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Sample records for corrected partition function

  1. Partition density functional theory

    NASA Astrophysics Data System (ADS)

    Nafziger, Jonathan

    Partition density functional theory (PDFT) is a method for dividing a molecular electronic structure calculation into fragment calculations. The molecular density and energy corresponding to Kohn Sham density-functional theory (KS-DFT) may be exactly recovered from these fragments. Each fragment acts as an isolated system except for the influence of a global one-body 'partition' potential which deforms the fragment densities. In this work, the developments of PDFT are put into the context of other fragment-based density functional methods. We developed three numerical implementations of PDFT: One within the NWChem computational chemistry package using basis sets, and the other two developed from scratch using real-space grids. It is shown that all three of these programs can exactly reproduce a KS-DFT calculation via fragment calculations. The first of our in-house codes handles non-interacting electrons in arbitrary one-dimensional potentials with any number of fragments. This code is used to explore how the exact partition potential changes for different partitionings of the same system and also to study features which determine which systems yield non-integer PDFT occupations and which systems are locked into integer PDFT occupations. The second in-house code, CADMium, performs real-space calculations of diatomic molecules. Features of the exact partition potential are studied for a variety of cases and an analytical formula determining singularities in the partition potential is derived. We introduce an approximation for the non-additive kinetic energy and show how this quantity can be computed exactly. Finally a PDFT functional is developed to address the issues of static correlation and delocalization errors in approximations within DFT. The functional is applied to the dissociation of H2 + and H2.

  2. Exact Abjm Partition Function from Tba

    NASA Astrophysics Data System (ADS)

    Putrov, Pavel; Yamazaki, Masahito

    2012-11-01

    We report on the exact computation of the S3 partition function of U(N)k × U(N)-k ABJM theory for k = 1, N = 1, …, 19. The result is a polynomial in π-1 with rational coefficients. As an application of our results, we numerically determine the coefficient of the membrane 1-instanton correction to the partition function.

  3. Exact instanton expansion of the ABJM partition function

    NASA Astrophysics Data System (ADS)

    Hatsuda, Yasuyuki; Moriyama, Sanefumi; Okuyama, Kazumi

    2015-11-01

    We review recent progress in determining the partition function of the ABJM theory in the large-N expansion, including all of the perturbative and non-perturbative corrections. In particular, we focus on how these exact expansions are obtained from various beautiful relations to the Fermi gas system, topological string theory, the integrable model, and the supergroup.

  4. Chiral partition functions of quantum Hall droplets

    SciTech Connect

    Cappelli, Andrea Viola, Giovanni; Zemba, Guillermo R.

    2010-02-15

    Chiral partition functions of conformal field theory describe the edge excitations of isolated Hall droplets. They are characterized by an index specifying the quasiparticle sector and transform among themselves by a finite-dimensional representation of the modular group. The partition functions are derived and used to describe electron transitions leading to Coulomb blockade conductance peaks. We find the peak patterns for Abelian hierarchical states and non-Abelian Read-Rezayi states, and compare them. Experimental observation of these features can check the qualitative properties of the conformal field theory description, such as the decomposition of the Hilbert space into sectors, involving charged and neutral parts, and the fusion rules.

  5. β-deformed matrix model and Nekrasov partition function

    NASA Astrophysics Data System (ADS)

    Nishinaka, Takahiro; Rim, Chaiho

    2012-02-01

    We study Penner type matrix models in relation with the Nekrasov partition function of four dimensional mathcal{N} = {2} , SU(2) supersymmetric gauge theories with N F = 2 , 3 and 4. By evaluating the resolvent using the loop equation for general β, we explicitly construct the first half-genus correction to the free energy and demonstrate the result coincides with the corresponding Nekrasov partition function with general Ω-background, including higher instanton contributions after modifying the relation of the Coulomb branch parameter with the filling fraction. Our approach complements the proof using the Selberg integrals directly which is useful to find the contribution in the series of instanton numbers for a given deformation parameter.

  6. Deformed topological partition function and Nekrasov backgrounds

    NASA Astrophysics Data System (ADS)

    Antoniadis, I.; Hohenegger, S.; Narain, K. S.; Taylor, T. R.

    2010-10-01

    A deformation of the N=2 topological string partition function is analyzed by considering higher-dimensional F-terms of the type W2gϒ, where W is the chiral Weyl superfield and each ϒ factor stands for the chiral projection of a real function of N=2 vector multiplets. These terms generate physical amplitudes involving two anti-self-dual Riemann tensors, 2g-2 anti-self-dual graviphoton field strengths and 2 n self-dual field strengths from the matter vector multiplets. Their coefficients F generalizing the genus g partition function F of the topological twisted type II theory, can be used to define a generating functional by introducing deformation parameters besides the string coupling. Choosing all matter field strengths to be that of the dual heterotic dilaton supermultiplet, one obtains two parameters that we argue should correspond to the deformation parameters of the Nekrasov partition function in the field theory limit, around the conifold singularity. Its perturbative part can be obtained from the one loop analysis on the heterotic side. This has been computed in Morales and Serone (1996) [1] and in the field theory limit shown to be given by the radius deformation of c=1 CFT coupled to two-dimensional gravity. Quite remarkably this result reproduces the gauge theory answer up to a phase difference that may be attributed to the regularization procedure. The type II results are expected to be exact and should also capture the part that is non-perturbative in heterotic dilaton.

  7. The minimal length and quantum partition functions

    NASA Astrophysics Data System (ADS)

    Abbasiyan-Motlaq, M.; Pedram, P.

    2014-08-01

    We study the thermodynamics of various physical systems in the framework of the generalized uncertainty principle that implies a minimal length uncertainty proportional to the Planck length. We present a general scheme to analytically calculate the quantum partition function of the physical systems to first order of the deformation parameter based on the behavior of the modified energy spectrum and compare our results with the classical approach. Also, we find the modified internal energy and heat capacity of the systems for the anti-Snyder framework.

  8. Octanol-Water Partition Coefficient from 3D-RISM-KH Molecular Theory of Solvation with Partial Molar Volume Correction.

    PubMed

    Huang, WenJuan; Blinov, Nikolay; Kovalenko, Andriy

    2015-04-30

    The octanol-water partition coefficient is an important physical-chemical characteristic widely used to describe hydrophobic/hydrophilic properties of chemical compounds. The partition coefficient is related to the transfer free energy of a compound from water to octanol. Here, we introduce a new protocol for prediction of the partition coefficient based on the statistical-mechanical, 3D-RISM-KH molecular theory of solvation. It was shown recently that with the compound-solvent correlation functions obtained from the 3D-RISM-KH molecular theory of solvation, the free energy functional supplemented with the correction linearly related to the partial molar volume obtained from the Kirkwood-Buff/3D-RISM theory, also called the "universal correction" (UC), provides accurate prediction of the hydration free energy of small compounds, compared to explicit solvent molecular dynamics [ Palmer , D. S. ; J. Phys.: Condens. Matter 2010 , 22 , 492101 ]. Here we report that with the UC reparametrized accordingly this theory also provides an excellent agreement with the experimental data for the solvation free energy in nonpolar solvent (1-octanol) and so accurately predicts the octanol-water partition coefficient. The performance of the Kovalenko-Hirata (KH) and Gaussian fluctuation (GF) functionals of the solvation free energy, with and without UC, is tested on a large library of small compounds with diverse functional groups. The best agreement with the experimental data for octanol-water partition coefficients is obtained with the KH-UC solvation free energy functional.

  9. Modular properties of full 5D SYM partition function

    NASA Astrophysics Data System (ADS)

    Qiu, Jian; Tizzano, Luigi; Winding, Jacob; Zabzine, Maxim

    2016-03-01

    We study properties of the full partition function for the U(1) 5D N = {2}^{ast } gauge theory with adjoint hypermultiplet of mass M . This theory is ultimately related to abelian 6D (2,0) theory. We construct the full non-perturbative partition function on toric Sasaki-Einstein manifolds by gluing flat copies of the Nekrasov partition function and we express the full partition function in terms of the generalized double elliptic gamma function G 2 C associated with a certain moment map cone C. The answer exhibits a curious SL(4 , ℤ) modular property. Finally, we propose a set of rules to construct the partition function that resembles the calculation of 5d supersymmetric partition function with the insert ion of defects of various co-dimensions.

  10. High-temperature asymptotics of supersymmetric partition functions

    NASA Astrophysics Data System (ADS)

    Ardehali, Arash Arabi

    2016-07-01

    We study the supersymmetric partition function of 4d supersymmetric gauge theories with a U(1) R-symmetry on Euclidean S 3 × S β 1 , with S 3 the unit-radius squashed three-sphere, and β the circumference of the circle. For superconformal theories, this partition function coincides (up to a Casimir energy factor) with the 4d superconformal index.

  11. Automorphic instanton partition functions on Calabi-Yau threefolds

    NASA Astrophysics Data System (ADS)

    Persson, Daniel

    2012-02-01

    We survey recent results on quantum corrections to the hypermultiplet moduli space Script M in type IIA/B string theory on a compact Calabi-Yau threefold X, or, equivalently, the vector multiplet moduli space in type IIB/A on X × S1. Our main focus lies on the problem of resumming the infinite series of D-brane and NS5-brane instantons, using the mathematical machinery of automorphic forms. We review the proposal that when the theory in three dimensions exhibits an arithmetic "U-duality" symmetry G(Bbb Z) the total instanton partition function arises from a certain unitary automorphic representation of G, whose Fourier coefficients reproduce the BPS-degeneracies. In the case of four-dimensional Script N = 2 theories on Bbb R × S1 we argue that the relevant automorphic representation falls in the quaternionic discrete series of G, and that the partition function is a holomorphic section on the twistor space over Script M.

  12. Level density of a Fermi gas and integer partitions: A Gumbel-like finite-size correction

    SciTech Connect

    Roccia, Jerome; Leboeuf, Patricio

    2010-04-15

    We investigate the many-body level density of a gas of noninteracting fermions. We determine its behavior as a function of the temperature and the number of particles. As the temperature increases, and beyond the usual Sommerfeld expansion that describes the degenerate gas behavior, corrections due to a finite number of particles lead to Gumbel-like contributions. We discuss connections with the partition problem in number theory, extreme value statistics, and differences with respect to the Bose gas.

  13. Reduced partition function ratios of iron and oxygen in goethite

    NASA Astrophysics Data System (ADS)

    Blanchard, M.; Dauphas, N.; Hu, M. Y.; Roskosz, M.; Alp, E. E.; Golden, D. C.; Sio, C. K.; Tissot, F. L. H.; Zhao, J.; Gao, L.; Morris, R. V.; Fornace, M.; Floris, A.; Lazzeri, M.; Balan, E.

    2015-02-01

    First-principles calculations based on the density functional theory (DFT) with or without the addition of a Hubbard U correction, are performed on goethite in order to determine the iron and oxygen reduced partition function ratios (β-factors). The calculated iron phonon density of states (pDOS), force constant and β-factor are compared with reevaluated experimental β-factors obtained from Nuclear Resonant Inelastic X-ray Scattering (NRIXS) measurements. The reappraisal of old experimental data is motivated by the erroneous previous interpretation of the low- and high-energy ends of the NRIXS spectrum of goethite and jarosite samples (Dauphas et al., 2012). Here the NRIXS data are analyzed using the SciPhon software that corrects for non-constant baseline. New NRIXS measurements also demonstrate the reproducibility of the results. Unlike for hematite and pyrite, a significant discrepancy remains between DFT, NRIXS and the existing Mössbauer-derived data. Calculations suggest a slight overestimation of the NRIXS signal possibly related to the baseline definition. The intrinsic features of the samples studied by NRIXS and Mössbauer spectroscopy may also contribute to the discrepancy (e.g., internal structural and/or chemical defects, microstructure, surface contribution). As for oxygen, DFT results indicate that goethite and hematite have similar β-factors, which suggests almost no fractionation between the two minerals at equilibrium.

  14. How Incorrect Is the Classical Partition Function for the Ideal Gas?

    ERIC Educational Resources Information Center

    Kroemer, Herbert

    1980-01-01

    Discussed is the classical partition function for the ideal gas and how it differs from the exact value for bosons or fermions in the classical regime. The differences in the two values are negligible hence the classical treatment leads in the end to correct answers for all observables. (Author/DS)

  15. One loop partition function of three-dimensional flat gravity

    NASA Astrophysics Data System (ADS)

    Barnich, G.; González, H. A.; Maloney, A.; Oblak, B.

    2015-04-01

    In this note we point out that the one-loop partition function of threedimensional flat gravity, computed along the lines originally developed for the anti-de Sitter case, reproduces characters of the BMS3 group.

  16. Dominant partition method. [based on a wave function formalism

    NASA Technical Reports Server (NTRS)

    Dixon, R. M.; Redish, E. F.

    1979-01-01

    By use of the L'Huillier, Redish, and Tandy (LRT) wave function formalism, a partially connected method, the dominant partition method (DPM) is developed for obtaining few body reductions of the many body problem in the LRT and Bencze, Redish, and Sloan (BRS) formalisms. The DPM maps the many body problem to a fewer body one by using the criterion that the truncated formalism must be such that consistency with the full Schroedinger equation is preserved. The DPM is based on a class of new forms for the irreducible cluster potential, which is introduced in the LRT formalism. Connectivity is maintained with respect to all partitions containing a given partition, which is referred to as the dominant partition. Degrees of freedom corresponding to the breakup of one or more of the clusters of the dominant partition are treated in a disconnected manner. This approach for simplifying the complicated BRS equations is appropriate for physical problems where a few body reaction mechanism prevails.

  17. ATOMIC PARTITION FUNCTION FOR STELLAR ATMOSPHERES AND PLASMA DIAGNOSTICS

    SciTech Connect

    Cardona, O.; Martinez-Arroyo, M.; Lopez-Castillo, M. A. E-mail: mmtz@inaoep.m

    2010-03-01

    A new approximate partition function is derived as a function of temperature and total number density of particles in the given system, and three adjustable parameters. The derivation assumes that we can simulate the calculations of the partition function for hydrogen by means of averages of the energies and sums of the statistical weights. We present the procedure and mathematical process to obtain an approximate analytic function and its derivatives that depend on those parameters. The comparisons with other calculations reported in the literature show good agreement. The free parameters of this function are calculated and given in a table for all the ions of the first 20 atomic species.

  18. A brief history of partitions of numbers, partition functions and their modern applications

    NASA Astrophysics Data System (ADS)

    Debnath, Lokenath

    2016-04-01

    'Number rules the universe.' The Pythagoras 'If you wish to forsee the future of mathematics our course is to study the history and present conditions of the science.' Henri Poincaré 'The primary source (Urqell) of all mathematics are integers.' Hermann Minkowski This paper is written to commemorate the centennial anniversary of the Mathematical Association of America. It deals with a short history of different kinds of natural numbers including triangular, square, pentagonal, hexagonal and k-gonal numbers, and their simple properties and their geometrical representations. Included are Euclid's and Pythagorean's main contributions to elementary number theory with the main contents of the Euclid Elements of the 13-volume masterpiece of mathematical work. This is followed by Euler's new discovery of the additive number theory based on partitions of numbers. Special attention is given to many examples, Euler's theorems on partitions of numbers with geometrical representations of Ferrers' graphs, Young's diagrams, Lagrange's four-square theorem and the celebrated Waring problem. Included are Euler's generating functions for the partitions of numbers, Euler's pentagonal number theorem, Gauss' triangular and square number theorems and the Jacobi triple product identity. Applications of the theory of partitions of numbers to different statistics such as the Bose- Einstein, Fermi- Dirac, Gentile, and Maxwell- Boltzmann statistics are briefly discussed. Special attention is given to pedagogical information through historical approach to number theory so that students and teachers at the school, college and university levels can become familiar with the basic concepts of partitions of numbers, partition functions and their modern applications, and can pursue advanced study and research in analytical and computational number theory.

  19. Quantum Mechanical Single Molecule Partition Function from PathIntegral Monte Carlo Simulations

    SciTech Connect

    Chempath, Shaji; Bell, Alexis T.; Predescu, Cristian

    2006-10-01

    An algorithm for calculating the partition function of a molecule with the path integral Monte Carlo method is presented. Staged thermodynamic perturbation with respect to a reference harmonic potential is utilized to evaluate the ratio of partition functions. Parallel tempering and a new Monte Carlo estimator for the ratio of partition functions are implemented here to achieve well converged simulations that give an accuracy of 0.04 kcal/mol in the reported free energies. The method is applied to various test systems, including a catalytic system composed of 18 atoms. Absolute free energies calculated by this method lead to corrections as large as 2.6 kcal/mol at 300 K for some of the examples presented.

  20. The partition function of the supersymmetric two-dimensional black hole and little string theory

    NASA Astrophysics Data System (ADS)

    Israel, Dan; Kounnas, Costas; Pakman, Ari; Troost, Jan

    2004-06-01

    We compute the partition function of the supersymmetric two-dimensional euclidean black hole geometry described by the SL(2,Bbb R)/U(1) superconformal field theory. We decompose the result in terms of characters of the N = 2 superconformal symmetry. We point out puzzling sectors of states besides finding expected discrete and continuous contributions to the partition function. By adding an N = 2 minimal model factor of the correct central charge and projecting on integral N = 2 charges we compute the partition function of the background dual to little string theory in a double scaling limit. We show the precise correspondence between this theory and the background for NS5-branes on a circle, due to an exact description of the background as a null gauging of SL(2,Bbb R) × SU(2). Finally, we discuss the interplay between GSO projection and target space geometry.

  1. A Pfaffian Formula for Monomer-Dimer Partition Functions

    NASA Astrophysics Data System (ADS)

    Giuliani, Alessandro; Jauslin, Ian; Lieb, Elliott H.

    2016-04-01

    We consider the monomer-dimer partition function on arbitrary finite planar graphs and arbitrary monomer and dimer weights, with the restriction that the only non-zero monomer weights are those on the boundary. We prove a Pfaffian formula for the corresponding partition function. As a consequence of this result, multipoint boundary monomer correlation functions at close packing are shown to satisfy fermionic statistics. Our proof is based on the celebrated Kasteleyn theorem, combined with a theorem on Pfaffians proved by one of the authors, and a careful labeling and directing procedure of the vertices and edges of the graph.

  2. Revisiting noninteracting string partition functions in Rindler space

    NASA Astrophysics Data System (ADS)

    Mertens, Thomas G.; Verschelde, Henri; Zakharov, Valentin I.

    2016-05-01

    We revisit noninteracting string partition functions in Rindler space by summing over fields in the spectrum. In field theory, the total partition function splits in a natural way into a piece that does not contain surface terms and a piece consisting of solely the so-called edge states. For open strings, we illustrate that surface contributions to the higher-spin fields correspond to open strings piercing the Rindler origin, unifying the higher-spin surface contributions in string language. For closed strings, we demonstrate that the string partition function is not quite the same as the sum over the partition functions of the fields in the spectrum: an infinite overcounting is present for the latter. Next we study the partition functions obtained by excluding the surface terms. Using recent results of He et al. [J. High Energy Phys. 05 (2015) 106], this construction, first done by Emparan [arXiv:hep-th/9412003], can be put on much firmer ground. We generalize to type II and heterotic superstrings and demonstrate modular invariance. All of these exhibit an IR divergence that can be interpreted as a maximal acceleration close to the black hole horizon. Ultimately, since these partition functions are only part of the full story, divergences here should not be viewed as a failure of string theory: maximal acceleration is a feature of a faulty treatment of the higher-spin fields in the string spectrum. We comment on the relevance of this to Solodukhin's recent proposal [Phys. Rev. D 91, 084028 (2015)]. A possible link with the firewall paradox is apparent.

  3. Further Stable methods for the calculation of partition functions

    SciTech Connect

    Wilson, B G; Gilleron, F; Pain, J

    2007-06-27

    The extension to recursion over holes of the Gilleron and Pain method for calculating partition functions of a canonical ensemble of non-interacting bound electrons is presented as well as a generalization for the efficient computation of collisional line broadening.

  4. Partition functions and concentrations in plasmas out of thermal equilibrium

    SciTech Connect

    Andre, P.

    1995-06-01

    Taking into account the disequilibrium between the temperatures (electronic, rotational, vibrational, translational) in a nitrogen-plasma out of thermal equilibrium, different partition function and chemical potential calculation method are described and applied. From the variation of the temperature hypotheses, their influence on the plasma concentration is shown.

  5. Polymer quantization and the saddle point approximation of partition functions

    NASA Astrophysics Data System (ADS)

    Morales-Técotl, Hugo A.; Orozco-Borunda, Daniel H.; Rastgoo, Saeed

    2015-11-01

    The saddle point approximation of the path integral partition functions is an important way of deriving the thermodynamical properties of black holes. However, there are certain black hole models and some mathematically analog mechanical models for which this method cannot be applied directly. This is due to the fact that their action evaluated on a classical solution is not finite and its first variation does not vanish for all consistent boundary conditions. These problems can be dealt with by adding a counterterm to the classical action, which is a solution of the corresponding Hamilton-Jacobi equation. In this work we study the effects of polymer quantization on a mechanical model presenting the aforementioned difficulties and contrast it with the above counterterm method. This type of quantization for mechanical models is motivated by the loop quantization of gravity, which is known to play a role in the thermodynamics of black hole systems. The model we consider is a nonrelativistic particle in an inverse square potential, and we analyze two polarizations of the polymer quantization in which either the position or the momentum is discrete. In the former case, Thiemann's regularization is applied to represent the inverse power potential, but we still need to incorporate the Hamilton-Jacobi counterterm, which is now modified by polymer corrections. In the latter, momentum discrete case, however, such regularization could not be implemented. Yet, remarkably, owing to the fact that the position is bounded, we do not need a Hamilton-Jacobi counterterm in order to have a well-defined saddle point approximation. Further developments and extensions are commented upon in the discussion.

  6. Hydrological modelling of a small catchment using SWAT-2000 Ensuring correct flow partitioning for contaminant modelling

    NASA Astrophysics Data System (ADS)

    Kannan, N.; White, S. M.; Worrall, F.; Whelan, M. J.

    2007-02-01

    SummaryThe performance of the SWAT-2000 model was evaluated using stream flow at the outlet of the 142 ha Colworth catchment (Bedfordshire, UK). This catchment has been monitored since October 1999. The soil type consists of clay loam soil over stony calcareous clay and a rotation of wheat, oil seed rape, grass, beans and peas is grown. Much of the catchment is tile drained. Acceptable performance in hydrological modelling, along with correct simulation of the processes driving the water balance were essential first requirements for predicting contaminant transport. Initial results from SWAT-2000 identified some necessary modifications in the model source code for correct simulation of processes driving water balance. After modification of the code, hydrological simulation, crop growth and evapotranspiration (ET) patterns were realistic when compared with empirical data. Acceptable model performance (based on a number of error measures) was obtained in final model runs, with reasonable runoff partitioning into overland flow, tile drainage and base flow.

  7. Unified approach to partition functions of RNA secondary structures.

    PubMed

    Bundschuh, Ralf

    2014-11-01

    RNA secondary structure formation is a field of considerable biological interest as well as a model system for understanding generic properties of heteropolymer folding. This system is particularly attractive because the partition function and thus all thermodynamic properties of RNA secondary structure ensembles can be calculated numerically in polynomial time for arbitrary sequences and homopolymer models admit analytical solutions. Such solutions for many different aspects of the combinatorics of RNA secondary structure formation share the property that the final solution depends on differences of statistical weights rather than on the weights alone. Here, we present a unified approach to a large class of problems in the field of RNA secondary structure formation. We prove a generic theorem for the calculation of RNA folding partition functions. Then, we show that this approach can be applied to the study of the molten-native transition, denaturation of RNA molecules, as well as to studies of the glass phase of random RNA sequences.

  8. Unified approach to partition functions of RNA secondary structures.

    PubMed

    Bundschuh, Ralf

    2014-11-01

    RNA secondary structure formation is a field of considerable biological interest as well as a model system for understanding generic properties of heteropolymer folding. This system is particularly attractive because the partition function and thus all thermodynamic properties of RNA secondary structure ensembles can be calculated numerically in polynomial time for arbitrary sequences and homopolymer models admit analytical solutions. Such solutions for many different aspects of the combinatorics of RNA secondary structure formation share the property that the final solution depends on differences of statistical weights rather than on the weights alone. Here, we present a unified approach to a large class of problems in the field of RNA secondary structure formation. We prove a generic theorem for the calculation of RNA folding partition functions. Then, we show that this approach can be applied to the study of the molten-native transition, denaturation of RNA molecules, as well as to studies of the glass phase of random RNA sequences. PMID:24177391

  9. High-temperature asymptotics of supersymmetric partition functions

    DOE PAGES

    Ardehali, Arash Arabi

    2016-07-05

    We study the supersymmetric partition function of 4d supersymmetric gauge theories with a U(1) R-symmetry on Euclidean S3 × Sβ1, with S3 the unit-radius squashed three-sphere, and β the circumference of the circle. For superconformal theories, this partition function coincides (up to a Casimir energy factor) with the 4d superconformal index. The partition function can be computed exactly using the supersymmetric localization of the gauge theory path-integral. It takes the form of an elliptic hypergeometric integral, which may be viewed as a matrix-integral over the moduli space of the holonomies of the gauge fields around Sβ1. At high temperatures (βmore » → 0, corresponding to the hyperbolic limit of the elliptic hypergeometric integral) we obtain from the matrix-integral a quantum effective potential for the holonomies. The effective potential is proportional to the temperature. Therefore the high-temperature limit further localizes the matrix-integral to the locus of the minima of the potential. If the effective potential is positive semi-definite, the leading high-temperature asymptotics of the partition function is given by the formula of Di Pietro and Komargodski, and the subleading asymptotics is connected to the Coulomb branch dynamics on R3 × S1. In theories where the effective potential is not positive semi-definite, the Di Pietro-Komargodski formula needs to be modified. In particular, this modification occurs in the SU(2) theory of Intriligator-Seiberg-Shenker, and the SO(N) theory of Brodie-Cho-Intriligator, both believed to exhibit “misleading” anomaly matchings, and both believed to yield interacting superconformal field theories with c < a. Lastly, two new simple tests for dualities between 4d supersymmetric gauge theories emerge as byproducts of our analysis.« less

  10. Partition functions for heterotic WZW conformal field theories

    NASA Astrophysics Data System (ADS)

    Gannon, Terry

    1993-08-01

    Thus far in the search for, and classification of, "physical" modular invariant partition functions ΣN LRχ Lχ R∗ the attention has been focused on the symmetric case where the holomorphic and anti-holomorphic sectors, and hence the characters χLand χR, are associated with the same Kac-Moody algebras ĝL = ĝR and levels κ L = κ R. In this paper we consider the more general possibility where ( ĝL, κ L) may not equal ( ĝR, κ R). We discuss which choices of algebras and levels may correspond to well-defined conformal field theories, we find the "smallest" such heterotic (i.e. asymmetric) partition functions, and we give a method, generalizing the Roberts-Terao-Warner lattice method, for explicitly constructing many other modular invariants. We conclude the paper by proving that this new lattice method will succeed in generating all the heterotic partition functions, for all choices of algebras and levels.

  11. Holonomy spin foam models: asymptotic geometry of the partition function

    NASA Astrophysics Data System (ADS)

    Hellmann, Frank; Kaminski, Wojciech

    2013-10-01

    We study the asymptotic geometry of the spin foam partition function for a large class of models, including the models of Barrett and Crane, Engle, Pereira, Rovelli and Livine, and, Freidel and Krasnov. The asymptotics is taken with respect to the boundary spins only, no assumption of large spins is made in the interior. We give a sufficient criterion for the existence of the partition function. We find that geometric boundary data is suppressed unless its interior continuation satisfies certain accidental curvature constraints. This means in particular that most Regge manifolds are suppressed in the asymptotic regime. We discuss this explicitly for the case of the configurations arising in the 3-3 Pachner move. We identify the origin of these accidental curvature constraints as an incorrect twisting of the face amplitude upon introduction of the Immirzi parameter and propose a way to resolve this problem, albeit at the price of losing the connection to the SU(2) boundary Hilbert space. The key methodological innovation that enables these results is the introduction of the notion of wave front sets, and the adaptation of tools for their study from micro local analysis to the case of spin foam partition functions.

  12. Supersymmetric partition functions in the AdS/CFT conjecture

    NASA Astrophysics Data System (ADS)

    Raju, Suvrat

    We study supersymmetric partition functions in several versions of the AdS/CFT correspondence. We present an Index for superconformal field theories in d = 3, 4, 5, 6. This captures all information about the spectrum that is protected, under continuous deformations of the theory, purely by group theory. We compute our Index in N = 4 SYM at weak coupling using gauge theory and at strong coupling using supergravity and find perfect agreement at large N. We also compute this Index for supergravity on AdS4 x S7 and AdS7 x S4 and for the recently constructed Chern Simons matter theories. We count 1/16 BPS states in the free gauge theory and find qualitative agreement with the entropy of big black holes in AdS5. We note that the near horizon geometry of some small supersymmetric black holes is an extremal BTZ black holes fibered on a compact base and propose a possible explanation for this, based on giant gravitons. We also find the partition function of the chiral ring of the N = 4 SYM theory at finite coupling and finite N. Turning to AdS3, we study the low energy 1/4 and 1/2 BPS partition functions by finding all classical supersymmetric probe brane solutions of string theory on this background. If the background BNS field and theta angle vanish, AdS3 x S 3 x T4/K3 supports supersymmetric probes: D1 branes, D5 branes and bound states of D5 and D1 branes. In global AdS, upon quantization, these solutions give rise to states in discrete representations of the SL(2,R) WZW model on AdS 3. We conclude that (a) the 1/4 BPS partition function jumps if we turn on a theta angle or NS-NS field (b) generic 1/2 BPS states are protected. We successfully compare our 1/2 BPS partition function with that of the symmetric product. We also discuss puzzles, and their possible resolutions, in reproducing the elliptic genus of the symmetric product. Finally, we comment on the spectrum of particles in the theory of gravity dual to non-supersymmetric Yang Mills theory on S3 x time.

  13. Generalised partition functions: inferences on phase space distributions

    NASA Astrophysics Data System (ADS)

    Treumann, Rudolf A.; Baumjohann, Wolfgang

    2016-06-01

    It is demonstrated that the statistical mechanical partition function can be used to construct various different forms of phase space distributions. This indicates that its structure is not restricted to the Gibbs-Boltzmann factor prescription which is based on counting statistics. With the widely used replacement of the Boltzmann factor by a generalised Lorentzian (also known as the q-deformed exponential function, where κ = 1/|q - 1|, with κ, q ∈ R) both the kappa-Bose and kappa-Fermi partition functions are obtained in quite a straightforward way, from which the conventional Bose and Fermi distributions follow for κ → ∞. For κ ≠ ∞ these are subject to the restrictions that they can be used only at temperatures far from zero. They thus, as shown earlier, have little value for quantum physics. This is reasonable, because physical κ systems imply strong correlations which are absent at zero temperature where apart from stochastics all dynamical interactions are frozen. In the classical large temperature limit one obtains physically reasonable κ distributions which depend on energy respectively momentum as well as on chemical potential. Looking for other functional dependencies, we examine Bessel functions whether they can be used for obtaining valid distributions. Again and for the same reason, no Fermi and Bose distributions exist in the low temperature limit. However, a classical Bessel-Boltzmann distribution can be constructed which is a Bessel-modified Lorentzian distribution. Whether it makes any physical sense remains an open question. This is not investigated here. The choice of Bessel functions is motivated solely by their convergence properties and not by reference to any physical demands. This result suggests that the Gibbs-Boltzmann partition function is fundamental not only to Gibbs-Boltzmann but also to a large class of generalised Lorentzian distributions as well as to the corresponding nonextensive statistical mechanics.

  14. Partition function zeros and finite size scaling for polymer adsorption

    SciTech Connect

    Taylor, Mark P.; Luettmer-Strathmann, Jutta

    2014-11-28

    The zeros of the canonical partition functions for a flexible polymer chain tethered to an attractive flat surface are computed for chains up to length N = 1536. We use a bond-fluctuation model for the polymer and obtain the density of states for the tethered chain by Wang-Landau sampling. The partition function zeros in the complex e{sup β}-plane are symmetric about the real axis and densest in a boundary region that has the shape of a nearly closed circle, centered at the origin, terminated by two flaring tails. This structure defines a root-free zone about the positive real axis and follows Yang-Lee theory. As the chain length increases, the base of each tail moves toward the real axis, converging on the phase-transition point in the thermodynamic limit. We apply finite-size scaling theory of partition-function zeros and show that the crossover exponent defined through the leading zero is identical to the standard polymer adsorption crossover exponent ϕ. Scaling analysis of the leading zeros locates the polymer adsorption transition in the thermodynamic (N → ∞) limit at reduced temperature T{sub c}{sup *}=1.027(3) [β{sub c}=1/T{sub c}{sup *}=0.974(3)] with crossover exponent ϕ = 0.515(25). Critical exponents for the order parameter and specific heat are determined to be β{sup ~}=0.97(5) and α = 0.03(4), respectively. A universal scaling function for the average number of surface contacts is also constructed.

  15. Partition function zeros and finite size scaling for polymer adsorption

    NASA Astrophysics Data System (ADS)

    Taylor, Mark P.; Luettmer-Strathmann, Jutta

    2014-11-01

    The zeros of the canonical partition functions for a flexible polymer chain tethered to an attractive flat surface are computed for chains up to length N = 1536. We use a bond-fluctuation model for the polymer and obtain the density of states for the tethered chain by Wang-Landau sampling. The partition function zeros in the complex eβ-plane are symmetric about the real axis and densest in a boundary region that has the shape of a nearly closed circle, centered at the origin, terminated by two flaring tails. This structure defines a root-free zone about the positive real axis and follows Yang-Lee theory. As the chain length increases, the base of each tail moves toward the real axis, converging on the phase-transition point in the thermodynamic limit. We apply finite-size scaling theory of partition-function zeros and show that the crossover exponent defined through the leading zero is identical to the standard polymer adsorption crossover exponent ϕ. Scaling analysis of the leading zeros locates the polymer adsorption transition in the thermodynamic (N → ∞) limit at reduced temperature T_c^*=1.027(3) [β _c=1/T_c^*=0.974(3)] with crossover exponent ϕ = 0.515(25). Critical exponents for the order parameter and specific heat are determined to be widetilde{β }=0.97(5) and α = 0.03(4), respectively. A universal scaling function for the average number of surface contacts is also constructed.

  16. Quantum algorithm for an additive approximation of Ising partition functions

    NASA Astrophysics Data System (ADS)

    Matsuo, Akira; Fujii, Keisuke; Imoto, Nobuyuki

    2014-08-01

    We investigate quantum-computational complexity of calculating partition functions of Ising models. We construct a quantum algorithm for an additive approximation of Ising partition functions on square lattices. To this end, we utilize the overlap mapping developed by M. Van den Nest, W. Dür, and H. J. Briegel [Phys. Rev. Lett. 98, 117207 (2007), 10.1103/PhysRevLett.98.117207] and its interpretation through measurement-based quantum computation (MBQC). We specify an algorithmic domain, on which the proposed algorithm works, and an approximation scale, which determines the accuracy of the approximation. We show that the proposed algorithm performs a nontrivial task, which would be intractable on any classical computer, by showing that the problem that is solvable by the proposed quantum algorithm is BQP-complete. In the construction of the BQP-complete problem coupling strengths and magnetic fields take complex values. However, the Ising models that are of central interest in statistical physics and computer science consist of real coupling strengths and magnetic fields. Thus we extend the algorithmic domain of the proposed algorithm to such a real physical parameter region and calculate the approximation scale explicitly. We found that the overlap mapping and its MBQC interpretation improve the approximation scale exponentially compared to a straightforward constant-depth quantum algorithm. On the other hand, the proposed quantum algorithm also provides partial evidence that there exist no efficient classical algorithm for a multiplicative approximation of the Ising partition functions even on the square lattice. This result supports the observation that the proposed quantum algorithm also performs a nontrivial task in the physical parameter region.

  17. Holographic partition functions and phases for higher genus Riemann surfaces

    NASA Astrophysics Data System (ADS)

    Maxfield, Henry; Ross, Simon F.; Way, Benson

    2016-06-01

    We describe a numerical method to compute the action of Euclidean saddle points for the partition function of a two-dimensional holographic CFT on a Riemann surface of arbitrary genus, with constant curvature metric. We explicitly evaluate the action for the saddles for genus two and map out the phase structure of dominant bulk saddles in a two-dimensional subspace of the moduli space. We discuss spontaneous breaking of discrete symmetries, and show that the handlebody bulk saddles always dominate over certain non-handlebody solutions.

  18. Chamber identity programs drive early functional partitioning of the heart.

    PubMed

    Mosimann, Christian; Panáková, Daniela; Werdich, Andreas A; Musso, Gabriel; Burger, Alexa; Lawson, Katy L; Carr, Logan A; Nevis, Kathleen R; Sabeh, M Khaled; Zhou, Yi; Davidson, Alan J; DiBiase, Anthony; Burns, Caroline E; Burns, C Geoffrey; MacRae, Calum A; Zon, Leonard I

    2015-01-01

    The vertebrate heart muscle (myocardium) develops from the first heart field (FHF) and expands by adding second heart field (SHF) cells. While both lineages exist already in teleosts, the primordial contributions of FHF and SHF to heart structure and function remain incompletely understood. Here we delineate the functional contribution of the FHF and SHF to the zebrafish heart using the cis-regulatory elements of the draculin (drl) gene. The drl reporters initially delineate the lateral plate mesoderm, including heart progenitors. Subsequent myocardial drl reporter expression restricts to FHF descendants. We harnessed this unique feature to uncover that loss of tbx5a and pitx2 affect relative FHF versus SHF contributions to the heart. High-resolution physiology reveals distinctive electrical properties of each heart field territory that define a functional boundary within the single zebrafish ventricle. Our data establish that the transcriptional program driving cardiac septation regulates physiologic ventricle partitioning, which successively provides mechanical advantages of sequential contraction. PMID:26306682

  19. Computing black hole partition functions from quasinormal modes

    DOE PAGES

    Arnold, Peter; Szepietowski, Phillip; Vaman, Diana

    2016-07-07

    We propose a method of computing one-loop determinants in black hole space-times (with emphasis on asymptotically anti-de Sitter black holes) that may be used for numerics when completely-analytic results are unattainable. The method utilizes the expression for one-loop determinants in terms of quasinormal frequencies determined by Denef, Hartnoll and Sachdev in [1]. A numerical evaluation must face the fact that the sum over the quasinormal modes, indexed by momentum and overtone numbers, is divergent. A necessary ingredient is then a regularization scheme to handle the divergent contributions of individual fixed-momentum sectors to the partition function. To this end, we formulatemore » an effective two-dimensional problem in which a natural refinement of standard heat kernel techniques can be used to account for contributions to the partition function at fixed momentum. We test our method in a concrete case by reproducing the scalar one-loop determinant in the BTZ black hole background. Furthermore, we then discuss the application of such techniques to more complicated spacetimes.« less

  20. Computing black hole partition functions from quasinormal modes

    NASA Astrophysics Data System (ADS)

    Arnold, Peter; Szepietowski, Phillip; Vaman, Diana

    2016-07-01

    We propose a method of computing one-loop determinants in black hole space-times (with emphasis on asymptotically anti-de Sitter black holes) that may be used for numerics when completely-analytic results are unattainable. The method utilizes the expression for one-loop determinants in terms of quasinormal frequencies determined by Denef, Hartnoll and Sachdev in [1]. A numerical evaluation must face the fact that the sum over the quasinormal modes, indexed by momentum and overtone numbers, is divergent. A necessary ingredient is then a regularization scheme to handle the divergent contributions of individual fixed-momentum sectors to the partition function. To this end, we formulate an effective two-dimensional problem in which a natural refinement of standard heat kernel techniques can be used to account for contributions to the partition function at fixed momentum. We test our method in a concrete case by reproducing the scalar one-loop determinant in the BTZ black hole background. We then discuss the application of such techniques to more complicated spacetimes.

  1. Structural and functional partitioning of bread wheat chromosome 3B.

    PubMed

    Choulet, Frédéric; Alberti, Adriana; Theil, Sébastien; Glover, Natasha; Barbe, Valérie; Daron, Josquin; Pingault, Lise; Sourdille, Pierre; Couloux, Arnaud; Paux, Etienne; Leroy, Philippe; Mangenot, Sophie; Guilhot, Nicolas; Le Gouis, Jacques; Balfourier, Francois; Alaux, Michael; Jamilloux, Véronique; Poulain, Julie; Durand, Céline; Bellec, Arnaud; Gaspin, Christine; Safar, Jan; Dolezel, Jaroslav; Rogers, Jane; Vandepoele, Klaas; Aury, Jean-Marc; Mayer, Klaus; Berges, Hélène; Quesneville, Hadi; Wincker, Patrick; Feuillet, Catherine

    2014-07-18

    We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- and intrachromosomal gene duplication activities that are potential sources of variability for adaption. In addition to providing a better understanding of the organization, function, and evolution of a large and polyploid genome, the availability of a high-quality sequence anchored to genetic maps will accelerate the identification of genes underlying important agronomic traits. PMID:25035497

  2. A simple way of approximating the canonical partition functions in statistical mechanics

    NASA Astrophysics Data System (ADS)

    Fernández, Francisco M.

    2015-09-01

    We propose a simple pedagogical way of introducing the Euler-MacLaurin summation formula in an undergraduate course on statistical mechanics. The reason is that the students may feel more comfortable and confident if they are able to deduce the main equations. To this end we put forward two alternative routes: the first one is the simplest and yields the first two terms of the expansion. The second one is somewhat more elaborate and takes into account all the correction terms. We apply both to the calculation of the simplest one-particle canonical partition functions for the translational, vibrational and rotational degrees of freedom. The more elaborate, systematic calculation of the correction terms is suitable for motivating the students to explore the possibility of using available computer algebra software that enable one to avoid long and tedious manipulation of algebraic equations.

  3. What is the correct value for the brain: blood partition coefficient for water

    SciTech Connect

    Herscovitch, P.; Raichle, M.E.

    1984-01-01

    A knowledge of the brain: blood partition coefficient (lambda) for water is usually required for the measurement of cerebral blood flow (CBF) with positron emission tomography (PET) and 0-15 labelled water. The correct calculation of this important parameter from the ratio of brain and blood water contents is reviewed, and the effect of physiological variations in these water contents on lambda is demonstrated. The currently accepted value for whole brain lambda is 0.95-0.96 ml/g, calculated from brain and blood water contents of 77g/100g and 80.5g/100g, respectively. However, this value for lambda is incorrect, because in the calculation the blood water content value was not adjusted for the density of blood. The correct value is 0.91 ml/g. Variations in brain or blood water content affect lambda. Over an hematocrit range of 25% to 55%, lambda varies from 0.86 to 0.93 ml/g, due to a decrease in blood water content. lambda changes with age, and varies regionally in the brain, as brain water content is inversely related to lipid and myelin content. The lambda of the human newborn brain, 1.10 ml/g, is considerably higher than in the adult. Differences in lambda between gray and white matter are well known. However, because of variations in water content, the lambda's of thalamus (0.88 ml/g) and caudate nucleus (0.96 ml/g) are less than that of cerebral cortex (0.99 ml/g), while the lambda of corpus callosum (0.89 ml/g) is greater than that of centrum semiovale (0.83 ml/g). These regional variations in lambda will assume more importance as PET resolution improves. The impact of using an incorrect lambda will depend upon the sensitivity of the particular CBF measurement technique to errors in lambda.

  4. From Special Geometry to Black Hole Partition Functions

    NASA Astrophysics Data System (ADS)

    Mohaupt, Thomas

    These notes are based on lectures given at the Erwin-Schrödinger Institute in Vienna in 2006/2007 and at the 2007 School on Attractor Mechanism in Frascati. Lecture I reviews special geometry from the superconformal point of view. Lecture II discusses the black hole attractor mechanism, the underlying variational principle and black hole partition functions. Lecture III applies the formalism introduced in the previous lectures to large and small BPS black holes in N = 4 supergravity. Lecture IV is devoted to the microscopic description of these black holes in N = 4 string compactifications. The lecture notes include problems which allow the readers to develop some of the key ideas by themselves. Appendix A reviews special geometry from the mathematical point of view. Appendix B provides the necessary background in modular forms needed for understanding S-duality and string state counting.

  5. Adiabatic corrections to density functional theory energies and wave functions.

    PubMed

    Mohallem, José R; Coura, Thiago de O; Diniz, Leonardo G; de Castro, Gustavo; Assafrão, Denise; Heine, Thomas

    2008-09-25

    The adiabatic finite-nuclear-mass-correction (FNMC) to the electronic energies and wave functions of atoms and molecules is formulated for density-functional theory and implemented in the deMon code. The approach is tested for a series of local and gradient corrected density functionals, using MP2 results and diagonal-Born-Oppenheimer corrections from the literature for comparison. In the evaluation of absolute energy corrections of nonorganic molecules the LDA PZ81 functional works surprisingly better than the others. For organic molecules the GGA BLYP functional has the best performance. FNMC with GGA functionals, mainly BLYP, show a good performance in the evaluation of relative corrections, except for nonorganic molecules containing H atoms. The PW86 functional stands out with the best evaluation of the barrier of linearity of H2O and the isotopic dipole moment of HDO. In general, DFT functionals display an accuracy superior than the common belief and because the corrections are based on a change of the electronic kinetic energy they are here ranked in a new appropriate way. The approach is applied to obtain the adiabatic correction for full atomization of alcanes C(n)H(2n+2), n = 4-10. The barrier of 1 mHartree is approached for adiabatic corrections, justifying its insertion into DFT. PMID:18537228

  6. Natural Microbial Assemblages Reflect Distinct Organismal and Functional Partitioning

    NASA Astrophysics Data System (ADS)

    Wilmes, P.; Andersson, A.; Kalnejais, L. H.; Verberkmoes, N. C.; Lefsrud, M. G.; Wexler, M.; Singer, S. W.; Shah, M.; Bond, P. L.; Thelen, M. P.; Hettich, R. L.; Banfield, J. F.

    2007-12-01

    The ability to link microbial community structure to function has long been a primary focus of environmental microbiology. With the advent of community genomic and proteomic techniques, along with advances in microscopic imaging techniques, it is now possible to gain insights into the organismal and functional makeup of microbial communities. Biofilms growing within highly acidic solutions inside the Richmond Mine (Iron Mountain, Redding, California) exhibit distinct macro- and microscopic morphologies. They are composed of microorganisms belonging to the three domains of life, including archaea, bacteria and eukarya. The proportion of each organismal type depends on sampling location and developmental stage. For example, mature biofilms floating on top of acid mine drainage (AMD) pools exhibit layers consisting of a densely packed bottom layer of the chemoautolithotroph Leptospirillum group II, a less dense top layer composed mainly of archaea, and fungal filaments spanning across the entire biofilm. The expression of cytochrome 579 (the most highly abundant protein in the biofilm, believed to be central to iron oxidation and encoded by Leptospirillum group II) is localized at the interface of the biofilm with the AMD solution, highlighting that biofilm architecture is reflected at the functional gene expression level. Distinct functional partitioning is also apparent in a biological wastewater treatment system that selects for distinct polyphosphate accumulating organisms. Community genomic data from " Candidatus Accumulibacter phosphatis" dominated activated sludge has enabled high mass-accuracy shotgun proteomics for identification of key metabolic pathways. Comprehensive genome-wide alignment of orthologous proteins suggests distinct partitioning of protein variants involved in both core-metabolism and specific metabolic pathways among the dominant population and closely related species. In addition, strain- resolved proteogenomic analysis of the AMD biofilms

  7. Partition function of the elliptic solid-on-solid model as a single determinant

    NASA Astrophysics Data System (ADS)

    Galleas, W.

    2016-07-01

    In this Rapid Communication we express the partition function of the integrable elliptic solid-on-solid model with domain-wall boundary conditions as a single determinant. This representation appears naturally as the solution of a system of functional equations governing the model's partition function.

  8. Reverse energy partitioning-An efficient algorithm for computing the density of states, partition functions, and free energy of solids.

    PubMed

    Do, Hainam; Wheatley, Richard J

    2016-08-28

    A robust and model free Monte Carlo simulation method is proposed to address the challenge in computing the classical density of states and partition function of solids. Starting from the minimum configurational energy, the algorithm partitions the entire energy range in the increasing energy direction ("upward") into subdivisions whose integrated density of states is known. When combined with the density of states computed from the "downward" energy partitioning approach [H. Do, J. D. Hirst, and R. J. Wheatley, J. Chem. Phys. 135, 174105 (2011)], the equilibrium thermodynamic properties can be evaluated at any temperature and in any phase. The method is illustrated in the context of the Lennard-Jones system and can readily be extended to other molecular systems and clusters for which the structures are known. PMID:27586913

  9. Three dimensional mirror symmetry and partition function on S 3

    NASA Astrophysics Data System (ADS)

    Dey, Anindya; Distler, Jacques

    2013-10-01

    We provide non-trivial checks of = 4 , D = 3 mirror symmetry in a large class of quiver gauge theories whose Type IIB (Hanany-Witten) descriptions involve D3 branes ending on orbifold/orientifold 5-planes at the boundary. From the M-theory perspective, such theories can be understood in terms of coincident M2 branes sitting at the origin of a product of an A-type and a D-type ALE (Asymtotically Locally Euclidean) space with G-fluxes. Families of mirror dual pairs, which arise in this fashion, can be labeled as ( A m-1 , D n ), where m and n are integers. For a large subset of such infinite families of dual theories, corresponding to generic values of n ≥ 4, arbitrary ranks of the gauge groups and varying m, we test the conjectured duality by proving the precise equality of the S 3 partition functions for dual gauge theories in the IR as functions of masses and FI parameters. The mirror map for a given pair of mirror dual theories can be read off at the end of this computation and we explicitly present these for the aforementioned examples. The computation uses non-trivial identities of hyperbolic functions including certain generalizations of Cauchy determinant identity and Schur's Pfaffian identity, which are discussed in the paper.

  10. Partition function and base pairing probabilities of RNA heterodimers

    PubMed Central

    Bernhart, Stephan H; Tafer, Hakim; Mückstein, Ulrike; Flamm, Christoph; Stadler, Peter F; Hofacker, Ivo L

    2006-01-01

    Background RNA has been recognized as a key player in cellular regulation in recent years. In many cases, non-coding RNAs exert their function by binding to other nucleic acids, as in the case of microRNAs and snoRNAs. The specificity of these interactions derives from the stability of inter-molecular base pairing. The accurate computational treatment of RNA-RNA binding therefore lies at the heart of target prediction algorithms. Methods The standard dynamic programming algorithms for computing secondary structures of linear single-stranded RNA molecules are extended to the co-folding of two interacting RNAs. Results We present a program, RNAcofold, that computes the hybridization energy and base pairing pattern of a pair of interacting RNA molecules. In contrast to earlier approaches, complex internal structures in both RNAs are fully taken into account. RNAcofold supports the calculation of the minimum energy structure and of a complete set of suboptimal structures in an energy band above the ground state. Furthermore, it provides an extension of McCaskill's partition function algorithm to compute base pairing probabilities, realistic interaction energies, and equilibrium concentrations of duplex structures. Availability RNAcofold is distributed as part of the Vienna RNA Package, . Contact Stephan H. Bernhart – berni@tbi.univie.ac.at PMID:16722605

  11. A simplified approach to calculate atomic partition functions in plasmas

    SciTech Connect

    D'Ammando, Giuliano; Colonna, Gianpiero

    2013-03-15

    A simplified method to calculate the electronic partition functions and the corresponding thermodynamic properties of atomic species is presented and applied to C(I) up to C(VI) ions. The method consists in reducing the complex structure of an atom to three lumped levels. The ground level of the lumped model describes the ground term of the real atom, while the second lumped level represents the low lying states and the last one groups all the other atomic levels. It is also shown that for the purpose of thermodynamic function calculation, the energy and the statistical weight of the upper lumped level, describing high-lying excited atomic states, can be satisfactorily approximated by an analytic hydrogenlike formula. The results of the simplified method are in good agreement with those obtained by direct summation over a complete set (i.e., including all possible terms and configurations below a given cutoff energy) of atomic energy levels. The method can be generalized to include more lumped levels in order to improve the accuracy.

  12. Dualities and Curved Space Partition Functions of Supersymmetric Theories

    NASA Astrophysics Data System (ADS)

    Agarwal, Prarit

    In this dissertation we discuss some conjectured dualities in supersymmetric field theories and provide non-trivial checks for these conjectures. A quick review of supersymmetry and related topics is provided in chapter 1. In chapter 2, we develop a method to identify the so called BPS states in the Hilbert space of a supersymmetric field theory (that preserves at least two real supercharges) on a generic curved space. As an application we obtain the superconformal index (SCI) of 4d theories. The large N SCI of quiver gauge theories has been previously noticed to factorize over the set of extremal BPS mesonic operators. In chapter 3, we reformulate this factorization in terms of the zigzag paths in the dimer model associated to the quiver and extend the factorization theorem of the index to include theories obtained from D-branes probing orbifold singularities. In chapter 4, we consider the dualities in two classes of 3 dimensional theories. The first class consist of dualities of certain necklace type Chern-Simons (CS) quiver gauge theories. A non trivial check of these dualities is provided by matching their squashed sphere partition functions. The second class consists of theories whose duals are described by a collection of free fields. In such cases, due to mixing between the superconformal R-symmetry and accidental symmetries, the matching of electric and magnetic partition functions is not straightforward. We provide a prescription to rectify this mismatch. In chapter 5, we consider some the N = 1 4d theories with orthogonal and symplectic gauge groups, arising from N = 1 preserving reduction of 6d theories on a Riemann surface. This construction allows us to dual descriptions of 4d theories. Some of the dual frames have no known Lagrangian description. We check the dualities by computing the anomaly coefficients and the superconformal indices. We also give a prescription to write the index of the theory obtained by reduction of 6d theories on a three

  13. Current density partitioning in time-dependent current density functional theory

    SciTech Connect

    Mosquera, Martín A.; Wasserman, Adam

    2014-05-14

    We adapt time-dependent current density functional theory to allow for a fragment-based solution of the many-electron problem of molecules in the presence of time-dependent electric and magnetic fields. Regarding a molecule as a set of non-interacting subsystems that individually evolve under the influence of an auxiliary external electromagnetic vector-scalar potential pair, the partition 4-potential, we show that there are one-to-one mappings between this auxiliary potential, a sharply-defined set of fragment current densities, and the total current density of the system. The partition electromagnetic (EM) 4-potential is expressed in terms of the real EM 4-potential of the system and a gluing EM 4-potential that accounts for exchange-correlation effects and mutual interaction forces between fragments that are required to yield the correct electron dynamics. We prove the zero-force theorem for the fragmented system, establish a variational formulation in terms of action functionals, and provide a simple illustration for a charged particle in a ring.

  14. Semiclassical limits of quantum partition functions on infinite graphs

    SciTech Connect

    Güneysu, Batu

    2015-02-15

    We prove that if H denotes the operator corresponding to the canonical Dirichlet form on a possibly locally infinite weighted graph (X, b, m), and if v : X → ℝ is such that H + v/ħ is well-defined as a form sum for all ħ > 0, then the quantum partition function tr(e{sup −βħ(H+v/ħ)}) converges to ∑{sub x∈X}e{sup −βv(x)} as ħ → 0 +, for all β > 0, regardless of the fact whether e{sup −βv} is a priori summable or not. This fact can be interpreted as a semiclassical limit, and it allows geometric Weyl-type convergence results. We also prove natural generalizations of this semiclassical limit to a large class of covariant Schrödinger operators that act on sections in Hermitian vector bundle over (X, m, b), a result that particularly applies to magnetic Schrödinger operators that are defined on (X, m, b)

  15. Computing the Partition Function for Kinetically Trapped RNA Secondary Structures

    PubMed Central

    Lorenz, William A.; Clote, Peter

    2011-01-01

    An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally optimal structure must involve energetically unfavorable folding steps. Here, we present a novel, efficient algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence. Our software, RNAlocopt runs in time and space. Additionally, RNAlocopt samples a user-specified number of structures from the Boltzmann subensemble of all locally optimal structures. We apply RNAlocopt to show that (1) the number of locally optimal structures is far fewer than the total number of structures – indeed, the number of locally optimal structures approximately equal to the square root of the number of all structures, (2) the structural diversity of this subensemble may be either similar to or quite different from the structural diversity of the entire Boltzmann ensemble, a situation that depends on the type of input RNA, (3) the (modified) maximum expected accuracy structure, computed by taking into account base pairing frequencies of locally optimal structures, is a more accurate prediction of the native structure than other current thermodynamics-based methods. The software RNAlocopt constitutes a technical breakthrough in our study of the folding landscape for RNA secondary structures. For the first time, locally optimal structures (kinetic traps in the Turner energy model) can be rapidly generated for long RNA sequences, previously impossible with methods that involved exhaustive enumeration. Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected accuracy. Web server

  16. Computing the partition function for kinetically trapped RNA secondary structures.

    PubMed

    Lorenz, William A; Clote, Peter

    2011-01-01

    An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally optimal structure must involve energetically unfavorable folding steps. Here, we present a novel, efficient algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence. Our software, RNAlocopt runs in O(n3) time and O(n2) space. Additionally, RNAlocopt samples a user-specified number of structures from the Boltzmann subensemble of all locally optimal structures. We apply RNAlocopt to show that (1) the number of locally optimal structures is far fewer than the total number of structures--indeed, the number of locally optimal structures approximately equal to the square root of the number of all structures, (2) the structural diversity of this subensemble may be either similar to or quite different from the structural diversity of the entire Boltzmann ensemble, a situation that depends on the type of input RNA, (3) the (modified) maximum expected accuracy structure, computed by taking into account base pairing frequencies of locally optimal structures, is a more accurate prediction of the native structure than other current thermodynamics-based methods. The software RNAlocopt constitutes a technical breakthrough in our study of the folding landscape for RNA secondary structures. For the first time, locally optimal structures (kinetic traps in the Turner energy model) can be rapidly generated for long RNA sequences, previously impossible with methods that involved exhaustive enumeration. Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected accuracy

  17. Region Graph Partition Function Expansion and Approximate Free Energy Landscapes: Theory and Some Numerical Results

    NASA Astrophysics Data System (ADS)

    Zhou, Haijun; Wang, Chuang

    2012-08-01

    Graphical models for finite-dimensional spin glasses and real-world combinatorial optimization and satisfaction problems usually have an abundant number of short loops. The cluster variation method and its extension, the region graph method, are theoretical approaches for treating the complicated short-loop-induced local correlations. For graphical models represented by non-redundant or redundant region graphs, approximate free energy landscapes are constructed in this paper through the mathematical framework of region graph partition function expansion. Several free energy functionals are obtained, each of which use a set of probability distribution functions or functionals as order parameters. These probability distribution function/functionals are required to satisfy the region graph belief-propagation equation or the region graph survey-propagation equation to ensure vanishing correction contributions of region subgraphs with dangling edges. As a simple application of the general theory, we perform region graph belief-propagation simulations on the square-lattice ferromagnetic Ising model and the Edwards-Anderson model. Considerable improvements over the conventional Bethe-Peierls approximation are achieved. Collective domains of different sizes in the disordered and frustrated square lattice are identified by the message-passing procedure. Such collective domains and the frustrations among them are responsible for the low-temperature glass-like dynamical behaviors of the system.

  18. Revealing how species loss affects ecosystem function: the trait-based Price Equation partition.

    PubMed

    Fox, Jeremy W; Harpole, W Stanley

    2008-01-01

    Species loss can alter ecosystem function. Recent work proposes a general theoretical framework, the "Price Equation partition," for understanding how species loss affects ecosystem functions that comprise the summed contributions of individual species (e.g., primary production). The Price Equation partition shows how the difference in function between a pre-species-loss site and a post-loss site can be partitioned into effects of random loss of species richness (species-richness effect; SRE), nonrandom loss of high- or low-functioning species (species-composition effect; SCE), and post-loss changes in the functional contributions of the remaining species (context-dependence effect; CDE). However, the Price Equation partition is silent on the underlying determinants of species' functional contributions. Here we extend the Price Equation partition by using multiple regression to describe how species' functional contributions depend on species' traits. This allows us to reexpress the SCE and CDE in terms of nonrandom loss of species with particular traits (trait-based SCE), and post-loss changes in species' traits and in the relationship between species' traits and species' functional contributions (trait-based CDE). We apply this new trait-based Price Equation partition to studies of species loss from grassland plant communities and protist microcosm food webs. In both studies, post-loss changes in the relationship between species' traits and their functional contributions alter ecosystem function more than nonrandom loss of species with particular traits. The protist microcosm data also illustrate how the trait-based Price Equation partition can be applied when species' functional contributions depend in part on the traits of other species. To do this, we define "synecological" traits that quantify how unique species are (e.g., in diet) compared to other species. Context dependence in the protist microcosm experiment arises in part because species loss alters the

  19. 1-loop partition function in AdS 3/ CFT 2

    NASA Astrophysics Data System (ADS)

    Chen, Bin; Wu, Jie-qiang

    2015-12-01

    The 1-loop partition function of the handlebody solutions in the AdS3 gravity have been derived some years ago using the heat kernel techniques and the method of images. In the semiclassical limit, such partition function should correspond to the order O( c 0) part in the partition function of dual conformal field theory(CFT) on the boundary Riemann surface. The higher genus partition function could be computed by the multi-point functions in the Riemann sphere via sewing prescription. In the large central charge limit, the CFT is effectively free in the sense that to the leading order of c the multi-point function is further simplified to be a summation over the products of two-point functions of single-particle states. Correspondingly in the bulk, the graviton is freely propagating without interaction. Furthermore the product of the two-point functions may define the links, each of which is in one-to-one correspondence with the conjugacy class of the Schottky group of the Riemann surface. Moreover, the value of a link is determined by the multiplier of the element in the conjugacy class. This allows us to reproduce exactly the gravitational 1-loop partition function. The proof can be generalized to the higher spin gravity and its dual CFT.

  20. Extending the applicability of the Tkatchenko-Scheffler dispersion correction via iterative Hirshfeld partitioning.

    PubMed

    Bučko, Tomáš; Lebègue, Sébastien; Ángyán, János G; Hafner, Jürgen

    2014-07-21

    Recently we have demonstrated that the applicability of the Tkatchenko-Scheffler (TS) method for calculating dispersion corrections to density-functional theory can be extended to ionic systems if the Hirshfeld method for estimating effective volumes and charges of atoms in molecules or solids (AIM's) is replaced by its iterative variant [T. Bučko, S. Lebègue, J. Hafner, and J. Ángyán, J. Chem. Theory Comput. 9, 4293 (2013)]. The standard Hirshfeld method uses neutral atoms as a reference, whereas in the iterative Hirshfeld (HI) scheme the fractionally charged atomic reference states are determined self-consistently. We show that the HI method predicts more realistic AIM charges and that the TS/HI approach leads to polarizabilities and C6 dispersion coefficients in ionic or partially ionic systems which are, as expected, larger for anions than for cations (in contrast to the conventional TS method). For crystalline materials, the new algorithm predicts polarizabilities per unit cell in better agreement with the values derived from the Clausius-Mosotti equation. The applicability of the TS/HI method has been tested for a wide variety of molecular and solid-state systems. It is demonstrated that for systems dominated by covalent interactions and/or dispersion forces the TS/HI method leads to the same results as the conventional TS approach. The difference between the TS/HI and TS approaches increases with increasing ionicity. A detailed comparison is presented for isoelectronic series of octet compounds, layered crystals, complex intermetallic compounds, and hydrides, and for crystals built of molecules or containing molecular anions. It is demonstrated that only the TS/HI method leads to accurate results for systems where both electrostatic and dispersion interactions are important, as illustrated for Li-intercalated graphite and for molecular adsorption on the surfaces in ionic solids and in the cavities of zeolites.

  1. Extending the applicability of the Tkatchenko-Scheffler dispersion correction via iterative Hirshfeld partitioning

    SciTech Connect

    Bučko, Tomáš; Lebègue, Sébastien; Ángyán, János G.; and others

    2014-07-21

    Recently we have demonstrated that the applicability of the Tkatchenko-Scheffler (TS) method for calculating dispersion corrections to density-functional theory can be extended to ionic systems if the Hirshfeld method for estimating effective volumes and charges of atoms in molecules or solids (AIM’s) is replaced by its iterative variant [T. Bučko, S. Lebègue, J. Hafner, and J. Ángyán, J. Chem. Theory Comput. 9, 4293 (2013)]. The standard Hirshfeld method uses neutral atoms as a reference, whereas in the iterative Hirshfeld (HI) scheme the fractionally charged atomic reference states are determined self-consistently. We show that the HI method predicts more realistic AIM charges and that the TS/HI approach leads to polarizabilities and C{sub 6} dispersion coefficients in ionic or partially ionic systems which are, as expected, larger for anions than for cations (in contrast to the conventional TS method). For crystalline materials, the new algorithm predicts polarizabilities per unit cell in better agreement with the values derived from the Clausius-Mosotti equation. The applicability of the TS/HI method has been tested for a wide variety of molecular and solid-state systems. It is demonstrated that for systems dominated by covalent interactions and/or dispersion forces the TS/HI method leads to the same results as the conventional TS approach. The difference between the TS/HI and TS approaches increases with increasing ionicity. A detailed comparison is presented for isoelectronic series of octet compounds, layered crystals, complex intermetallic compounds, and hydrides, and for crystals built of molecules or containing molecular anions. It is demonstrated that only the TS/HI method leads to accurate results for systems where both electrostatic and dispersion interactions are important, as illustrated for Li-intercalated graphite and for molecular adsorption on the surfaces in ionic solids and in the cavities of zeolites.

  2. Genus Two Partition and Correlation Functions for Fermionic Vertex Operator Superalgebras I

    NASA Astrophysics Data System (ADS)

    Tuite, Michael P.; Zuevsky, Alexander

    2011-09-01

    We define the partition and n-point correlation functions for a vertex operator superalgebra on a genus two Riemann surface formed by sewing two tori together. For the free fermion vertex operator superalgebra we obtain a closed formula for the genus two continuous orbifold partition function in terms of an infinite dimensional determinant with entries arising from torus Szegő kernels. We prove that the partition function is holomorphic in the sewing parameters on a given suitable domain and describe its modular properties. Using the bosonized formalism, a new genus two Jacobi product identity is described for the Riemann theta series. We compute and discuss the modular properties of the generating function for all n-point functions in terms of a genus two Szegő kernel determinant. We also show that the Virasoro vector one point function satisfies a genus two Ward identity.

  3. Coexistence via resource partitioning fails to generate an increase in community function.

    PubMed

    DeLong, John P; Vasseur, David A

    2012-01-01

    Classic ecological theory suggests that resource partitioning facilitates the coexistence of species by reducing inter-specific competition. A byproduct of this process is an increase in overall community function, because a greater spectrum of resources can be used. In contrast, coexistence facilitated by neutral mechanisms is not expected to increase function. We studied coexistence in laboratory microcosms of the bactivorous ciliates Paramecium aurelia and Colpidium striatum to understand the relationship between function and coexistence mechanism. We quantified population and community-level function (biomass and oxygen consumption), competitive interactions, and resource partitioning. The two ciliates partitioned their bacterial resource along a size axis, with the larger ciliate consuming larger bacteria than the smaller ciliate. Despite this, there was no gain in function at the community level for either biomass or oxygen consumption, and competitive effects were symmetrical within and between species. Because other potential coexistence mechanisms can be ruled out, it is likely that inter-specific interference competition diminished the expected gain in function generated by resource partitioning, leading to a system that appeared competitively neutral even when structured by niche partitioning. We also analyzed several previous studies where two species of protists coexisted and found that the two-species communities showed a broad range of biomass levels relative to the single-species states.

  4. Coexistence via Resource Partitioning Fails to Generate an Increase in Community Function

    PubMed Central

    DeLong, John P.; Vasseur, David A.

    2012-01-01

    Classic ecological theory suggests that resource partitioning facilitates the coexistence of species by reducing inter-specific competition. A byproduct of this process is an increase in overall community function, because a greater spectrum of resources can be used. In contrast, coexistence facilitated by neutral mechanisms is not expected to increase function. We studied coexistence in laboratory microcosms of the bactivorous ciliates Paramecium aurelia and Colpidium striatum to understand the relationship between function and coexistence mechanism. We quantified population and community-level function (biomass and oxygen consumption), competitive interactions, and resource partitioning. The two ciliates partitioned their bacterial resource along a size axis, with the larger ciliate consuming larger bacteria than the smaller ciliate. Despite this, there was no gain in function at the community level for either biomass or oxygen consumption, and competitive effects were symmetrical within and between species. Because other potential coexistence mechanisms can be ruled out, it is likely that inter-specific interference competition diminished the expected gain in function generated by resource partitioning, leading to a system that appeared competitively neutral even when structured by niche partitioning. We also analyzed several previous studies where two species of protists coexisted and found that the two-species communities showed a broad range of biomass levels relative to the single-species states. PMID:22253888

  5. 3D-partition functions on the sphere: exact evaluation and mirror symmetry

    NASA Astrophysics Data System (ADS)

    Benvenuti, Sergio; Pasquetti, Sara

    2012-05-01

    We study {N} = {4} quiver theories on the three-sphere. We compute partition functions using the localisation method by Kapustin et al. solving exactly the matrix integrals at finite N, as functions of mass and Fayet-Iliopoulos parameters. We find a simple explicit formula for the partition function of the quiver tail T(SU( N)). This formula opens the way for the analysis of star-shaped quivers and their mirrors (that are the Gaiotto-type theories arising from M5 branes on punctured Riemann surfaces). We provide non-perturbative checks of mirror symmetry for infinite classes of theories and find the partition functions of the T N theory, the building block of generalised quiver theories.

  6. Iterating free-field AdS/CFT: higher spin partition function relations

    NASA Astrophysics Data System (ADS)

    Beccaria, Matteo; Tseytlin, Arkady A.

    2016-07-01

    We find a simple relation between a free higher spin partition function on the thermal quotient of {{AdS}}d+1 and the partition function of the associated d-dimensional conformal higher spin field defined on the thermal quotient of {{AdS}}d. Starting with a conformal higher spin field defined in {{AdS}}d, one may also associate to with another conformal field in d-1 dimensions, thus iterating AdS/CFT. We observe that in the case of d=4, this iteration leads to a trivial 3d higher spin conformal theory with parity-even non-local action: it describes a zero total number of dynamical degrees of freedom and the corresponding partition function is equal to 1.

  7. Anharmonic state counts and partition functions for molecules via classical phase space integrals in curvilinear coordinates.

    PubMed

    Kamarchik, Eugene; Jasper, Ahren W

    2013-05-21

    An algorithm is presented for calculating fully anharmonic vibrational state counts, state densities, and partition functions for molecules using Monte Carlo integration of classical phase space. The algorithm includes numerical evaluations of the elements of the Jacobian and is general enough to allow for sampling in arbitrary curvilinear or rectilinear coordinate systems. Invariance to the choice of coordinate system is demonstrated for vibrational state densities of methane, where we find comparable sampling efficiency when using curvilinear z-matrix and rectilinear Cartesian normal mode coordinates. In agreement with past work, we find that anharmonicity increases the vibrational state density of methane by a factor of ∼2 at its dissociation threshold. For the vinyl radical, we find a significant (∼10×) improvement in sampling efficiency when using curvilinear z-matrix coordinates relative to Cartesian normal mode coordinates. We attribute this improved efficiency, in part, to a more natural curvilinear coordinate description of the double well associated with the H2C-C-H wagging motion. The anharmonicity correction for the vinyl radical state density is ∼1.4 at its dissociation threshold. Finally, we demonstrate that with trivial parallelizations of the Monte Carlo step, tractable calculations can be made for the vinyl radical using direct ab initio potential energy surface evaluations and a composite QCISD(T)/MP2 method.

  8. Quasiclassical approach to partition functions of ions in a chemical plasma model

    SciTech Connect

    Shpatakovskaya, G. V.

    2008-03-15

    The partition functions of ions that are used in a chemical plasma model are estimated by the Thomas-Fermi free ion model without reference to empirical data. Different form factors limiting the number of the excitation levels taken into account are considered, namely, those corresponding to the average atomic radius criterion, the temperature criterion, and the Planck-Brillouin-Larkin approximation. Expressions are presented for the average excitation energy and for the temperature and volume derivatives of the partition function. A comparison with the results of the empirical approach is made for the aluminum and iron plasmas.

  9. Compactified strings as quantum statistical partition function on the Jacobian torus.

    PubMed

    Matone, Marco; Pasti, Paolo; Shadchin, Sergey; Volpato, Roberto

    2006-12-31

    We show that the solitonic contribution of toroidally compactified strings corresponds to the quantum statistical partition function of a free particle living on higher dimensional spaces. In the simplest case of compactification on a circle, the Hamiltonian is the Laplacian on the 2g-dimensional Jacobian torus associated with the genus g Riemann surface corresponding to the string world sheet. T duality leads to a symmetry of the partition function mixing time and temperature. Such a classical-quantum correspondence and T duality shed some light on the well-known interplay between time and temperature in quantum field theory and classical statistical mechanics.

  10. Use of JANAF Tables in Equilibrium Calculations and Partition Function Calculations for an Undergraduate Physical Chemistry Course

    ERIC Educational Resources Information Center

    Cleary, David A.

    2014-01-01

    The usefulness of the JANAF tables is demonstrated with specific equilibrium calculations. An emphasis is placed on the nature of standard chemical potential calculations. Also, the use of the JANAF tables for calculating partition functions is examined. In the partition function calculations, the importance of the zero of energy is highlighted.

  11. Equivalent Structures on Sets: Equivalence Classes, Partitions and Fiber Structures of Functions

    ERIC Educational Resources Information Center

    Hamdan, May

    2006-01-01

    This study reports on how students can be led to make meaningful connections between such structures on a set as a partition, the set of equivalence classes determined by an equivalence relation and the fiber structure of a function on that set (i.e., the set of preimages of all sets {b} for b in the range of the function). In this paper, I first…

  12. Algorithm for finding partitionings of hard variants of boolean satisfiability problem with application to inversion of some cryptographic functions.

    PubMed

    Semenov, Alexander; Zaikin, Oleg

    2016-01-01

    In this paper we propose an approach for constructing partitionings of hard variants of the Boolean satisfiability problem (SAT). Such partitionings can be used for solving corresponding SAT instances in parallel. For the same SAT instance one can construct different partitionings, each of them is a set of simplified versions of the original SAT instance. The effectiveness of an arbitrary partitioning is determined by the total time of solving of all SAT instances from it. We suggest the approach, based on the Monte Carlo method, for estimating time of processing of an arbitrary partitioning. With each partitioning we associate a point in the special finite search space. The estimation of effectiveness of the particular partitioning is the value of predictive function in the corresponding point of this space. The problem of search for an effective partitioning can be formulated as a problem of optimization of the predictive function. We use metaheuristic algorithms (simulated annealing and tabu search) to move from point to point in the search space. In our computational experiments we found partitionings for SAT instances encoding problems of inversion of some cryptographic functions. Several of these SAT instances with realistic predicted solving time were successfully solved on a computing cluster and in the volunteer computing project SAT@home. The solving time agrees well with estimations obtained by the proposed method. PMID:27190753

  13. Algorithm for finding partitionings of hard variants of boolean satisfiability problem with application to inversion of some cryptographic functions.

    PubMed

    Semenov, Alexander; Zaikin, Oleg

    2016-01-01

    In this paper we propose an approach for constructing partitionings of hard variants of the Boolean satisfiability problem (SAT). Such partitionings can be used for solving corresponding SAT instances in parallel. For the same SAT instance one can construct different partitionings, each of them is a set of simplified versions of the original SAT instance. The effectiveness of an arbitrary partitioning is determined by the total time of solving of all SAT instances from it. We suggest the approach, based on the Monte Carlo method, for estimating time of processing of an arbitrary partitioning. With each partitioning we associate a point in the special finite search space. The estimation of effectiveness of the particular partitioning is the value of predictive function in the corresponding point of this space. The problem of search for an effective partitioning can be formulated as a problem of optimization of the predictive function. We use metaheuristic algorithms (simulated annealing and tabu search) to move from point to point in the search space. In our computational experiments we found partitionings for SAT instances encoding problems of inversion of some cryptographic functions. Several of these SAT instances with realistic predicted solving time were successfully solved on a computing cluster and in the volunteer computing project SAT@home. The solving time agrees well with estimations obtained by the proposed method.

  14. Partition functions of superconformal Chern-Simons theories from Fermi gas approach

    NASA Astrophysics Data System (ADS)

    Moriyama, Sanefumi; Nosaka, Tomoki

    2014-11-01

    We study the partition function of three-dimensional superconformal Chern-Simons theories of the circular quiver type, which are natural generalizations of the ABJM theory, the worldvolume theory of M2-branes. In the ABJM case, it was known that the perturbative part of the partition function sums up to the Airy function as Z( N) = e A C -1/3Ai[ C -1/3( N - B)] with coefficients C, B and A and that for the non-perturbative part the divergences coming from the coefficients of worldsheet instantons and membrane instantons cancel among themselves. We find that many of the interesting properties in the ABJM theory are extended to the general superconformal Chern-Simons theories. Especially, we find an explicit expression of B for general theories, a conjectural form of A for a special class of theories, and cancellation in the non-perturbative coefficients for the simplest theory next to the ABJM theory.

  15. Superconformal Chern-Simons partition functions of affine D-type quiver from Fermi gas

    NASA Astrophysics Data System (ADS)

    Moriyama, Sanefumi; Nosaka, Tomoki

    2015-09-01

    We consider the partition function of the superconformal Chern-Simons theories with the quiver diagram being the affine D-type Dynkin diagram. Rewriting the partition function into that of a Fermi gas system, we show that the perturbative expansions in 1 /N are summed up to an Airy function, as in the ABJM theory or more generally the theories of the affine A-type quiver. As a corollary, this provides a proof for the previous proposal in the large N limit. For special values of the Chern-Simons levels, we further identify three species of the membrane instantons and also conjecture an exact expression of the overall constant, which corresponds to the constant map in the topological string theory. [Figure not available: see fulltext.

  16. Heat capacity decomposition by partition function zeros for interacting self-avoiding walks

    NASA Astrophysics Data System (ADS)

    Chen, Chi-Ning; Hsieh, Yu-Hsin; Hu, Chin-Kun

    2013-10-01

    A novel method based on partition function zeros is developed to demonstrate the additional advantages by considering both loci of partition function zeros and thermodynamical functions associated with them. With this method, the first pair of complex conjugate zeros (first zeros) can be defined without ambiguity and the critical point of a small system can be defined as the peak position of the heat capacity component associated with the first zeros. For the system with two phase transitions, two pairs of first zeros corresponding to two phase transitions can be identified and two overlapping phase transitions can be well separated. This method is applied to the interacting self-avoiding walk (ISAW) of homopolymer with N monomers on the simple cubic lattice, which has a collapse transition at a higher temperature and a freezing transition at a low temperature. The exact partition functions ZN with N up to 27 are calculated and our approach gives a clear scenario for the collapse and the freezing transitions.

  17. Long-Range Corrected Hybrid Density Functionals with Damped Atom-Atom Dispersion Corrections

    SciTech Connect

    Chai, Jeng-Da; Head-Gordon, Martin

    2008-06-14

    We report re-optimization of a recently proposed long-range corrected (LC) hybrid density functionals [J.-D. Chai and M. Head-Gordon, J. Chem. Phys. 128, 084106 (2008)] to include empirical atom-atom dispersion corrections. The resulting functional, {omega}B97X-D yields satisfactory accuracy for thermochemistry, kinetics, and non-covalent interactions. Tests show that for non-covalent systems, {omega}B97X-D shows slight improvement over other empirical dispersion-corrected density functionals, while for covalent systems and kinetics, it performs noticeably better. Relative to our previous functionals, such as {omega}B97X, the new functional is significantly superior for non-bonded interactions, and very similar in performance for bonded interactions.

  18. Relation between the 4d superconformal index and the S 3 partition function

    NASA Astrophysics Data System (ADS)

    Imamura, Yosuke

    2011-09-01

    A relation between the 4d superconformal index and the S 3 partition function is studied with focus on the 4d and 3d actions used in localization. In the case of vanishing Chern-Simons levels and round S 3 we explicitly show that the 3d action is obtained from the4d action by dimensional reduction up to terms which do not affect the exact results. By combining this fact and a recent proposal concerning a squashing of S 3 and SU(2) Wilson line, we obtain a formula which gives the partition function depending on the Weyl weight of chiral multiplets, real mass parameters, FI parameters, and a squashing parameter as a limit of the index of a parent 4d theory.

  19. Boundary conditions and partition functions in higher spin AdS3/CFT2

    NASA Astrophysics Data System (ADS)

    de Boer, Jan; Jottar, Juan I.

    2016-04-01

    We discuss alternative definitions of the semiclassical partition function in two-dimensional CFTs with higher spin symmetry, in the presence of sources for the higher spin currents. Theories of this type can often be described via Hamiltonian reduction of current algebras, and a holographic description in terms of three-dimensional Chern-Simons theory with generalized AdS boundary conditions becomes available. By studying the CFT Ward identities in the presence of sources, we determine the appropriate choice of boundary terms and boundary conditions in Chern-Simons theory for the various types of partition functions considered. In particular, we compare the Chern-Simons description of deformations of the field theory Hamiltonian versus those encoding deformations of the CFT action. Our analysis clarifies various issues and confusions that have permeated the literature on this subject.

  20. Towards a classification of modular invariant partition functions for theories based on N=4 superconformal algebras

    NASA Astrophysics Data System (ADS)

    Taormina, Anne

    1993-05-01

    The representation theory of the doubly extended N=4 superconformal algebra is reviewed. The modular properties of the corresponding characters can be derived, using characters sumrules for coset realizations of these N=4 algebras. Some particular combinations of massless characters are shown to transform as affine SU(2) characters under S and T, a fact used to completely classify the massless sector of the partition function.

  1. An efficient algorithm for upper bound on the partition function of nucleic acids.

    PubMed

    Chitsaz, Hamidreza; Forouzmand, Elmirasadat; Haffari, Gholamreza

    2013-07-01

    It has been shown that minimum free-energy structure for RNAs and RNA-RNA interaction is often incorrect due to inaccuracies in the energy parameters and inherent limitations of the energy model. In contrast, ensemble-based quantities such as melting temperature and equilibrium concentrations can be more reliably predicted. Even structure prediction by sampling from the ensemble and clustering those structures by Sfold has proven to be more reliable than minimum free energy structure prediction. The main obstacle for ensemble-based approaches is the computational complexity of the partition function and base-pairing probabilities. For instance, the space complexity of the partition function for RNA-RNA interaction is O(n4) and the time complexity is O(n6), which is prohibitively large. Our goal in this article is to present a fast algorithm, based on sparse folding, to calculate an upper bound on the partition function. Our work is based on the recent algorithm of Hazan and Jaakkola (2012). The space complexity of our algorithm is the same as that of sparse folding algorithms, and the time complexity of our algorithm is O(MFE(n)ℓ) for single RNA and O(MFE(m, n)ℓ) for RNA-RNA interaction in practice, in which MFE is the running time of sparse folding and ℓ≤n (ℓ≤n+m) is a sequence-dependent parameter.

  2. Function approximation based on fuzzy rules extracted from partitioned numerical data.

    PubMed

    Thawonmas, R; Abe, S

    1999-01-01

    We present an efficient method for extracting fuzzy rules directly from numerical input-output data for function approximation problems. First, we convert a given function approximation problem into a pattern classification problem. This is done by dividing the universe of discourse of the output variable into multiple intervals, each regarded as a class, and then by assigning a class to each of the training data according to the desired value of the output variable. Next, we partition the data of each class in the input space to achieve a higher accuracy in approximation of class regions. Partition terminates according to a given criterion to prevent excessive partition. For class region approximation, we discuss two different types of representations using hyperboxes and ellipsoidal regions, respectively. Based on a selected representation, we then extract fuzzy rules from the approximated class regions. For a given input datum, we convert, or in other words, defuzzify, the resulting vector of the class membership degrees into a single real value. This value represents the final result approximated by the method. We test the presented method on a synthetic nonlinear function approximation problem and a real-world problem in an application to a water purification plant. We also compare the presented method with a method based on neural networks.

  3. Verifying Correct Functionality of Avionics Subsystems

    NASA Technical Reports Server (NTRS)

    Meuer, Ben t.

    2005-01-01

    This project focuses on the testing of the telecommunications interface subsystem of the Multi-Mission System Architecture Platform to ensure proper functionality. The Multi-Mission System Architecture Platform is a set of basic tools designed to be used in future spacecraft. The responsibilities of the telecommunications interface include communication between the spacecraft and ground teams as well as acting as the bus controller for the system. The tests completed include bit wise read\\write tests to each register, testing of status bits, and verifying various bus controller activities. Testing is accomplished through the use of software-based simulations run on an electronic design of the system. The tests are written in Verilog Hardware Definition Language and they simulate specific states and conditions in telecommunication interfaces. Upon successful completion, the output is examined to verify that the system responded appropriately.

  4. Arbitrary function generator for APS injector synchrotron correction magnets

    SciTech Connect

    Despe, O.D.

    1990-11-07

    The APS injector synchrotron ring measures about 368 m in circumference. In order to obtain the precision of the magnetic field required for the positron acceleration from 450 Mev to 7.7 Gev with low beam loss, eighty correction magnets are distributed around its circumference. These magnets provide the vernier field changes required for beam orbit correction during the acceleration phase of the injector synchrotron cycle. Because of mechanical imperfections in the construction, as well as installation of real dipole and multi-pole magnets, the exact field correction required at each correction magnet location is not known until a beam is actually accelerated. It is therefore essential that a means is provided to generate a correction field that is a function of the beam energy from injection until extraction for each correction magnet. The fairly large number of correction magnets in the system requires that the arbitrary function generator design be as simple as possible yet provide the required performance. An important, required performance feature is that the function can be changed or modified ``on the fly``, to provide the operator with a real-time feel during the tune up process. The arbitrary function generator described in this report satisfies these requirements.

  5. Rovibrational energies, partition functions and equilibrium fractionation of the CO2 isotopologues

    NASA Astrophysics Data System (ADS)

    Cerezo, J.; Bastida, A.; Requena, A.; Zúñiga, J.

    2014-11-01

    Rovibrational energy levels, partition functions and relative abundances of the stable isotopologues of CO2 in gas phase at equilibrium are calculated using an empirical Morse-cosine potential energy surface (PES) refined by fitting to the updated pure (l2=0) vibrational frequencies observed for the main 12C16O2 isotopologue. The rovibrational energy levels are calculated variationally using a system of optimized hyperspherical normal coordinates, and from these the vibrational terms Gv and rotational constants Bv of the isotopologues are determined. The refined potential surface is shown to be clearly superior to the original potential surface, with the former reproducing the observed values of the spectroscopic constants Gv and Bv with accuracies of about 0.1 cm-1 and 0.00020 cm-1, respectively, for levels with l2≥0 up to 10,000 cm-1 above the ground state. The internal partition functions of the isotopologues are calculated by approximated direct summation over the rovibrational energies and compared with both previous partition sums and values obtained from analytical expressions based on the harmonic oscillator and rigid rotor models. The partition functions calculated by approximated direct summation are then used to determine the abundances of the CO2 isotopologues at thermodynamic equilibrium using the method developed by Wang et al. [74]. Significant variations in the relative abundances of some of the CO2 multiple substituted isotopologues at terrestrial temperatures with respect to those provided by the classical harmonic-based Urey theory are found, which may be of relevance in geochemical processes.

  6. Overlap Correction Function For an Airborne Based Lidar

    NASA Astrophysics Data System (ADS)

    Adam, Mariana; Marenco, Franco

    2016-06-01

    The present research envisages the estimation of the overlap correction function for an airborne nadir-mounted lidar using multi-angle measurements. We have scanned a series of offnadir angles and after data processing we have been able to determine the instrument's overlap function down to 95m from the lidar. This function can be used for the correction of lidar profiles and hence reduce the near-range uncertainty of lidar measurements. To our knowledge, the estimation of the overlap function using multi-angle method for a nadir pointing lidar is a première.

  7. Self-interaction corrections in density functional theory

    SciTech Connect

    Tsuneda, Takao; Hirao, Kimihiko

    2014-05-14

    Self-interaction corrections for Kohn-Sham density functional theory are reviewed for their physical meanings, formulations, and applications. The self-interaction corrections get rid of the self-interaction error, which is the sum of the Coulomb and exchange self-interactions that remains because of the use of an approximate exchange functional. The most frequently used self-interaction correction is the Perdew-Zunger correction. However, this correction leads to instabilities in the electronic state calculations of molecules. To avoid these instabilities, several self-interaction corrections have been developed on the basis of the characteristic behaviors of self-interacting electrons, which have no two-electron interactions. These include the von Weizsäcker kinetic energy and long-range (far-from-nucleus) asymptotic correction. Applications of self-interaction corrections have shown that the self-interaction error has a serious effect on the states of core electrons, but it has a smaller than expected effect on valence electrons. This finding is supported by the fact that the distribution of self-interacting electrons indicates that they are near atomic nuclei rather than in chemical bonds.

  8. Self-interaction corrections in density functional theory

    NASA Astrophysics Data System (ADS)

    Tsuneda, Takao; Hirao, Kimihiko

    2014-05-01

    Self-interaction corrections for Kohn-Sham density functional theory are reviewed for their physical meanings, formulations, and applications. The self-interaction corrections get rid of the self-interaction error, which is the sum of the Coulomb and exchange self-interactions that remains because of the use of an approximate exchange functional. The most frequently used self-interaction correction is the Perdew-Zunger correction. However, this correction leads to instabilities in the electronic state calculations of molecules. To avoid these instabilities, several self-interaction corrections have been developed on the basis of the characteristic behaviors of self-interacting electrons, which have no two-electron interactions. These include the von Weizsäcker kinetic energy and long-range (far-from-nucleus) asymptotic correction. Applications of self-interaction corrections have shown that the self-interaction error has a serious effect on the states of core electrons, but it has a smaller than expected effect on valence electrons. This finding is supported by the fact that the distribution of self-interacting electrons indicates that they are near atomic nuclei rather than in chemical bonds.

  9. VizieR Online Data Catalog: Partition functions for molecules and atoms (Barklem+, 2016)

    NASA Astrophysics Data System (ADS)

    Barklem, P. S.; Collet, R.

    2016-02-01

    The results and input data are presented in the following files. Table 1 contains dissociation energies from the literature, and final adopted values, for 291 molecules. The literature values are from the compilations of Huber & Herzberg (1979, Constants of Diatomic Molecules (Van Nostrand Reinhold), Luo (2007, Comprehensive Handbook of Chemical Bond Energies (CRC Press)) and G2 theory calculations of Curtiss et al. (1991, J. Chem. Phys., 94, 7221). Table 2 contains the input data for the molecular calculations including adopted dissociation energy, nuclear spins, molecular spectroscopic constants and their sources. There are 291 files, one for each molecule, labelled by the molecule name. The various molecular spectroscopic constants are as defined in the paper. Table 4 contains the first, second and third ionisation energies for all chemical elements from H to U. The data comes from the CRC Handbook of Chemistry and Physics (Haynes, W.M. 2010, CRC Handbook of Chemistry and Physics, 91st edn. (CRC Press, Taylor and Francis Group)). Table 5a contains a list of keys to bibliographic references for the atomic energy level data that was extracted from NIST Atomic Spectra Database and used in the present work to compute atomic partition functions. The citation keys are abbreviations of the full bibliographic references which are made available in Table 5b in BibTeX format. Table 5b contains the full bibliographic references for the atomic energy level data that was extracted from the NIST Atomic Spectra Database. Table 6 contains tabulated partition function data as a function of temperature for 291 molecules. Table 7 contains tabulated equilibrium constant data as a function of temperature for 291 molecules. Table 8 contains tabulated partition function data as a function of temperature for 284 atoms and ions. The paper should be consulted for further details. (10 data files).

  10. Partition functions of classical Heisenberg spin chains with arbitrary and different exchange

    NASA Astrophysics Data System (ADS)

    Cregg, P. J.; García-Palacios, J. L.; Svedlindh, P.

    2008-10-01

    The classical Heisenberg model has been effective in modelling exchange interactions in molecular magnets. In this model, the partition function is important as it allows the calculation of the magnetization and susceptibility. For an ensemble of N-spin sites, this typically involves integrals in 2N dimensions. Here, for two-, three- and four-spin nearest neighbour open linear Heisenberg chains these integrals are reduced to sums of known functions, using a result due to Gegenbauer. For the case of the three- and four-spin chains, the sums are equivalent in form to the results of Joyce. The general result for an N-spin chain is also obtained.

  11. Analysis of Different Cost Functions in the Geosect Airspace Partitioning Tool

    NASA Technical Reports Server (NTRS)

    Wong, Gregory L.

    2010-01-01

    A new cost function representing air traffic controller workload is implemented in the Geosect airspace partitioning tool. Geosect currently uses a combination of aircraft count and dwell time to select optimal airspace partitions that balance controller workload. This is referred to as the aircraft count/dwell time hybrid cost function. The new cost function is based on Simplified Dynamic Density, a measure of different aspects of air traffic controller workload. Three sectorizations are compared. These are the current sectorization, Geosect's sectorization based on the aircraft count/dwell time hybrid cost function, and Geosect s sectorization based on the Simplified Dynamic Density cost function. Each sectorization is evaluated for maximum and average workload along with workload balance using the Simplified Dynamic Density as the workload measure. In addition, the Airspace Concept Evaluation System, a nationwide air traffic simulator, is used to determine the capacity and delay incurred by each sectorization. The sectorization resulting from the Simplified Dynamic Density cost function had a lower maximum workload measure than the other sectorizations, and the sectorization based on the combination of aircraft count and dwell time did a better job of balancing workload and balancing capacity. However, the current sectorization had the lowest average workload, highest sector capacity, and the least system delay.

  12. A novel brain partition highlights the modular skeleton shared by structure and function

    PubMed Central

    Diez, Ibai; Bonifazi, Paolo; Escudero, Iñaki; Mateos, Beatriz; Muñoz, Miguel A.; Stramaglia, Sebastiano; Cortes, Jesus M.

    2015-01-01

    Elucidating the intricate relationship between brain structure and function, both in healthy and pathological conditions, is a key challenge for modern neuroscience. Recent progress in neuroimaging has helped advance our understanding of this important issue, with diffusion images providing information about structural connectivity (SC) and functional magnetic resonance imaging shedding light on resting state functional connectivity (rsFC). Here, we adopt a systems approach, relying on modular hierarchical clustering, to study together SC and rsFC datasets gathered independently from healthy human subjects. Our novel approach allows us to find a common skeleton shared by structure and function from which a new, optimal, brain partition can be extracted. We describe the emerging common structure-function modules (SFMs) in detail and compare them with commonly employed anatomical or functional parcellations. Our results underline the strong correspondence between brain structure and resting-state dynamics as well as the emerging coherent organization of the human brain. PMID:26037235

  13. A novel brain partition highlights the modular skeleton shared by structure and function.

    PubMed

    Diez, Ibai; Bonifazi, Paolo; Escudero, Iñaki; Mateos, Beatriz; Muñoz, Miguel A; Stramaglia, Sebastiano; Cortes, Jesus M

    2015-06-03

    Elucidating the intricate relationship between brain structure and function, both in healthy and pathological conditions, is a key challenge for modern neuroscience. Recent progress in neuroimaging has helped advance our understanding of this important issue, with diffusion images providing information about structural connectivity (SC) and functional magnetic resonance imaging shedding light on resting state functional connectivity (rsFC). Here, we adopt a systems approach, relying on modular hierarchical clustering, to study together SC and rsFC datasets gathered independently from healthy human subjects. Our novel approach allows us to find a common skeleton shared by structure and function from which a new, optimal, brain partition can be extracted. We describe the emerging common structure-function modules (SFMs) in detail and compare them with commonly employed anatomical or functional parcellations. Our results underline the strong correspondence between brain structure and resting-state dynamics as well as the emerging coherent organization of the human brain.

  14. A logarithmic correction in the entropy functional formalism

    NASA Astrophysics Data System (ADS)

    Hammad, Fayçal; Faizal, Mir

    2016-04-01

    The entropy functional formalism allows one to recover general relativity, modified gravity theories, as well as the Bekenstein-Hawking entropy formula. In most approaches to quantum gravity, the Bekenstein-Hawking’s entropy formula acquires a logarithmic correction term. As such terms occur almost universally in most approaches to quantum gravity, we analyze the effect of such terms on the entropy functional formalism. We demonstrate that the leading correction to the micro-canonical entropy in the entropy functional formalism can be used to recover modified theories of gravity already obtained with an uncorrected micro-canonical entropy. Furthermore, since the entropy functional formalism reproduces modified gravity, the rise of gravity-dependent logarithmic corrections turns out to be one way to impose constraints on these theories of modified gravity. The constraints found here for the simple case of an ℱ(R)-gravity are the same as those obtained in the literature from cosmological considerations.

  15. Chemical Assignment of Symmetry-Adapted Perturbation Theory Interaction Energy Components: The Functional-Group SAPT Partition.

    PubMed

    Parrish, Robert M; Parker, Trent M; Sherrill, C David

    2014-10-14

    Recently, we introduced an effective atom-pairwise partition of the many-body symmetry-adapted perturbation theory (SAPT) interaction energy decomposition, producing a method known as atomic SAPT (A-SAPT) [Parrish, R. M.; Sherrill, C. D. J. Chem. Phys. 2014, 141, 044115]. A-SAPT provides ab initio atom-pair potentials for force field development and also automatic visualizations of the spatial contributions of noncovalent interactions, but often has difficulty producing chemically useful partitions of the electrostatic energy, due to the buildup of oscillating partial charges on adjacent functional groups. In this work, we substitute chemical functional groups in place of atoms as the relevant local quasiparticles in the partition, resulting in a functional-group-pairwise partition denoted as functional-group SAPT (F-SAPT). F-SAPT assigns integral sets of local occupied electronic orbitals and protons to chemical functional groups and linking σ bonds. Link-bond contributions can be further assigned to chemical functional groups to simplify the analysis. This approach yields a SAPT partition between pairs of functional groups with integral charge (usually neutral), preventing oscillations in the electrostatic partition. F-SAPT qualitatively matches chemical intuition and the cut-and-cap fragmentation technique but additionally yields the quantitative many-body SAPT interaction energy. The conceptual simplicity, chemical utility, and computational efficiency of F-SAPT is demonstrated in the context of phenol dimer, proflavine(+)-DNA intercalation, and a cucurbituril host-guest inclusion complex. PMID:26588139

  16. Chemical Assignment of Symmetry-Adapted Perturbation Theory Interaction Energy Components: The Functional-Group SAPT Partition.

    PubMed

    Parrish, Robert M; Parker, Trent M; Sherrill, C David

    2014-10-14

    Recently, we introduced an effective atom-pairwise partition of the many-body symmetry-adapted perturbation theory (SAPT) interaction energy decomposition, producing a method known as atomic SAPT (A-SAPT) [Parrish, R. M.; Sherrill, C. D. J. Chem. Phys. 2014, 141, 044115]. A-SAPT provides ab initio atom-pair potentials for force field development and also automatic visualizations of the spatial contributions of noncovalent interactions, but often has difficulty producing chemically useful partitions of the electrostatic energy, due to the buildup of oscillating partial charges on adjacent functional groups. In this work, we substitute chemical functional groups in place of atoms as the relevant local quasiparticles in the partition, resulting in a functional-group-pairwise partition denoted as functional-group SAPT (F-SAPT). F-SAPT assigns integral sets of local occupied electronic orbitals and protons to chemical functional groups and linking σ bonds. Link-bond contributions can be further assigned to chemical functional groups to simplify the analysis. This approach yields a SAPT partition between pairs of functional groups with integral charge (usually neutral), preventing oscillations in the electrostatic partition. F-SAPT qualitatively matches chemical intuition and the cut-and-cap fragmentation technique but additionally yields the quantitative many-body SAPT interaction energy. The conceptual simplicity, chemical utility, and computational efficiency of F-SAPT is demonstrated in the context of phenol dimer, proflavine(+)-DNA intercalation, and a cucurbituril host-guest inclusion complex.

  17. Resource partitioning in a ladybird, Menochilus sexmaculatus: function of body size and prey density.

    PubMed

    Chaudhary, D D; Kumar, B; Mishra, G; Omkar

    2015-02-01

    In the present study, resource partitioning by natural conspecific size variants (small and large) of ladybird, Menochilus sexmaculatus (Fabricius) females, in response to varying prey densities was assessed using functional and numerical responses as measures of prey density. The prey provided was small (second) and large (fourth) instars of Aphis craccivora Koch. Results revealed that under choice condition, small and large females of M. sexmaculatus consumed higher number of small and large instars, respectively. Small females exhibited a modified Type II functional response on small aphid instars and a Type II functional response on fourth aphid instars. Large females exhibited a Type II functional response when provided either second or fourth aphid instars. Numerical response in terms of numbers of eggs laid by both the females increased with increase in the density of either of the aphid instars. However, in small females, oviposition had a positive correlation with the numbers of small and large aphid instars consumed; being strong for the small aphid instars. While in large females, oviposition was positively correlated with the numbers of large aphid instars consumed and not small aphid instars. It therefore seems that intraspecific resource partitioning in M. sexmaculatus occurs prominently in large females than the small females. PMID:25467186

  18. Resource partitioning in a ladybird, Menochilus sexmaculatus: function of body size and prey density.

    PubMed

    Chaudhary, D D; Kumar, B; Mishra, G; Omkar

    2015-02-01

    In the present study, resource partitioning by natural conspecific size variants (small and large) of ladybird, Menochilus sexmaculatus (Fabricius) females, in response to varying prey densities was assessed using functional and numerical responses as measures of prey density. The prey provided was small (second) and large (fourth) instars of Aphis craccivora Koch. Results revealed that under choice condition, small and large females of M. sexmaculatus consumed higher number of small and large instars, respectively. Small females exhibited a modified Type II functional response on small aphid instars and a Type II functional response on fourth aphid instars. Large females exhibited a Type II functional response when provided either second or fourth aphid instars. Numerical response in terms of numbers of eggs laid by both the females increased with increase in the density of either of the aphid instars. However, in small females, oviposition had a positive correlation with the numbers of small and large aphid instars consumed; being strong for the small aphid instars. While in large females, oviposition was positively correlated with the numbers of large aphid instars consumed and not small aphid instars. It therefore seems that intraspecific resource partitioning in M. sexmaculatus occurs prominently in large females than the small females.

  19. Geometry of Spin and SPINc Structures in the M-Theory Partition Function

    NASA Astrophysics Data System (ADS)

    Sati, Hisham

    We study the effects of having multiple Spin structures on the partition function of the spacetime fields in M-theory. This leads to a potential anomaly which appears in the eta invariants upon variation of the Spin structure. The main sources of such spaces are manifolds with nontrivial fundamental group, which are also important in realistic models. We extend the discussion to the Spinc case and find the phase of the partition function, and revisit the quantization condition for the C-field in this case. In type IIA string theory in 10 dimensions, the (mod 2) index of the Dirac operator is the obstruction to having a well-defined partition function. We geometrically characterize manifolds with and without such an anomaly and extend to the case of nontrivial fundamental group. The lift to KO-theory gives the α-invariant, which in general depends on the Spin structure. This reveals many interesting connections to positive scalar curvature manifolds and constructions related to the Gromov-Lawson-Rosenberg conjecture. In the 12-dimensional theory bounding M-theory, we study similar geometric questions, including choices of metrics and obtaining elements of K-theory in 10 dimensions by pushforward in K-theory on the disk fiber. We interpret the latter in terms of the families index theorem for Dirac operators on the M-theory circle and disk. This involves superconnections, eta forms, and infinite-dimensional bundles, and gives elements in Deligne cohomology in lower dimensions. We illustrate our discussion with many examples throughout.

  20. On a Gopakumar-Vafa form of partition function of Chern-Simons theory on classical and exceptional lines

    NASA Astrophysics Data System (ADS)

    Mkrtchyan, R. L.

    2014-12-01

    We show that partition function of Chern-Simons theory on three-sphere with classical and exceptional groups (actually on the whole corresponding lines in Vogel's plane) can be represented as ratio of respectively triple and double sine functions (last function is essentially a modular quantum dilogarithm). The product representation of sine functions gives Gopakumar-Vafa structure form of partition function, which in turn gives a corresponding integer invariants of manifold after geometrical transition. In this way we suggest to extend gauge/string duality to exceptional groups, although one still have to resolve few problems. In both classical and exceptional cases an additional terms, non-perturbative w.r.t. the string coupling constant, appear. The full universal partition function of ChernSimons theory on three-sphere is shown to be the ratio of quadruple sine functions. We also briefly discuss the matrix model for exceptional line.

  1. Airy Equation for the Topological String Partition Function in a Scaling Limit

    NASA Astrophysics Data System (ADS)

    Alim, Murad; Yau, Shing-Tung; Zhou, Jie

    2016-06-01

    We use the polynomial formulation of the holomorphic anomaly equations governing perturbative topological string theory to derive the free energies in a scaling limit to all orders in perturbation theory for any Calabi-Yau threefold. The partition function in this limit satisfies an Airy differential equation in a rescaled topological string coupling. One of the two solutions of this equation gives the perturbative expansion and the other solution provides geometric hints of the non-perturbative structure of topological string theory. Both solutions can be expanded naturally around strong coupling.

  2. Sampling from the Thermal Quantum Gibbs State and Evaluating Partition Functions with a Quantum Computer

    SciTech Connect

    Poulin, David; Wocjan, Pawel

    2009-11-27

    We present a quantum algorithm to prepare the thermal Gibbs state of interacting quantum systems. This algorithm sets a universal upper bound D{sup {alpha}} on the thermalization time of a quantum system, where D is the system's Hilbert space dimension and {alpha}<=(1/2) is proportional to the Helmholtz free energy density. We also derive an algorithm to evaluate the partition function of a quantum system in a time proportional to the system's thermalization time and inversely proportional to the targeted accuracy squared.

  3. Exact Partition Functions of Interacting Self-Avoiding Walks on Lattices

    NASA Astrophysics Data System (ADS)

    Hsieh, Yu-Hsin; Chen, Chi-Ning; Hu, Chin-Kun

    2016-02-01

    Ideas and methods of statistical physics have been shown to be useful for understanding some interesting problems in physical systems, e.g. universality and scaling in critical systems. The interacting self-avoiding walk (ISAW) on a lattice is the simplest model for homopolymers and serves as the framework of simple models for biopolymers, such as DNA, RNA, and protein, which are important components in complex systems in biology. In this paper, we briefly review our recent work on exact partition functions of ISAW. Based on zeros of these exact partition functions, we have developed a novel method in which both loci of zeros and thermodynamic functions associated with them are considered. With this method, the first zeros can be identified clearly without ambiguity. The critical point of a small system can then be defined as the peak position of the heat capacity component associated with the first zeros. For the system with two phase transitions, two pairs of first zeros corresponding to two phase transitions can be identified and overlapping Cυ can be well separated. ISAW on the simple cubic lattice is such a system where in addition to a standard collapse transition, there is another freezing transition occurring at a lower temperature. Our approach can give a clear scenario for the collapse and the freezing transitions.

  4. Partition functions and equilibrium constants for diatomic molecules and atoms of astrophysical interest

    NASA Astrophysics Data System (ADS)

    Barklem, P. S.; Collet, R.

    2016-04-01

    Partition functions and dissociation equilibrium constants are presented for 291 diatomic molecules for temperatures in the range from near absolute zero to 10 000 K, thus providing data for many diatomic molecules of astrophysical interest at low temperature. The calculations are based on molecular spectroscopic data from the book of Huber & Herzberg (1979, Constants of Diatomic Molecules) with significant improvements from the literature, especially updated data for ground states of many of the most important molecules by Irikura (2007, J. Phys. Chem. Ref. Data, 36, 389). Dissociation energies are collated from compilations of experimental and theoretical values. Partition functions for 284 species of atoms for all elements from H to U are also presented based on data collected at NIST. The calculated data are expected to be useful for modelling a range of low density astrophysical environments, especially star-forming regions, protoplanetary disks, the interstellar medium, and planetary and cool stellar atmospheres. The input data, which will be made available electronically, also provides a possible foundation for future improvement by the community. Full Tables 1-8 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/588/A96

  5. Partition functions of mini-F affect plasmid DNA topology in Escherichia coli.

    PubMed

    Biek, D P; Strings, J

    1995-02-24

    Efficient segregation of the low copy number plasmid mini-F is dependent on partition functions encoded by the plasmid sopABC genes. The sop region encodes proteins SopA and SopB and a cis-acting element, sopC, which may function as a centromere analog. The SopC segment contains 12 imperfect 43 bp repeats to which the SopB protein binds. We have found that mutations in the sop genes affect superhelicity of isolated plasmid DNA. Plasmids with mutations in sopB or a deletion of the sopC segment were more highly negatively supercoiled than normal. In contrast, a mutation in the autoregulatory SopA protein resulted in plasmid DNA that was more relaxed. The SopAB proteins provided in trans to a pBR322 plasmid carrying sopC resulted in the relaxation of negative supercoils. We suggest that binding of SopB protein to the cis-acting sopC segment in vivo, alone or in conjunction with other proteins, produced a change in DNA topology in which positive superhelical turns were introduced locally. This higher-order nucleoprotein structure may allow interaction of plasmid mini-F with the partition apparatus.

  6. Does mass play a role in partition functions even in low Reynolds number systems?

    NASA Astrophysics Data System (ADS)

    Perry, Rebecca W.; Franklin, Nica; Manoharan, Vinothan N.

    2014-03-01

    Classical statistical mechanics predicts that heavy components of a reconfigurable object will preferentially occupy positions at the edges of the object while lighter components will most often reside near the object's center of mass. This predicted influence of mass comes in through the rotational component of the partition function, which favors configurations with larger moments of inertia. It is tempting to apply these findings of statistical mechanics directly to colloidal systems, but is this appropriate when colloidal systems are immersed in liquid rather than surrounded by vaccuum? Does mass have a place in the partition function of colloidal clusters at low Reynolds numbers where we are accustomed to ignoring inertia? Here, we measure how silica microspheres distribute themselves when mixed with identically-sized polystyrene microspheres to form weakly-bound clusters of up to ten spheres. Using an array of microwells, we observe thousands of two-dimensional clusters to answer these fundamental questions. This work is funded by the NSF through grant no. 1306410.

  7. Nested sampling of isobaric phase space for the direct evaluation of the isothermal-isobaric partition function of atomic systems

    SciTech Connect

    Wilson, Blake A.; Nielsen, Steven O.; Gelb, Lev D.

    2015-10-21

    Nested Sampling (NS) is a powerful athermal statistical mechanical sampling technique that directly calculates the partition function, and hence gives access to all thermodynamic quantities in absolute terms, including absolute free energies and absolute entropies. NS has been used predominately to compute the canonical (NVT) partition function. Although NS has recently been used to obtain the isothermal-isobaric (NPT) partition function of the hard sphere model, a general approach to the computation of the NPT partition function has yet to be developed. Here, we describe an isobaric NS (IBNS) method which allows for the computation of the NPT partition function of any atomic system. We demonstrate IBNS on two finite Lennard-Jones systems and confirm the results through comparison to parallel tempering Monte Carlo. Temperature-entropy plots are constructed as well as a simple pressure-temperature phase diagram for each system. We further demonstrate IBNS by computing part of the pressure-temperature phase diagram of a Lennard-Jones system under periodic boundary conditions.

  8. Statistical mechanics of partially ionized stellar plasma - The Planck-Larkin partition function, polarization shifts, and simulations of optical spectra

    NASA Astrophysics Data System (ADS)

    Dappen, Werner; Anderson, Lawrence; Mihalas, Dimitri

    1987-08-01

    We discuss a recent controversy about the Planck-Larkin partition function, and present optical simulations of high-quality spectra from laboratory hydrogen plasmas (Wiese, Kelleher, and Paquette) using several partition function formalisms. We point out that the controversy has arisen from a misunderstanding about the use of the Planck-Larkin partition function. A Planck-Larkin cancellation may still have its place in equations of state that are based on quantum-statistical many-body theory (i.e., the "physical picture"). However, experimental evidence shows that it is inconsistent to use the Planck-Larkin partition function as the internal partition function in simple models of reacting gases (i.e., the "chemical picture"). Moreover, the more sophisticated equations of state of the physical picture will have to be subjected to the same comparison with experimental data. We also address the question of plasma polarization shifts of bound-state energies. We discuss the static-screened Coulomb potential (SSCP) as an atomic potential: from theoretical considerations and observational constraints we conclude that it should not be used. The only useful result of the SSCP potential its prediction of the number of excited be obtained by alternative means, e.g., by an occupation probability formalism.

  9. Local-scale Partitioning of Functional and Phylogenetic Beta Diversity in a Tropical Tree Assemblage.

    PubMed

    Yang, Jie; Swenson, Nathan G; Zhang, Guocheng; Ci, Xiuqin; Cao, Min; Sha, Liqing; Li, Jie; Ferry Slik, J W; Lin, Luxiang

    2015-01-01

    The relative degree to which stochastic and deterministic processes underpin community assembly is a central problem in ecology. Quantifying local-scale phylogenetic and functional beta diversity may shed new light on this problem. We used species distribution, soil, trait and phylogenetic data to quantify whether environmental distance, geographic distance or their combination are the strongest predictors of phylogenetic and functional beta diversity on local scales in a 20-ha tropical seasonal rainforest dynamics plot in southwest China. The patterns of phylogenetic and functional beta diversity were generally consistent. The phylogenetic and functional dissimilarity between subplots (10 × 10 m, 20 × 20 m, 50 × 50 m and 100 × 100 m) was often higher than that expected by chance. The turnover of lineages and species function within habitats was generally slower than that across habitats. Partitioning the variation in phylogenetic and functional beta diversity showed that environmental distance was generally a better predictor of beta diversity than geographic distance thereby lending relatively more support for deterministic environmental filtering over stochastic processes. Overall, our results highlight that deterministic processes play a stronger role than stochastic processes in structuring community composition in this diverse assemblage of tropical trees. PMID:26235237

  10. Local-scale Partitioning of Functional and Phylogenetic Beta Diversity in a Tropical Tree Assemblage

    PubMed Central

    Yang, Jie; Swenson, Nathan G.; Zhang, Guocheng; Ci, Xiuqin; Cao, Min; Sha, Liqing; Li, Jie; Ferry Slik, J. W.; Lin, Luxiang

    2015-01-01

    The relative degree to which stochastic and deterministic processes underpin community assembly is a central problem in ecology. Quantifying local-scale phylogenetic and functional beta diversity may shed new light on this problem. We used species distribution, soil, trait and phylogenetic data to quantify whether environmental distance, geographic distance or their combination are the strongest predictors of phylogenetic and functional beta diversity on local scales in a 20-ha tropical seasonal rainforest dynamics plot in southwest China. The patterns of phylogenetic and functional beta diversity were generally consistent. The phylogenetic and functional dissimilarity between subplots (10 × 10 m, 20 × 20 m, 50 × 50 m and 100 × 100 m) was often higher than that expected by chance. The turnover of lineages and species function within habitats was generally slower than that across habitats. Partitioning the variation in phylogenetic and functional beta diversity showed that environmental distance was generally a better predictor of beta diversity than geographic distance thereby lending relatively more support for deterministic environmental filtering over stochastic processes. Overall, our results highlight that deterministic processes play a stronger role than stochastic processes in structuring community composition in this diverse assemblage of tropical trees. PMID:26235237

  11. Assessment of a long-range corrected hybrid functional

    SciTech Connect

    Vydrov, Oleg A.; Scuseria, Gustavo E.

    2006-12-21

    Common approximate exchange-correlation functionals suffer from self-interaction error, and as a result, their corresponding potentials have incorrect asymptotic behavior. The exact asymptote can be imposed by introducing range separation into the exchange component and replacing the long-range portion of the approximate exchange by the Hartree-Fock counterpart. The authors show that this long-range correction works particularly well in combination with the short-range variant of the Perdew-Burke-Ernzerhof (PBE) exchange functional. This long-range-corrected hybrid, here denoted LC-{omega}PBE, is remarkably accurate for a broad range of molecular properties, such as thermochemistry, barrier heights of chemical reactions, bond lengths, and most notably, description of processes involving long-range charge transfer.

  12. Modular invariant partition functions for the doubly extended N = 4 superconformal algebras

    NASA Astrophysics Data System (ADS)

    Ooguri, Hirosi; Petersen, Jens Lyng; Taormina, Anne

    1992-01-01

    Non-trivial modular properties of characters of the doubly extended N = 4 superconformal algebras Aγ, Ãγ are derived from two different points of view. First, we use realizations on Wolf spaces, in particular when one of the levels of the two commuting affine SU(2) subalgebras takes the value 2. We emphasize how these realizations involve rational torus theories, and how some specific combinations of massless characters transform under the modular group as affine SU(2) characters. Second, we show how these combinations, and generalizations thereof, emerge from a study of the explicit form of the characters when angular variables are partly restricted, but the levels are not. The two results are then combined to give stringent constraints on the modular invariant Ãγ partition functions and they give rise to a partial classification of the latter, closely related to that of affine SU(2).

  13. Simultaneous correction of functional posterior cross bite and midline shift

    PubMed Central

    Arvinth, R.; Rana, Shailendra Singh; Duggal, Ritu; Kharbanda, Om Prakash

    2016-01-01

    The most frequent cause of functional posterior crossbite is the reduction in width of the maxillary dental arch. This posterior crossbite is associated with anterior crowding which is presented as an infrapositioned canine or a palatally positioned lateral incisor on one side; this leads to an upper midline shift toward the crowded side. The present case report shows the management of posterior crossbite with functional shift and upper midline shift simultaneously without adverse side effects. In this case, rapid maxillary expansion along with fixed appliance is used to correct posterior crossbite with the upper dental midline shift using reciprocal action of elastic transseptal fibers.

  14. Simultaneous correction of functional posterior cross bite and midline shift

    PubMed Central

    Arvinth, R.; Rana, Shailendra Singh; Duggal, Ritu; Kharbanda, Om Prakash

    2016-01-01

    The most frequent cause of functional posterior crossbite is the reduction in width of the maxillary dental arch. This posterior crossbite is associated with anterior crowding which is presented as an infrapositioned canine or a palatally positioned lateral incisor on one side; this leads to an upper midline shift toward the crowded side. The present case report shows the management of posterior crossbite with functional shift and upper midline shift simultaneously without adverse side effects. In this case, rapid maxillary expansion along with fixed appliance is used to correct posterior crossbite with the upper dental midline shift using reciprocal action of elastic transseptal fibers. PMID:27630513

  15. Simultaneous correction of functional posterior cross bite and midline shift.

    PubMed

    Arvinth, R; Rana, Shailendra Singh; Duggal, Ritu; Kharbanda, Om Prakash

    2016-01-01

    The most frequent cause of functional posterior crossbite is the reduction in width of the maxillary dental arch. This posterior crossbite is associated with anterior crowding which is presented as an infrapositioned canine or a palatally positioned lateral incisor on one side; this leads to an upper midline shift toward the crowded side. The present case report shows the management of posterior crossbite with functional shift and upper midline shift simultaneously without adverse side effects. In this case, rapid maxillary expansion along with fixed appliance is used to correct posterior crossbite with the upper dental midline shift using reciprocal action of elastic transseptal fibers. PMID:27630513

  16. Adaptive cyclic physiologic noise modeling and correction in functional MRI.

    PubMed

    Beall, Erik B

    2010-03-30

    Physiologic noise in BOLD-weighted MRI data is known to be a significant source of the variance, reducing the statistical power and specificity in fMRI and functional connectivity analyses. We show a dramatic improvement on current noise correction methods in both fMRI and fcMRI data that avoids overfitting. The traditional noise model is a Fourier series expansion superimposed on the periodicity of parallel measured breathing and cardiac cycles. Correction using this model results in removal of variance matching the periodicity of the physiologic cycles. Using this framework allows easy modeling of noise. However, using a large number of regressors comes at the cost of removing variance unrelated to physiologic noise, such as variance due to the signal of functional interest (overfitting the data). It is our hypothesis that there are a small variety of fits that describe all of the significantly coupled physiologic noise. If this is true, we can replace a large number of regressors used in the model with a smaller number of the fitted regressors and thereby account for the noise sources with a smaller reduction in variance of interest. We describe these extensions and demonstrate that we can preserve variance in the data unrelated to physiologic noise while removing physiologic noise equivalently, resulting in data with a higher effective SNR than with current corrections techniques. Our results demonstrate a significant improvement in the sensitivity of fMRI (up to a 17% increase in activation volume for fMRI compared with higher order traditional noise correction) and functional connectivity analyses.

  17. A phyletic perspective on the allometry of plant biomass-partitioning patterns and functionally equivalent organ-categories.

    PubMed

    Niklas, Karl J

    2006-01-01

    Biomass-partitioning patterns influence the functioning of aquatic and terrestrial vegetation at all levels, ranging from individual growth and reproduction to the flow of mass and energy through entire communities. For this reason, leaf, stem and root dry biomass-partitioning patterns across taxonomically and ecologically diverse seed plants (spermatophytes) have been intensively investigated, both empirically and theoretically. By contrast, phyletically disparate plants (e.g. green and brown algal macrophytes, mosses and pteridophytes) have not been examined to determine whether the partitioning of their body parts into 'leaf', 'stem' and 'root' analogs accords with that of spermatophytes. In this review, the biomass-partitioning patterns of siphonous and brown algal macrophytes, mosses and pteridophytes were compared allometrically with those of spermatophytes and were shown to be largely in statistical accordance (thus lending support to the hypothesis that a single scaling relationship exists across eukaryotic photoautotrophs). This concordance is argued to support the hypothesis of functional equivalence across analogous, but developmentally different, body parts, a feature that permits the use of simpler biological model systems with which to derive analytical explanations for the biomass-partitioning patterns reported for more complex seed plants.

  18. Exact partition functions for the Ω-deformed {N}={2}^{ast } SU(2) gauge theory

    NASA Astrophysics Data System (ADS)

    Beccaria, Matteo; Macorini, Guido

    2016-07-01

    We study the low energy effective action of the Ω-deformed {N}={2}^{ast } SU(2) gauge theory. It depends on the deformation parameters ɛ 1, ɛ 2, the scalar field expectation value a, and the hypermultiplet mass m. We explore the plane (m/ɛ_1,ɛ_2/ɛ_1) looking for special features in the multi-instanton contributions to the prepotential, motivated by what happens in the Nekrasov-Shatashvili limit ɛ 2 → 0. We propose a simple condition on the structure of poles of the k-instanton prepotential and show that it is admissible at a finite set of points in the above plane. At these special points, the prepotential has poles at fixed positions independent on the instanton number. Besides and remarkably, both the instanton partition function and the full prepotential, including the perturbative contribution, may be given in closed form as functions of the scalar expectation value a and the modular parameter q appearing in special combinations of Eisenstein series and Dedekind η function. As a byproduct, the modular anomaly equation can be tested at all orders at these points. We discuss these special features from the point of view of the AGT correspondence and provide explicit toroidal 1-blocks in non-trivial closed form. The full list of solutions with 1, 2, 3, and 4 poles is determined and described in details.

  19. Hierarchical Partitioning of Metazoan Protein Conservation Profiles Provides New Functional Insights

    PubMed Central

    Witztum, Jonathan; Persi, Erez; Horn, David; Pasmanik-Chor, Metsada; Chor, Benny

    2014-01-01

    The availability of many complete, annotated proteomes enables the systematic study of the relationships between protein conservation and functionality. We explore this question based solely on the presence or absence of protein homologues (a.k.a. conservation profiles). We study 18 metazoans, from two distinct points of view: the human's and the fly's. Using the GOrilla gene ontology (GO) analysis tool, we explore functional enrichment of the “universal proteins”, those with homologues in all 17 other species, and of the “non-universal proteins”. A large number of GO terms are strongly enriched in both human and fly universal proteins. Most of these functions are known to be essential. A smaller number of GO terms, exhibiting markedly different properties, are enriched in both human and fly non-universal proteins. We further explore the non-universal proteins, whose conservation profiles are consistent with the “tree of life” (TOL consistent), as well as the TOL inconsistent proteins. Finally, we applied Quantum Clustering to the conservation profiles of the TOL consistent proteins. Each cluster is strongly associated with one or a small number of specific monophyletic clades in the tree of life. The proteins in many of these clusters exhibit strong functional enrichment associated with the “life style” of the related clades. Most previous approaches for studying function and conservation are “bottom up”, studying protein families one by one, and separately assessing the conservation of each. By way of contrast, our approach is “top down”. We globally partition the set of all proteins hierarchically, as described above, and then identify protein families enriched within different subdivisions. While supporting previous findings, our approach also provides a tool for discovering novel relations between protein conservation profiles, functionality, and evolutionary history as represented by the tree of life. PMID:24594619

  20. 2D quantum gravity on compact Riemann surfaces and two-loop partition function: A first principles approach

    NASA Astrophysics Data System (ADS)

    Bilal, Adel; Leduc, Laetitia

    2015-07-01

    We study two-dimensional quantum gravity on arbitrary genus Riemann surfaces in the Kähler formalism where the basic quantum field is the (Laplacian of the) Kähler potential. We do a careful first-principles computation of the fixed-area partition function Z [ A ] up to and including all two-loop contributions. This includes genuine two-loop diagrams as determined by the Liouville action, one-loop diagrams resulting from the non-trivial measure on the space of metrics, as well as one-loop diagrams involving various counterterm vertices. Contrary to what is often believed, several such counterterms, in addition to the usual cosmological constant, do and must occur. We consistently determine the relevant counterterms from a one-loop computation of the full two-point Green's function of the Kähler field. Throughout this paper we use the general spectral cutoff regularization developed recently and which is well-suited for multi-loop computations on curved manifolds. At two loops, while all "unwanted" contributions to ln ⁡ (Z [ A ] / Z [A0 ]) correctly cancel, it appears that the finite coefficient of ln ⁡ (A /A0) does depend on the finite part of a certain counterterm coefficient, i.e. on the finite renormalization conditions one has to impose. There exists a choice that reproduces the famous KPZ-scaling, but it seems to be only one consistent choice among others. Maybe, this hints at the possibility that other renormalization conditions could eventually provide a way to circumvent the famous c = 1 barrier.

  1. Correction.

    PubMed

    2015-11-01

    In the article by Heuslein et al, which published online ahead of print on September 3, 2015 (DOI: 10.1161/ATVBAHA.115.305775), a correction was needed. Brett R. Blackman was added as the penultimate author of the article. The article has been corrected for publication in the November 2015 issue. PMID:26490278

  2. Reverse energy partitioning—An efficient algorithm for computing the density of states, partition functions, and free energy of solids

    NASA Astrophysics Data System (ADS)

    Do, Hainam; Wheatley, Richard J.

    2016-08-01

    A robust and model free Monte Carlo simulation method is proposed to address the challenge in computing the classical density of states and partition function of solids. Starting from the minimum configurational energy, the algorithm partitions the entire energy range in the increasing energy direction ("upward") into subdivisions whose integrated density of states is known. When combined with the density of states computed from the "downward" energy partitioning approach [H. Do, J. D. Hirst, and R. J. Wheatley, J. Chem. Phys. 135, 174105 (2011)], the equilibrium thermodynamic properties can be evaluated at any temperature and in any phase. The method is illustrated in the context of the Lennard-Jones system and can readily be extended to other molecular systems and clusters for which the structures are known.

  3. Partitioning heritability by functional annotation using genome-wide association summary statistics.

    PubMed

    Finucane, Hilary K; Bulik-Sullivan, Brendan; Gusev, Alexander; Trynka, Gosia; Reshef, Yakir; Loh, Po-Ru; Anttila, Verneri; Xu, Han; Zang, Chongzhi; Farh, Kyle; Ripke, Stephan; Day, Felix R; Purcell, Shaun; Stahl, Eli; Lindstrom, Sara; Perry, John R B; Okada, Yukinori; Raychaudhuri, Soumya; Daly, Mark J; Patterson, Nick; Neale, Benjamin M; Price, Alkes L

    2015-11-01

    Recent work has demonstrated that some functional categories of the genome contribute disproportionately to the heritability of complex diseases. Here we analyze a broad set of functional elements, including cell type-specific elements, to estimate their polygenic contributions to heritability in genome-wide association studies (GWAS) of 17 complex diseases and traits with an average sample size of 73,599. To enable this analysis, we introduce a new method, stratified LD score regression, for partitioning heritability from GWAS summary statistics while accounting for linked markers. This new method is computationally tractable at very large sample sizes and leverages genome-wide information. Our findings include a large enrichment of heritability in conserved regions across many traits, a very large immunological disease-specific enrichment of heritability in FANTOM5 enhancers and many cell type-specific enrichments, including significant enrichment of central nervous system cell types in the heritability of body mass index, age at menarche, educational attainment and smoking behavior. PMID:26414678

  4. Flow partitioning in regional groundwater flow systems as a function of recharge and topography

    NASA Astrophysics Data System (ADS)

    Goderniaux, P.; Davy, P.; Bresciani, E.; De Dreuzy, J.; Le Borgne, T.

    2013-12-01

    The distribution of groundwater fluxes in aquifers is strongly influenced by topography, and organized between hillslope and regional scales. In this study, we use a finite-difference flow model to quantify the partitioning of recharge and compartmentalization of aquifers between shallow/local and deep/regional groundwater transfers. The flow structure is analyzed for a regional aquifers, as a function of recharge (from 20 to 500 mm/yr), in 3-dimensions, and accounting for variable groundwater discharge zones. The Probability Density Function of transit times shows two different parts, interpreted using a two-compartment model, related to regional and local groundwater flows. The role of recharge on the size and nature of the flow regimes, including groundwater pathways, transit time distributions, and volumes associated to the two compartments is investigated. Results show that topography control on the water table and groundwater compartmentalization varies with the recharge rate applied. The volume associated to the regional compartment is calculated from the exponential part of the two-compartment model, and is nearly insensitive to the total recharge fluctuations. The model also allows visualizing 3D circulations, as those provided by Tothian models in 2D, and shows local and regional transfers, with 3D effects. Results are presented for a specific basin (1400 km2) in Brittany (France). Preliminary results using different kinds of topography are presented and compared.

  5. Temperature-dependent nuclear partition functions and abundances in the stellar interior

    NASA Astrophysics Data System (ADS)

    Nabi, Jameel-Un; Nasser Tawfik, Abdel; Ezzelarab, Nada; Abas Khan, Ali

    2016-05-01

    We calculate the temperature-dependent nuclear partition functions (TDNPFs) and nuclear abundances for 728 nuclei, assuming nuclear statistical equilibrium (NSE). The theories of stellar evolution support NSE. Discrete nuclear energy levels have been calculated microscopically, using the pn-QRPA theory, up to an excitation energy of 10 MeV in the calculation of the TDNPFs. This feature of our paper distinguishes it from previous calculations. Experimental data is also incorporated wherever available to ensure the reliability of our results. Beyond 10 MeV, we employ a simple Fermi gas model and perform integration over the nuclear level densities to approximate the TDNPFs. We calculate nuclidic abundances, using the Saha equation, as a function of three parameters: stellar density, stellar temperature and the lepton-to-baryon content of stellar matter. All these physical parameters are considered to be extremely important in the stellar interior. The results obtained in this paper show that the equilibrium configuration of nuclei remains unaltered by increasing the stellar density (only the calculated nuclear abundances increase by roughly the same order of magnitude). Increasing the stellar temperature smoothes the equilibrium configuration showing peaks at the neutron-number magic nuclei.

  6. Influence of pressure derivative of partition function on thermodynamic properties of non-local thermodynamic equilibrium thermal plasma

    NASA Astrophysics Data System (ADS)

    Singh, Gurpreet; Sharma, Rohit; Singh, Kuldip

    2015-09-01

    Thermodynamic properties (compressibility coefficient Z γ , specific heat at constant volume c v , adiabatic coefficient γ a , isentropic coefficient γ i s e n , and sound speed c s ) of non-local thermodynamic equilibrium hydrogen thermal plasma have been investigated for different values of pressure and non-equilibrium parameter θ (=Te/Th) in the electron temperature range from 6000 K to 60 000 K. In order to estimate the influence of pressure derivative of partition function on thermodynamic properties, two cases have been considered: (a) in which pressure derivative of partition function is taken into account in the expressions and (b) without pressure derivative of partition function in their expressions. Here, the case (b) represents expressions already available in literature. It has been observed that the temperature from which pressure derivative of partition function starts influencing a given thermodynamic property increases with increase of pressure and non-equilibrium parameter θ. Thermodynamic property in the case (a) is always greater than its value in the case (b) for compressibility coefficient and specific heat at constant volume, whereas for adiabatic coefficient, isentropic coefficient, and sound speed, its value in the case (a) is always less than its value in the case (b). For a given value of θ, the relationship of compressibility coefficient with degree of ionization depends upon pressure in the case (a), whereas it is independent of pressure in the case (b). Relative deviation between the two cases shows that the influence of pressure derivative of partition function is significantly large and increases with the augmentation of pressure and θ for compressibility coefficient, specific heat at constant volume, and adiabatic coefficient, whereas for isentropic coefficient and sound speed, it is marginal even at high values of pressure and non-equilibrium parameter θ.

  7. First hyperpolarizability of polymethineimine with long-range corrected functionals

    NASA Astrophysics Data System (ADS)

    Jacquemin, Denis; Perpète, Eric A.; Medved', Miroslav; Scalmani, Giovanni; Frisch, Michael J.; Kobayashi, Rika; Adamo, Carlo

    2007-05-01

    Using the long-range corrected (LC) density functional theory (DFT) scheme introduced by Iikura et al. [J. Chem. Phys. 115, 3540 (2001)] and the Coulomb-attenuating model (CAM-B3LYP) of Yanai et al. [Chem. Phys. Lett. 393, 51 (2004)], we have calculated the longitudinal dipole moments and static electronic first hyperpolarizabilities of increasingly long polymehtineimine oligomers. For comparison purposes Hartree-Fock (HF), Møller-Plesset perturbation theory (MP2), and conventional pure and hybrid functionals have been considered as well. HF, generalized gradient approximation (GGA), and conventional hybrids provide too large dipole moments for long oligomers, while LC-DFT allows to reduce the discrepancy with respect to MP2 by a factor of 3. For the first hyperpolarizability, the incorrect evolution with the chain length predicted by HF is strongly worsened by BLYP, Perdew-Burke-Ernzerhof (PBE), and also by B3LYP and PBE0. On the reverse, LC-BLYP and LC-PBE hyperpolarizabilities are correctly predicted to be positive (but for the two smallest chains). Indeed, for medium and long oligomers LC hyperpolarizabilities are slightly smaller than MP2 hyperpolarizabilities, as it should be. CAM-B3LYP also strongly improves the B3LYP results, though a bit less impressively for small chain lengths. The present study demonstrates the efficiency of long-range DFT, even in very pathological cases.

  8. Semilocal density functional theory with correct surface asymptotics

    NASA Astrophysics Data System (ADS)

    Constantin, Lucian A.; Fabiano, Eduardo; Pitarke, J. M.; Della Sala, Fabio

    2016-03-01

    Semilocal density functional theory is the most used computational method for electronic structure calculations in theoretical solid-state physics and quantum chemistry of large systems, providing good accuracy with a very attractive computational cost. Nevertheless, because of the nonlocality of the exchange-correlation hole outside a metal surface, it was always considered inappropriate to describe the correct surface asymptotics. Here, we derive, within the semilocal density functional theory formalism, an exact condition for the imagelike surface asymptotics of both the exchange-correlation energy per particle and potential. We show that this condition can be easily incorporated into a practical computational tool, at the simple meta-generalized-gradient approximation level of theory. Using this tool, we also show that the Airy-gas model exhibits asymptotic properties that are closely related to those at metal surfaces. This result highlights the relevance of the linear effective potential model to the metal surface asymptotics.

  9. Quantum partition functions of composite particles in a hydrogen-helium plasma via path integral Monte Carlo

    SciTech Connect

    Wendland, D.; Ballenegger, V.; Alastuey, A.

    2014-11-14

    We compute two- and three-body cluster functions that describe contributions of composite entities, like hydrogen atoms, ions H{sup −}, H{sub 2}{sup +}, and helium atoms, and also charge-charge and atom-charge interactions, to the equation of state of a hydrogen-helium mixture at low density. A cluster function has the structure of a truncated virial coefficient and behaves, at low temperatures, like a usual partition function for the composite entity. Our path integral Monte Carlo calculations use importance sampling to sample efficiently the cluster partition functions even at low temperatures where bound state contributions dominate. We also employ a new and efficient adaptive discretization scheme that allows one not only to eliminate Coulomb divergencies in discretized path integrals, but also to direct the computational effort where particles are close and thus strongly interacting. The numerical results for the two-body function agree with the analytically known quantum second virial coefficient. The three-body cluster functions are compared at low temperatures with familiar partition functions for composite entities.

  10. Impaired Error Monitoring and Correction Function in Autism

    PubMed Central

    Sokhadze, Estate; Baruth, Joshua; El-Baz, Ayman; Horrell, Timothy; Sokhadze, Guela; Carroll, Thomas; Tasman, Allan; Sears, Lonnie; Casanova, Manuel F.

    2010-01-01

    Introduction Error monitoring and correction is one of the executive functions and is important for effective goal directed behavior. Deficient executive functioning, including reduced error monitoring ability, is one of the typical features of such neurodevelopmental disorders as autism, probably related to perseverative responding, stereotyped repetitive behaviors, and an inability to accurately monitor ongoing behavior. Our prior studies of behavioral and event-related potential (ERP) measures during performance on visual oddball tasks in high-functioning autistic (HFA) children showed that despite only minor differences in reaction times HFA children committed significantly more errors. Methods This study investigated error monitoring in children with autism spectrum disorder (ASD) with response-locked event-related potentials - the Error-related Negativity (ERN) and Error-related Positivity (Pe) recorded at fronto-central sites. The ERN reflects early error detection processes, while the Pe has been associated with later conscious error evaluation and attention re-allocation. Reaction times (RT) in correct trials and post-error slowing in reaction times were measured. In this study fourteen subjects with ASD and 14 age- and IQ- matched controls received a three-category visual oddball task with novel distracters. Results ERN had a lower amplitude and longer latency in the ASD group but was localized in the caudal part of anterior cingulate cortex (ACC) in both groups. The Pe component was significantly prolonged in the ASD group but did not reach significance in amplitude differences compared to controls. We found significant post-error slowing in RTs in controls, and post-error acceleration in RTs in the ASD group. Conclusions The reduced ERN and altered Pe along with a lack of post-error RT slowing in autism might be interpreted as insensitivity in the detection and monitoring of response errors and a reduced ability of execute corrective actions. This might

  11. Partition function and thermodynamic parameters of the all-particle cosmic-ray flux

    NASA Astrophysics Data System (ADS)

    Tomaschitz, Roman

    2016-11-01

    The all-particle cosmic-ray energy spectrum is studied in the 1 GeV-1011 GeV interval, the relativistic nuclei being treated as a free multi-component gas in stationary non-equilibrium. A phase-space derivation of the spectral number density, partition function and entropy is given, and an analytic expression for the flux density of the all-particle spectrum is semi-empirically obtained from a wideband spectral fit. The all-particle spectrum is the additive superposition of four strongly overlapping peaks with exponential cutoffs at the spectral breaks. The analytic flux density covers the mentioned interval ranging over eleven decades and accurately reproduces the spectral fine-structure, such as two weak spectral breaks between knee and ankle emerging in the IceTop-73 and KASCADE-Grande data sets. In the low-energy range below 104 GeV, the all-particle flux is approximated by adding the proton and helium flux densities obtained from fits to the AMS-02 and CREAM spectra, the contribution of heavier nuclei being negligible in this energy range. Estimates of the thermodynamic parameters (number count, internal energy, entropy and pressure) of the all-particle flux and the partial fluxes generating the spectral peaks are derived.

  12. The oxygen isotope partition function ratio of water and the structure of liquid water

    USGS Publications Warehouse

    O'Neil, J.R.; Adami, L.H.

    1969-01-01

    By means of the CO2-equilibration technique, the temperature dependence and absolute values of the oxygen isotope partition function ratio of liquid water have been determined, often at 1?? intervals, from -2 to 85??. A linear relationship between In (Q2/Q1) (H2O) and T-1 was obtained that is explicable in terms of the Bigeleisen-Mayer theory of isotopic fractionation. The data are incompatible with conventional, multicomponent mixture models of water because liquid water behaves isotopically as a singly structured homogeneous substance over the entire temperature range studied. A two-species model of water is proposed in which approximately 30% of the hydrogen bonds in ice are broken on melting at 0?? and in which this per cent of monomer changes by only a small amount over the entire liquid range. Because of the high precision and the fundamental property determined, the isotopic fractionation technique is particularly well suited to the detection of thermal anomalies. No anomalies were observed and those previously reported are ascribed to under-estimates of experimental error.

  13. Partitioning taxonomic diversity of aquatic insect assemblages and functional feeding groups in Neotropical Savanna headwater streams

    EPA Science Inventory

    Biological diversity can be divided into: alpha (α, local), beta (β, difference in assemblage composition among locals), and gamma (γ, total diversity). We assessed the partitioning of taxonomic diversity of Ephemeroptera, Plecoptera and Trichoptera (EPT) and of ...

  14. Partition function of a Wilson loop in a strongly coupled N=4 supersymmetric Yang-Mills plasma with fluctuations

    SciTech Connect

    Hou Defu; Liu, James T.; Ren Haicang

    2009-08-15

    We examine the one-loop partition function describing the fluctuations of the superstring in a Schwarzschild-AdS{sub 5}xS{sup 5} background. On the bosonic side, we demonstrate the one-loop equivalence of the Nambu-Goto action and the Polyakov action for a general world sheet, while on the fermionic side, we consider the reduction of the ten-dimensional Green-Schwarz fermion action to a two-dimensional world sheet action. We derive the partition functions of the world sheets corresponding to both straight and parallel Wilson lines. We discuss the cancellation of the UV divergences of the functional determinants in the thermal AdS background.

  15. Ocean color remote sensing: choosing the correct depth weighting function.

    PubMed

    Piskozub, Jacek; Neumann, Tomasz; Woźniak, Ludomir

    2008-09-15

    Values of reflectance and remote sensing reflectance are proportional to the ratio of sea water backscattering to absorption. However, in vertically non-homogeneous waters, this fraction needs to be depth weighted. The usual practice uses normalized vertical transmittance profiles as the weighting function. Recently, it was shown that the correct approach is to use, instead of transmittance, its first derivative. We used both approaches to calculate spectral reflectance and remote sensing reflectance over a submerged bubble cloud and chlorophyll rich layer and compared the results with a radiative transfer Monte Carlo code. We also compared several methods of approximating diffuse attenuation (not measured directly) to estimate the effect on calculating reflectance. Our results show that the traditional method of IOP weighting is inadequate in the presence of bubble clouds and/or chlorophyll rich layers. This is relevant for both "ground truth" studies and inverse methods of remote sensing (including lidar ones) for vertically inhomogeneous ocean sea waters.

  16. A whole-path importance-sampling scheme for Feynman path integral calculations of absolute partition functions and free energies.

    PubMed

    Mielke, Steven L; Truhlar, Donald G

    2016-01-21

    Using Feynman path integrals, a molecular partition function can be written as a double integral with the inner integral involving all closed paths centered at a given molecular configuration, and the outer integral involving all possible molecular configurations. In previous work employing Monte Carlo methods to evaluate such partition functions, we presented schemes for importance sampling and stratification in the molecular configurations that constitute the path centroids, but we relied on free-particle paths for sampling the path integrals. At low temperatures, the path sampling is expensive because the paths can travel far from the centroid configuration. We now present a scheme for importance sampling of whole Feynman paths based on harmonic information from an instantaneous normal mode calculation at the centroid configuration, which we refer to as harmonically guided whole-path importance sampling (WPIS). We obtain paths conforming to our chosen importance function by rejection sampling from a distribution of free-particle paths. Sample calculations on CH4 demonstrate that at a temperature of 200 K, about 99.9% of the free-particle paths can be rejected without integration, and at 300 K, about 98% can be rejected. We also show that it is typically possible to reduce the overhead associated with the WPIS scheme by sampling the paths using a significantly lower-order path discretization than that which is needed to converge the partition function.

  17. A whole-path importance-sampling scheme for Feynman path integral calculations of absolute partition functions and free energies.

    PubMed

    Mielke, Steven L; Truhlar, Donald G

    2016-01-21

    Using Feynman path integrals, a molecular partition function can be written as a double integral with the inner integral involving all closed paths centered at a given molecular configuration, and the outer integral involving all possible molecular configurations. In previous work employing Monte Carlo methods to evaluate such partition functions, we presented schemes for importance sampling and stratification in the molecular configurations that constitute the path centroids, but we relied on free-particle paths for sampling the path integrals. At low temperatures, the path sampling is expensive because the paths can travel far from the centroid configuration. We now present a scheme for importance sampling of whole Feynman paths based on harmonic information from an instantaneous normal mode calculation at the centroid configuration, which we refer to as harmonically guided whole-path importance sampling (WPIS). We obtain paths conforming to our chosen importance function by rejection sampling from a distribution of free-particle paths. Sample calculations on CH4 demonstrate that at a temperature of 200 K, about 99.9% of the free-particle paths can be rejected without integration, and at 300 K, about 98% can be rejected. We also show that it is typically possible to reduce the overhead associated with the WPIS scheme by sampling the paths using a significantly lower-order path discretization than that which is needed to converge the partition function. PMID:26801023

  18. Computing the partition function, ensemble averages, and density of states for lattice spin systems by sampling the mean

    SciTech Connect

    Gillespie, Dirk

    2013-10-01

    An algorithm to approximately calculate the partition function (and subsequently ensemble averages) and density of states of lattice spin systems through non-Monte-Carlo random sampling is developed. This algorithm (called the sampling-the-mean algorithm) can be applied to models where the up or down spins at lattice nodes interact to change the spin states of other lattice nodes, especially non-Ising-like models with long-range interactions such as the biological model considered here. Because it is based on the Central Limit Theorem of probability, the sampling-the-mean algorithm also gives estimates of the error in the partition function, ensemble averages, and density of states. Easily implemented parallelization strategies and error minimizing sampling strategies are discussed. The sampling-the-mean method works especially well for relatively small systems, systems with a density of energy states that contains sharp spikes or oscillations, or systems with little a priori knowledge of the density of states.

  19. Source water partitioning as a means of characterizing hydrologic function in mangroves

    USGS Publications Warehouse

    Drexler, J.Z.; De Carlo, E. W.

    2002-01-01

    Mangrove ecosystems rely on seawater, rain-derived flow, and groundwater for hydrologic sustenance, flushing, and inflow of nutrients and sediments. The relative contribution of these source waters and their variability through time and space can provide key information concerning the hydrologic function of ecosystems. We used hydrologic tracers to partition source waters and trace their movements in the Enipoas stream, a river-dominated mangrove ecosystem on the island of Pohnpei, Federated States of Micronesia (FSM) and in the Yela watershed, an interior mangrove ecosystem on the island of Kosrae, FSM. The Enipoas site was characterized as a salt wedge estuary whose source water contributions alternated between predominantly seawater and rain-derived flow, depending on the tide. The source waters in the interior Yela site were also predominantly seawater and rain-derived flow, however the relative contribution of each was much more stable. The mean groundwater contribution was 5% (SD = 5.5) for the Enipoas site and 20% (SD = 11.0) for the Yela site. Although a small contributor to flow, groundwater was a steady source of freshwater for both systems. Hydrologic linkages between mangroves and adjacent ecosystems were demonstrated by the temporal and spatial distribution of source waters. The 0.8 km Enipoas estuary, with its highly dynamic bi-directional flows, transported source waters along a hydrologic continuum comprised of coral reef, mangroves, and palm forest. In the interior mangroves of the Yela watershed, the presence of rain-derived flow and groundwater demonstrated a hydraulic connection between the mangroves and an upstream freshwater swamp. Interior mangroves with such linkages avoid stresses such as desiccation and heightened salinity, and thus are more productive than those with little or no freshwater flows.

  20. Dual function of partitioning-defective 3 in the regulation of YAP phosphorylation and activation

    PubMed Central

    Zhang, Peng; Wang, Shuting; Wang, Sai; Qiao, Jing; Zhang, Lei; Zhang, Zhe; Chen, Zhengjun

    2016-01-01

    Partitioning-defective 3 (Par3), a key component of the evolutionarily conserved polarity PAR complex (Par3/Par6/aPKC), controls cell polarity and contributes to cell migration, proliferation and tumor development. Emerging evidence indicates that cell polarity proteins function as upstream modulators that regulate the Hippo pathway. However, little is known about Par3’s involvement in the Hippo pathway. Here, we find Par3 and YAP dynamically co-localize in different subcellular compartments; that is, the membrane, cytoplasm and nucleus, in a cell-density-dependent manner. Interestingly, Par3 knockdown promotes YAP phosphorylation, leading to a significant impairment of YAP nuclear translocation at low cell density, but not at high density, in MDCK cells. Furthermore, via its third PDZ domain, Par3 directly binds to the PDZ-binding motif of YAP. The interaction is required for regulating YAP phosphorylation and nuclear localization. Mechanistically, Par3, as a scaffold protein, associates with LATS1 and protein phosphatase 1, α subunit (PP1A) in the cytoplasm and nucleus. Par3 promotes the dephosphorylation of LATS1 and YAP, thus enhancing YAP activation and cell proliferation. Strikingly, we also find that under the condition of PP1A knockdown, Par3 expression promotes YAP hyperphosphorylation, leading to the suppression of YAP activity and its downstream targets. Par3 expression results in differential effects on YAP phosphorylation and activation in different tumor cell lines. These findings indicate that Par3 may have a dual role in regulating the activation of the Hippo pathway, in a manner possibly dependent on cellular context or cell type in response to cell–cell contact and cell polarity signals. PMID:27462467

  1. Metallophilic interactions from dispersion-corrected density-functional theory.

    PubMed

    Otero-de-la-Roza, Alberto; Mallory, Joel D; Johnson, Erin R

    2014-05-14

    In this article, we present the first comprehensive study of metallophilic (aurophilic) interactions using dispersion-corrected density-functional theory. Dispersion interactions (an essential component of metallophilicity) are treated using the exchange-hole dipole moment (XDM) model. By comparing against coupled-cluster benchmark calculations on simple dimers, we show that LC-ωPBE-XDM is a viable functional to study interactions between closed-shell transition metals and that it performs uniformly better than second-order Møller-Plesset theory, the basic computational technique used in previous works. We apply LC-ωPBE-XDM to address several open questions regarding metallophilicity, such as the interplay between dispersion and relativistic effects, the interaction strength along group 11, the additivity of homo- and hetero-metallophilic effects, the stability of [E(AuPH3)4](+) cations (E = N, P, As, Sb), and the role of metallophilic effects in crystal packing. We find that relativistic effects explain the prevalence of aurophilicity not by stabilizing metal-metal contacts, but by preventing gold from forming ionic structures involving bridge anions (which are otherwise common for Ag and Cu) as a result of the increased electron affinity of the metal. Dispersion effects are less important than previously assumed and their stabilization contribution is relatively independent of the metal.

  2. Metallophilic interactions from dispersion-corrected density-functional theory

    NASA Astrophysics Data System (ADS)

    Otero-de-la-Roza, Alberto; Mallory, Joel D.; Johnson, Erin R.

    2014-05-01

    In this article, we present the first comprehensive study of metallophilic (aurophilic) interactions using dispersion-corrected density-functional theory. Dispersion interactions (an essential component of metallophilicity) are treated using the exchange-hole dipole moment (XDM) model. By comparing against coupled-cluster benchmark calculations on simple dimers, we show that LC-ωPBE-XDM is a viable functional to study interactions between closed-shell transition metals and that it performs uniformly better than second-order Møller-Plesset theory, the basic computational technique used in previous works. We apply LC-ωPBE-XDM to address several open questions regarding metallophilicity, such as the interplay between dispersion and relativistic effects, the interaction strength along group 11, the additivity of homo- and hetero-metallophilic effects, the stability of [E(AuPH3)4]+ cations (E = N, P, As, Sb), and the role of metallophilic effects in crystal packing. We find that relativistic effects explain the prevalence of aurophilicity not by stabilizing metal-metal contacts, but by preventing gold from forming ionic structures involving bridge anions (which are otherwise common for Ag and Cu) as a result of the increased electron affinity of the metal. Dispersion effects are less important than previously assumed and their stabilization contribution is relatively independent of the metal.

  3. Effect of partition board color on mood and autonomic nervous function.

    PubMed

    Sakuragi, Sokichi; Sugiyama, Yoshiki

    2011-12-01

    The purpose of this study was to evaluate the effects of the presence or absence (control) of a partition board and its color (red, yellow, blue) on subjective mood ratings and changes in autonomic nervous system indicators induced by a video game task. The increase in the mean Profile of Mood States (POMS) Fatigue score and mean Oppressive feeling rating after the task was lowest with the blue partition board. Multiple-regression analysis identified oppressive feeling and error scores on the second half of the task as statistically significant contributors to Fatigue. While explanatory variables were limited to the physiological indices, multiple-regression analysis identified a significant contribution of autonomic reactivity (assessed by heart rate variability) to Fatigue. These results suggest that a blue partition board would reduce task-induced subjective fatigue, in part by lowering the oppressive feeling of being enclosed during the task, possibly by increasing autonomic reactivity.

  4. Electric-magnetic duality of Abelian gauge theory on the four-torus, from the fivebrane on T 2 × T 4, via their partition functions

    NASA Astrophysics Data System (ADS)

    Dolan, Louise; Sun, Yang

    2015-06-01

    We compute the partition function of four-dimensional abelian gauge theory on a general four-torus T 4 with flat metric using Dirac quantization. In addition to an symmetry, it possesses symmetry that is electromagnetic S-duality. We show explicitly how this S-duality of the 4 d abelian gauge theory has its origin in symmetries of the 6 d (2 , 0) tensor theory, by computing the partition function of a single fivebrane compactified on T 2 times T 4, which has symmetry. If we identify the couplings of the abelian gauge theory with the complex modulus of the T 2 torus , then in the small T 2 limit, the partition function of the fivebrane tensor field can be factorized, and contains the partition function of the 4 d gauge theory. In this way the symmetry of the 6d tensor partition function is identified with the S-duality symmetry of the 4d gauge partition function. Each partition function is the product of zero mode and oscillator contributions, where the acts suitably. For the 4d gauge theory, which has a Lagrangian, this product redistributes when using path integral quantization.

  5. Corrections

    NASA Astrophysics Data System (ADS)

    2012-09-01

    The feature article "Material advantage?" on the effects of technology and rule changes on sporting performance (July pp28-30) stated that sprinters are less affected by lower oxygen levels at high altitudes because they run "aerobically". They run anaerobically. The feature about the search for the Higgs boson (August pp22-26) incorrectly gave the boson's mass as roughly 125 MeV it is 125 GeV, as correctly stated elsewhere in the issue. The article also gave a wrong value for the intended collision energy of the Superconducting Super Collider, which was designed to collide protons with a total energy of 40 TeV.

  6. Correction.

    PubMed

    2015-05-22

    The Circulation Research article by Keith and Bolli (“String Theory” of c-kitpos Cardiac Cells: A New Paradigm Regarding the Nature of These Cells That May Reconcile Apparently Discrepant Results. Circ Res. 2015:116:1216-1230. doi: 10.1161/CIRCRESAHA.116.305557) states that van Berlo et al (2014) observed that large numbers of fibroblasts and adventitial cells, some smooth muscle and endothelial cells, and rare cardiomyocytes originated from c-kit positive progenitors. However, van Berlo et al reported that only occasional fibroblasts and adventitial cells derived from c-kit positive progenitors in their studies. Accordingly, the review has been corrected to indicate that van Berlo et al (2014) observed that large numbers of endothelial cells, with some smooth muscle cells and fibroblasts, and more rarely cardiomyocytes, originated from c-kit positive progenitors in their murine model. The authors apologize for this error, and the error has been noted and corrected in the online version of the article, which is available at http://circres.ahajournals.org/content/116/7/1216.full ( PMID:25999426

  7. Marine microalgae growth and carbon partitioning as a function of nutrient availability.

    PubMed

    Fernandes, Tomásia; Fernandes, Igor; Andrade, Carlos A P; Cordeiro, Nereida

    2016-08-01

    To understand in which way the structural differences of three marine microalgae (Nannochloropsis gaditana, Rhodomonas marina and Isochrysis sp.) affect their carbon partitioning, growth and applicability; a stoichiometric imbalance was imposed by steady carbon and other nutrients variation. Towards high nutrients concentrations/low carbon availability a decrease of 12-51% in C/N microalgae ratio was observed and maximum cell densities were achieved. Moreover, linear correlation between the nutrient input and microalgae protein content were observed. The macromolecular ratios pointed that carbohydrate was the main contributor for the C/N decrement. Although lipid content in R. marina remained constant throughout the experiment, a rise of 37-107% in N. gaditana and Isochrysis sp. was verified. Lipid fractions revealed high percentages of glycolipids in all microalgae (57-73% of total lipids). The present study shows an easy way to understand and modulate microalgae carbon partitioning relying on the field of application. PMID:27179298

  8. Concerted action of plasmid maintenance functions: partition complexes create a requirement for dimer resolution.

    PubMed

    Bouet, Jean-Yves; Bouvier, Marie; Lane, David

    2006-12-01

    Partition of prokaryotic DNA requires formation of specific protein-centromere complexes, but an excess of the protein can disrupt segregation. The mechanisms underlying this destabilization are unknown. We have found that destabilization by the F plasmid partition protein, SopB, of plasmids carrying the F centromere, sopC, results from the capacity of the SopB-sopC partition complex to stimulate plasmid multimerization. Mutant SopBs unable to destabilize failed to increase multimerization. Stability of wild-type mini-F, whose ResD/rfsF site-specific recombination system enables it to resolve multimers to monomers, was barely affected by excess SopB. Destabilization of plasmids lacking the rfsF site was suppressed by recF, recO and recR, but not by recB, mutant alleles, indicating that multimerization is initiated from single-strand gaps. SopB did not alter the amounts or distribution of replication intermediates, implying that SopB-DNA complexes do not create single-strand gaps by blocking replication forks. Rather, the results are consistent with SopB-DNA complexes channelling gapped molecules into the RecFOR recombination pathway. We suggest that extended SopB-DNA complexes increase the likelihood of recombination between sibling plasmids by keeping them in close contact prior to SopA-mediated segregation. These results cast plasmid site-specific resolution in a new role - compensation for untoward consequences of partition complex formation. PMID:17059567

  9. Relationship between whole-body macronutrient oxidative partitioning and pancreatic insulin secretion/β-cell function in non-diabetic humans

    PubMed Central

    Galgani, J. E.; Mizgier, M. L.; Mari, A.; Ravussin, E.

    2014-01-01

    Background Glucose-stimulated insulin secretion correlates inversely with the degree of whole-body insulin sensitivity suggesting a crosstalk between peripheral organs and pancreas. Such sensing mechanism could be mediated by changes in glucose flux (uptake, oxidation or storage) in peripheral tissues that may drive insulin secretion. Aim To relate whole-body non-protein respiratory quotient (npRQ), an index of macronutrient oxidative partitioning, with insulin secretion and β-cell function in non-diabetic individuals. Methods Macronutrient oxidation was measured after an overnight fast and for 4 hours after a 75-g oral glucose tolerance test (OGTT) in 30 participants (15/15 males/females; 35±12 y; 27±4 kg/m2). Furthermore, npRQ was assessed for 24 hours in a metabolic chamber. Insulin secretion was estimated by deconvolution of serum C-peptide concentration (fasting and 4-h OGTT) and from 24-h urinary C-peptide excretion corrected for energy intake (metabolic chamber). β-cell function parameters were obtained by mathematical modelling, while insulin sensitivity was determined by a euglycemic-hyperinsulinemic clamp (120 mU·m−2·min). Results Insulin secretion (from 24-h urinary C-peptide) correlated inversely with 24-h npRQ (r=−0.61; p=0.001), even after controlling for insulin sensitivity, energy balance, age and body mass index (r=−0.52; p=0.01). In turn, insulin secretion (from serum C-peptide) was not associated with fasting or OGTT npRQ. However, fasting npRQ was positively correlated with rate sensitivity (r=0.40; p<0.05) and marginally with glucose sensitivity (r=0.34; p=0.08). Conclusion Macronutrient oxidative partitioning, specifically glucose oxidation, might play a role on the regulation of insulin secretion. Further studies should aim at identifying the signals linking these processes. PMID:25176602

  10. Corrections of arterial input function for dynamic H215O PET to assess perfusion of pelvic tumours: arterial blood sampling versus image extraction

    NASA Astrophysics Data System (ADS)

    Lüdemann, L.; Sreenivasa, G.; Michel, R.; Rosner, C.; Plotkin, M.; Felix, R.; Wust, P.; Amthauer, H.

    2006-06-01

    Assessment of perfusion with 15O-labelled water (H215O) requires measurement of the arterial input function (AIF). The arterial time activity curve (TAC) measured using the peripheral sampling scheme requires corrections for delay and dispersion. In this study, parametrizations with and without arterial spillover correction for fitting of the tissue curve are evaluated. Additionally, a completely noninvasive method for generation of the AIF from a dynamic positron emission tomography (PET) acquisition is applied to assess perfusion of pelvic tumours. This method uses a volume of interest (VOI) to extract the TAC from the femoral artery. The VOI TAC is corrected for spillover using a separate tissue TAC and for recovery by determining the recovery coefficient on a coregistered CT data set. The techniques were applied in five patients with pelvic tumours who underwent a total of 11 examinations. Delay and dispersion correction of the blood TAC without arterial spillover correction yielded in seven examinations solutions inconsistent with physiology. Correction of arterial spillover increased the fitting accuracy and yielded consistent results in all patients. Generation of an AIF from PET image data was investigated as an alternative to arterial blood sampling and was shown to have an intrinsic potential to determine the AIF noninvasively and reproducibly. The AIF extracted from a VOI in a dynamic PET scan was similar in shape to the blood AIF but yielded significantly higher tissue perfusion values (mean of 104.0 ± 52.0%) and lower partition coefficients (-31.6 ± 24.2%). The perfusion values and partition coefficients determined with the VOI technique have to be corrected in order to compare the results with those of studies using a blood AIF.

  11. An extended hindered-rotor model with incorporation of Coriolis and vibrational-rotational coupling for calculating partition functions and derived quantities

    NASA Astrophysics Data System (ADS)

    Vansteenkiste, P.; Van Neck, D.; Van Speybroeck, V.; Waroquier, M.

    2006-01-01

    Large-amplitude motions, particularly internal rotations, are known to affect substantially thermodynamic functions and rate constants of reactions in which flexible molecules are involved. Up to now all methods for computing the partition functions of these motions rely on the Pitzer approximation of more than 50 years ago, in which the large-amplitude motion is treated in complete independence of the other (vibrational) degrees of freedom. In this paper an extended hindered-rotor model (EHR) is developed in which the vibrational modes, treated harmonically, are correctly separated from the large-amplitude motion and in which relaxation effects (the changes in the kinetic-energy matrix and potential curvature) are taken into account as one moves along the large-amplitude path. The model also relies on a specific coordinate system in which the Coriolis terms vanish at all times in the Hamiltonian. In this way an increased level of consistency between the various internal modes is achieved, as compared with the more usual hindered-rotor (HR) description. The method is illustrated by calculating the entropies and heat capacities on 1,3-butadiene and 1-butene (with, respectively, one and two internal rotors) and the rate constant for the addition reaction of a vinyl radical to ethene. We also discuss various variants of the one-dimensional hindered-rotor scheme existing in the literature and its relation with the EHR model. It is argued why in most cases the HR approach is already quite successful.

  12. An extended hindered-rotor model with incorporation of Coriolis and vibrational-rotational coupling for calculating partition functions and derived quantities.

    PubMed

    Vansteenkiste, P; Van Neck, D; Van Speybroeck, V; Waroquier, M

    2006-01-28

    Large-amplitude motions, particularly internal rotations, are known to affect substantially thermodynamic functions and rate constants of reactions in which flexible molecules are involved. Up to now all methods for computing the partition functions of these motions rely on the Pitzer approximation of more than 50 years ago, in which the large-amplitude motion is treated in complete independence of the other (vibrational) degrees of freedom. In this paper an extended hindered-rotor model (EHR) is developed in which the vibrational modes, treated harmonically, are correctly separated from the large-amplitude motion and in which relaxation effects (the changes in the kinetic-energy matrix and potential curvature) are taken into account as one moves along the large-amplitude path. The model also relies on a specific coordinate system in which the Coriolis terms vanish at all times in the Hamiltonian. In this way an increased level of consistency between the various internal modes is achieved, as compared with the more usual hindered-rotor (HR) description. The method is illustrated by calculating the entropies and heat capacities on 1,3-butadiene and 1-butene (with, respectively, one and two internal rotors) and the rate constant for the addition reaction of a vinyl radical to ethene. We also discuss various variants of the one-dimensional hindered-rotor scheme existing in the literature and its relation with the EHR model. It is argued why in most cases the HR approach is already quite successful.

  13. Extended Function of Plasmid Partition Genes: the Sop System of Linear Phage-Plasmid N15 Facilitates Late Gene Expression▿

    PubMed Central

    Ravin, Nikolai V.; Rech, Jérôme; Lane, David

    2008-01-01

    The mitotic stability of the linear plasmid-prophage N15 of Escherichia coli depends on a partition system closely related to that of the F plasmid SopABC. The two Sop systems are distinguished mainly by the arrangement of their centromeric SopB-binding sites, clustered in F (sopC) and dispersed in N15 (IR1 to IR4). Because two of the N15 inverted repeat (IR) sites are located close to elements presumed (by analogy with phage λ) to regulate late gene expression during the lytic growth of N15, we asked whether Sop partition functions play a role in this process. In N15, a putative Q antiterminator gene is located 6 kb upstream of the probable major late promoter and two intrinsic terminator-like sequences, in contrast to λ, where the Q gene is adjacent to the late promoter. Northern hybridization and lacZ reporter activity confirmed the identity of the N15 late promoter (p52), demonstrated antiterminator activity of the Q analogue, and located terminator sequences between p52 and the first open reading frame. Following prophage induction, N15 mutated in IR2 (downstream from gene Q) or IR3 (upstream of p52) showed a pronounced delay in lysis relative to that for wild-type N15. Expression of ir3−-p52::lacZ during N15 wild-type lytic growth was strongly reduced relative to the equivalent ir3+ fusion. The provision of Q protein and the IR2 and SopAB proteins in trans to ir3+-p52::lacZ increased expression beyond that seen in the absence of any one of these factors. These results indicate that the N15 Sop system has a dual role: partition and regulation of late gene transcription during lytic growth. PMID:18359814

  14. Extended function of plasmid partition genes: the Sop system of linear phage-plasmid N15 facilitates late gene expression.

    PubMed

    Ravin, Nikolai V; Rech, Jérôme; Lane, David

    2008-05-01

    The mitotic stability of the linear plasmid-prophage N15 of Escherichia coli depends on a partition system closely related to that of the F plasmid SopABC. The two Sop systems are distinguished mainly by the arrangement of their centromeric SopB-binding sites, clustered in F (sopC) and dispersed in N15 (IR1 to IR4). Because two of the N15 inverted repeat (IR) sites are located close to elements presumed (by analogy with phage lambda) to regulate late gene expression during the lytic growth of N15, we asked whether Sop partition functions play a role in this process. In N15, a putative Q antiterminator gene is located 6 kb upstream of the probable major late promoter and two intrinsic terminator-like sequences, in contrast to lambda, where the Q gene is adjacent to the late promoter. Northern hybridization and lacZ reporter activity confirmed the identity of the N15 late promoter (p52), demonstrated antiterminator activity of the Q analogue, and located terminator sequences between p52 and the first open reading frame. Following prophage induction, N15 mutated in IR2 (downstream from gene Q) or IR3 (upstream of p52) showed a pronounced delay in lysis relative to that for wild-type N15. Expression of ir3(-)-p52::lacZ during N15 wild-type lytic growth was strongly reduced relative to the equivalent ir3(+) fusion. The provision of Q protein and the IR2 and SopAB proteins in trans to ir3(+)-p52::lacZ increased expression beyond that seen in the absence of any one of these factors. These results indicate that the N15 Sop system has a dual role: partition and regulation of late gene transcription during lytic growth.

  15. Climate Change and Water Use Partitioning by Different Plant Functional Groups in a Grassland on the Tibetan Plateau

    PubMed Central

    Hu, Jia; Hopping, Kelly A.; Bump, Joseph K.; Kang, Sichang; Klein, Julia A.

    2013-01-01

    The Tibetan Plateau (TP) is predicted to experience increases in air temperature, increases in snowfall, and decreases in monsoon rains; however, there is currently a paucity of data that examine the ecological responses to such climate changes. In this study, we examined the effects of increased air temperature and snowfall on: 1) water use partitioning by different plant functional groups, and 2) ecosystem CO2 fluxes throughout the growing season. At the individual plant scale, we used stable hydrogen isotopes (δD) to partition water use between shallow- and deep-rooted species. Prior to the arrival of summer precipitation (typically mid-July), snowmelt was the main water source in the soils. During this time, shallow and deep-rooted species partitioned water use by accessing water from shallow and deep soils, respectively. However, once the monsoon rains arrived, all plants used rainwater from the upper soils as the main water source. Snow addition did not result in increased snowmelt use throughout the growing season; instead, snowmelt water was pushed down into deeper soils when the rains arrived. At the larger plot scale, CO2 flux measurements demonstrated that rain was the main driver for net ecosystem productivity (NEP). NEP rates were low during June and July and reached a maximum during the monsoon season in August. Warming decreased NEP through a reduction in gross primary productivity (GPP), and snow additions did not mitigate the negative effects of warming by increasing NEP or GPP. Both the isotope and CO2 flux results suggest that rain drives productivity in the Nam Tso region on the TP. This also suggests that the effects of warming-induced drought on the TP may not be mitigated by increased snowfall. Further decreases in summer monsoon rains may affect ecosystem productivity, with large implications for livestock-based livelihoods. PMID:24069425

  16. Fixed conditions for achieving the real-valued partition function of one-dimensional Gross-Pitaevskii equation coupled with time-dependent potential

    SciTech Connect

    Prayitno, T. B.

    2014-03-24

    We have imposed the conditions in order to preserve the real-valued partition function in the case of onedimensional Gross-Pitaevskii equation coupled by time-dependent potential. In this case we have solved the Gross-Pitaevskii equation by means of the time-dependent perturbation theory by extending the previous work of Kivshar et al. [Phys. Lett A 278, 225–230 (2001)]. To use the method, we have treated the equation as the macroscopic quantum oscillator and found that the expression of the partition function explicitly has complex values. In fact, we have to choose not only the appropriate functions but also the suitable several values of the potential to keep the real-valued partition function.

  17. Prospective motion correction for functional MRI using sparsity and Kalman filtering

    NASA Astrophysics Data System (ADS)

    Weller, Daniel S.; Noll, Douglas C.; Fessler, Jeffrey A.

    2013-09-01

    We propose a novel algorithm to adaptively correct head motion during functional magnetic resonance imaging scans. Our method combines a Kalman-filter-like motion tracker and a registration cost function based on a sparse residual image model. Using simulated data, we compare a time series correlation analysis of our prospectively corrected reconstruction against the same analysis using post-scan motion correction provided by standard software. Our experiments demonstrate our prospective correction method is capable of mitigating motion effects and improving the sensitivity and specificity of the correlation analysis, without relying on costly external tracking hardware or separate navigational data that would take extra time to acquire during each time frame.

  18. Metal-Silicate Partitioning of Bi, In, and Cd as a Function of Temperature and Melt Composition

    NASA Technical Reports Server (NTRS)

    Marin, Nicole; Righter, K.; Danielson, L.; Pando, K.; Lee, C.

    2013-01-01

    The origin of volatile elements in the Earth, Moon and Mars is not known; however, several theories have been proposed based on volatile elements such as In, As, Se, Te and Zn which are in lower concentration in the Earth, Moon, and Mars than in chondrites. Explanations for these low concentrations are based on two contrasting theories for the origin of Earth: equilibrium core formation versus late accretion. One idea is that the volatiles were added during growth of the planets and Moon, and some mobilized into the metallic core while others stayed in the mantle (e.g., [1]). The competing idea is that they were added to the mantles after core formation had completed (e.g., [2]). Testing these ideas involves quantitative modeling which can only be performed after data is obtained on the systematic metal-silicate partitioning behavior of volatile elements with temperature, pressure and melt composition. Until now, such data for Bi, In, and Cd has been lacking. After conducting a series of high pressure, high temperature experiments, the metal-silicate partition coefficients of Bi, In, and Cd as a function of temperature and melt composition can be used to evaluate potential conditions under which terrestrial planets differentiated into core and mantle, and how they acquired volatiles.

  19. Partition search

    SciTech Connect

    Ginsberg, M.L.

    1996-12-31

    We introduce a new form of game search called partition search that incorporates dependency analysis, allowing substantial reductions in the portion of the tree that needs to be expanded. Both theoretical results and experimental data are presented. For the game of bridge, partition search provides approximately as much of an improvement over existing methods as {alpha}-{beta} pruning provides over minimax.

  20. A Systematic Approach for Computing Zero-Point Energy, Quantum Partition Function, and Tunneling Effect Based on Kleinert's Variational Perturbation Theory.

    PubMed

    Wong, Kin-Yiu; Gao, Jiali

    2008-09-01

    In this paper, we describe an automated integration-free path-integral (AIF-PI) method, based on Kleinert's variational perturbation (KP) theory, to treat internuclear quantum-statistical effects in molecular systems. We have developed an analytical method to obtain the centroid potential as a function of the variational parameter in the KP theory, which avoids numerical difficulties in path-integral Monte Carlo or molecular dynamics simulations, especially at the limit of zero-temperature. Consequently, the variational calculations using the KP theory can be efficiently carried out beyond the first order, i.e., the Giachetti-Tognetti-Feynman-Kleinert variational approach, for realistic chemical applications. By making use of the approximation of independent instantaneous normal modes (INM), the AIF-PI method can readily be applied to many-body systems. Previously, we have shown that in the INM approximation, the AIF-PI method is accurate for computing the quantum partition function of a water molecule (3 degrees of freedom) and the quantum correction factor for the collinear H(3) reaction rate (2 degrees of freedom). In this work, the accuracy and properties of the KP theory are further investigated by using the first three order perturbations on an asymmetric double-well potential, the bond vibrations of H(2), HF, and HCl represented by the Morse potential, and a proton-transfer barrier modeled by the Eckart potential. The zero-point energy, quantum partition function, and tunneling factor for these systems have been determined and are found to be in excellent agreement with the exact quantum results. Using our new analytical results at the zero-temperature limit, we show that the minimum value of the computed centroid potential in the KP theory is in excellent agreement with the ground state energy (zero-point energy) and the position of the centroid potential minimum is the expectation value of particle position in wave mechanics. The fast convergent property

  1. A Systematic Approach for Computing Zero-Point Energy, Quantum Partition Function, and Tunneling Effect Based on Kleinert’s Variational Perturbation Theory

    PubMed Central

    Wong, Kin-Yiu; Gao, Jiali

    2009-01-01

    In this paper, we describe an automated integration-free path-integral (AIF-PI) method, based on Kleinert’s variational perturbation (KP) theory, to treat internuclear quantum-statistical effects in molecular systems. We have developed an analytical method to obtain the centroid potential as a function of the variational parameter in the KP theory, which avoids numerical difficulties in path-integral Monte Carlo or molecular dynamics simulations, especially at the limit of zero-temperature. Consequently, the variational calculations using the KP theory can be efficiently carried out beyond the first order, i.e., the Giachetti-Tognetti-Feynman-Kleinert variational approach, for realistic chemical applications. By making use of the approximation of independent instantaneous normal modes (INM), the AIF-PI method can readily be applied to many-body systems. Previously, we have shown that in the INM approximation, the AIF-PI method is accurate for computing the quantum partition function of a water molecule (3 degrees of freedom) and the quantum correction factor for the collinear H3 reaction rate (2 degrees of freedom). In this work, the accuracy and properties of the KP theory are further investigated by using the first three order perturbations on an asymmetric double-well potential, the bond vibrations of H2, HF, and HCl represented by the Morse potential, and a proton-transfer barrier modeled by the Eckart potential. The zero-point energy, quantum partition function, and tunneling factor for these systems have been determined and are found to be in excellent agreement with the exact quantum results. Using our new analytical results at the zero-temperature limit, we show that the minimum value of the computed centroid potential in the KP theory is in excellent agreement with the ground state energy (zero-point energy) and the position of the centroid potential minimum is the expectation value of particle position in wave mechanics. The fast convergent property of

  2. Umbrella motion of the methyl cation, radical, and anion molecules. I. Potentials, energy levels and partition functions

    NASA Astrophysics Data System (ADS)

    Ragni, Mirco; Bitencourt, Ana Carla P.; Prudente, Frederico V.; Barreto, Patricia R. P.; Posati, Tamara

    2016-03-01

    A study of the umbrella motion of the methyl cation, radical, and anion molecules is presented. This is the floppiest mode of vibration of all three species and its characterization is of fundamental importance for understanding their reactivity. Minimum Energy Paths of the umbrella motions according to the hyperspherical treatment were obtained, by single point calculations, at the CCSD(T)/aug-cc-pVQT level of theory in the Born-Oppenheimer approximation. These energy profiles permit us to calculate the vibrational levels through the Hyperquantization algorithm, which is shown appropriated for the description of the umbrella motion of these three molecules. The adiabatic electron affinity and ionization potentials were estimated to good accuracy. Partition functions are also calculated in order to obtain information on the reaction rates involving these groups.

  3. Relations Among Two Methods for Computing the Partition Function of the Two-Dimensional One-Component Plasma

    NASA Astrophysics Data System (ADS)

    Grimaldo, Johnny Alejandro Mora; Téllez, Gabriel

    2015-07-01

    The two-dimensional one-component plasma—2dOCP—is a system composed by mobile particles with charge over a neutralizing background in a two-dimensional surface. The Boltzmann factor of this system, at temperature , takes the form of a Vandermonde determinant to the power , where is the coupling constant of this Coulomb system. The partition function of the model has been computed exactly for the even values of the coupling constant , and a finite number of particles , by two means: (1) by recognizing that the Boltzmann factor is the square of a Jack polynomial and expanding it in an appropriate monomial base, and (2) by mapping the system onto a 1-dimensional chain of interacting fermions. In this work the connection among the two methods is derived, and some properties of the expansion coefficients for the power of the Vandermonde determinant are explored.

  4. Thermal Corrections to Density Functional Simulations of Warm Dense Matter

    NASA Astrophysics Data System (ADS)

    Smith, Justin; Pribram-Jones, Aurora; Burke, Kieron

    Present density functional calculations of warm dense matter often use the Mermin-Kohn-Sham (MKS) scheme at finite temperature, but employ ground-state approximations to the exchange-correlation (XC) free energy. In the simplest solvable non-trivial model, an asymmetric Hubbard dimer, we calculate the exact many-body energies, the exact Mermin-Kohn-Sham functionals for this system, and extract the exact XC free energy. For moderate temperatures and weak correlation, we show this approximation is excellent, but fails for stronger correlations. Additionally, we use this system to test various conditions that must be satisfied.

  5. Spatial Distribution of Cellular Function: The Partitioning of Proteins between Mitochondria and the Nucleus in MCF7 Breast Cancer Cells

    PubMed Central

    Qattan, Amal T.; Radulovic, Marko; Crawford, Mark; Godovac-Zimmermann, Jasminka

    2014-01-01

    Concurrent proteomics analysis of the nuclei and mitochondria of MCF7 breast cancer cells identified 985 proteins (40% of all detected proteins) present in both organelles. Numerous proteins from all five complexes involved in oxidative phosphorylation (e.g., NDUFA5, NDUFB10, NDUFS1, NDUF2, SDHA, UQRB, UQRC2, UQCRH, COX5A, COX5B, MT-CO2, ATP5A1, ATP5B, ATP5H, etc.), from the TCA-cycle (DLST, IDH2, IDH3A, OGDH, SUCLAG2, etc.), and from glycolysis (ALDOA, ENO1, FBP1, GPI, PGK1, TALDO1, etc.) were distributed to both the nucleus and mitochondria. In contrast, proteins involved in nuclear/mitochondrial RNA processing/translation and Ras/Rab signaling showed different partitioning patterns. The identity of the OxPhos, TCA-cycle, and glycolysis proteins distributed to both the nucleus and mitochondria provides evidence for spatio-functional integration of these processes over the two different subcellular organelles. We suggest that there are unrecognized aspects of functional coordination between the nucleus and mitochondria, that integration of core functional processes via wide subcellular distribution of constituent proteins is a common characteristic of cells, and that subcellular spatial integration of function may be a vital aspect of cancer. PMID:23051583

  6. Different functional states of ram spermatozoa analysed by partition in an aqueous two-phase system.

    PubMed

    Grasa, P; Martí, J I; Muiño-Blanco, T; Cebrián-Pérez, J A

    2003-09-25

    The surface of spermatozoa plays a critical role in many stages involved in fertilisation. The plasma membrane undergoes important alterations in the male and female reproductive tract, which result in the ability of spermatozoa to fertilise eggs. One of these membrane modifications is sperm capacitation, a process by which sperm interacts with the zona pellucida receptors leading to the acrosome reaction. It has been proposed that the freezing process induces capacitation-like changes to spermatozoa, and that this premature capacitation could explain the reduction in longevity and fertilising capacity of cryopreserved mammalian spermatozoa. Our research focused on the relationship between membrane alterations occurring throughout freezing-thawing and the processes of capacitation and acrosome reaction. We used centrifugal countercurrent distribution (CCCD) analysis to compare the partition behaviour of ram spermatozoa that was either subjected to cold-shock or frozen-thawed with capacitated and acrosome reacted samples. In addition, the effect of the induced acrosome reaction on membrane integrity of ram spermatozoa was studied using biochemical markers and electron microscopy scanning. The CCCD analysis revealed important similarities between the surface characteristics of capacitated and cold-shocked sperm as well as between acrosome-reacted and frozen-thawed sperm. Cold-shocked and capacitated sperm showed an increased cell affinity for the lower dextran-rich phase as well as a decreased heterogeneity. Likewise, the induction of the acrosome reaction resulted in a loss of viability and an important decrease in cell surface heterogeneity compared to the untreated-control sample. Similar surface changes were found when semen samples were frozen with either Fiser or milk-yolk extender. These results confirm those obtained for membrane integrity by fluorescence markers. Thus, the high cell viability value found in the control sample (74.5%) was greatly decreased

  7. Approach to a correct function of stuffing boxes

    SciTech Connect

    Bartonicek, J.; Schoeckle, F.

    1996-12-01

    Stuff boxes are often used to tighten the gaps between valve stems and the housing. The stuffing box packing material is compressed axially to achieve a radial stress value, which is necessary for tightness. Tightness is achieved, if the sealing materials are seated properly and if a sufficient stress value is acting in radial direction during all states of operation. High prestress values are necessary for tightening purposes, lower values are better for the function of the valve. As the seating and the prestressing force is applied axially (using the bolts of a gland), gasket factors must be known, that characterize the deformation behavior and the transmission (relation between radial/axial stress). Furthermore, gasket factors, that characterize the tightening behavior, are necessary. Such gasket factors give the relation between radial stress and leakage of the packing materials. A friction coefficient -- this parameter determines the function of the valve (together with the radial stress) -- is another important gasket factor. Additionally the relaxation of the stuffing box packing material between the assembly and the operating state must be known. In the paper definitions for the most important gasket factors of stuffing box materials are provided. Test procedures and test rigs for the determination of the gasket factors are discussed. Gasket factors, which have been measured with these newly developed test rigs, are related to experiences with real applications. Finally a method for a controlled prestressing of gland packings is described.

  8. [Correcting influence of music on the students' functional state].

    PubMed

    Gevorkian, É S; Minasian, S M; Abraamian, É T; Adamian, Ts I

    2013-01-01

    The influence of listening to classical music on integral indices of the activity of the regulatory mechanisms of the heart rhythm in students after teaching load was tested with the method of variational pulsometry accordingly to R.M Baevsky procedure. Registration and analysis of ECG was realized on Pentium 4 in three experimental situations: before the start of lessons (norm), after lessons, after listening to the music. Two types of response of students 'functional state to the teaching load: sympathetic and parasympathetic have been established. After teaching load music therapy session was found to led to the shift of levels of all examined indices of heart rhythm toward the original data (norm), most expressed in students with a sympathetic response type.

  9. Resource partitioning along multiple niche axes drives functional diversity in parrotfishes on Caribbean coral reefs.

    PubMed

    Adam, Thomas C; Kelley, Megan; Ruttenberg, Benjamin I; Burkepile, Deron E

    2015-12-01

    The recent loss of key consumers to exploitation and habitat degradation has significantly altered community dynamics and ecosystem function across many ecosystems worldwide. Predicting the impacts of consumer losses requires knowing the level of functional diversity that exists within a consumer assemblage. In this study, we document functional diversity among nine species of parrotfishes on Caribbean coral reefs. Parrotfishes are key herbivores that facilitate the maintenance and recovery of coral-dominated reefs by controlling algae and provisioning space for the recruitment of corals. We observed large functional differences among two genera of parrotfishes that were driven by differences in diet. Fishes in the genus Scarus targeted filamentous algal turf assemblages, crustose coralline algae, and endolithic algae and avoided macroalgae, while fishes in the genus Sparisoma preferentially targeted macroalgae. However, species with similar diets were dissimilar in other attributes, including the habitats they frequented, the types of substrate they fed from, and the spatial scale at which they foraged. These differences indicate that species that appear to be functionally redundant when looking at diet alone exhibit high levels of complementarity when we consider multiple functional traits. By identifying key functional differences among parrotfishes, we provide critical information needed to manage parrotfishes to enhance the resilience of coral-dominated reefs and reverse phase shifts on algal-dominated reefs throughout the wider Caribbean. Further, our study provides a framework for predicting the impacts of consumer losses in other species rich ecosystems. PMID:26245147

  10. Resource partitioning along multiple niche axes drives functional diversity in parrotfishes on Caribbean coral reefs.

    PubMed

    Adam, Thomas C; Kelley, Megan; Ruttenberg, Benjamin I; Burkepile, Deron E

    2015-12-01

    The recent loss of key consumers to exploitation and habitat degradation has significantly altered community dynamics and ecosystem function across many ecosystems worldwide. Predicting the impacts of consumer losses requires knowing the level of functional diversity that exists within a consumer assemblage. In this study, we document functional diversity among nine species of parrotfishes on Caribbean coral reefs. Parrotfishes are key herbivores that facilitate the maintenance and recovery of coral-dominated reefs by controlling algae and provisioning space for the recruitment of corals. We observed large functional differences among two genera of parrotfishes that were driven by differences in diet. Fishes in the genus Scarus targeted filamentous algal turf assemblages, crustose coralline algae, and endolithic algae and avoided macroalgae, while fishes in the genus Sparisoma preferentially targeted macroalgae. However, species with similar diets were dissimilar in other attributes, including the habitats they frequented, the types of substrate they fed from, and the spatial scale at which they foraged. These differences indicate that species that appear to be functionally redundant when looking at diet alone exhibit high levels of complementarity when we consider multiple functional traits. By identifying key functional differences among parrotfishes, we provide critical information needed to manage parrotfishes to enhance the resilience of coral-dominated reefs and reverse phase shifts on algal-dominated reefs throughout the wider Caribbean. Further, our study provides a framework for predicting the impacts of consumer losses in other species rich ecosystems.

  11. Recursive Partitioning to Identify Potential Causes of Differential Item Functioning in Cross-National Data

    ERIC Educational Resources Information Center

    Finch, W. Holmes; Hernández Finch, Maria E.; French, Brian F.

    2016-01-01

    Differential item functioning (DIF) assessment is key in score validation. When DIF is present scores may not accurately reflect the construct of interest for some groups of examinees, leading to incorrect conclusions from the scores. Given rising immigration, and the increased reliance of educational policymakers on cross-national assessments…

  12. A new strategy for exploring the hierarchical structure of cancers by adaptively partitioning functional modules from gene expression network

    PubMed Central

    Xu, Junmei; Jing, Runyu; Liu, Yuan; Dong, Yongcheng; Wen, Zhining; Li, Menglong

    2016-01-01

    The interactions among the genes within a disease are helpful for better understanding the hierarchical structure of the complex biological system of it. Most of the current methodologies need the information of known interactions between genes or proteins to create the network connections. However, these methods meet the limitations in clinical cancer researches because different cancers not only share the common interactions among the genes but also own their specific interactions distinguished from each other. Moreover, it is still difficult to decide the boundaries of the sub-networks. Therefore, we proposed a strategy to construct a gene network by using the sparse inverse covariance matrix of gene expression data, and divide it into a series of functional modules by an adaptive partition algorithm. The strategy was validated by using the microarray data of three cancers and the RNA-sequencing data of glioblastoma. The different modules in the network exhibited specific functions in cancers progression. Moreover, based on the gene expression profiles in the modules, the risk of death was well predicted in the clustering analysis and the binary classification, indicating that our strategy can be benefit for investigating the cancer mechanisms and promoting the clinical applications of network-based methodologies in cancer researches. PMID:27349736

  13. Automatic correction scheme for the temperature dependent overlap function of CHM15k ceilometers

    NASA Astrophysics Data System (ADS)

    Haefele, Alexander; Poltera, Yann; Hervo, Maxime

    2016-04-01

    Imperfections in a lidar's overlap function lead to artefacts in the background, range and overlap corrected lidar signals. These artefacts can erroneously be interpreted as aerosol gradient or, in extreme cases, as cloud base leading to false cloud detection. A correct specification of the overlap function is hence crucial to use automatic elastic lidars (ceilometers) for the detection of the planetary boundary layer or low clouds. In this study an algorithm is presented to correct such artefacts. It is based on the assumption of a homogeneous boundary layer and a correct specification of the overlap function down to a minimum range, which must be situated within the boundary layer. The strength of the algorithm lies in a sophisticated quality check scheme which allows to reliably identify favorable atmospheric conditions. The algorithm has been applied to 2 years of data from a CHM15k ceilometer from Lufft. Backscatter signals corrected for background, range and overlap have been compared using the overlap function provided by the manufacturer and the one corrected with the presented algorithm. Differences between corrected and uncorrected signals reach up to 45% in the first 300m above ground. The amplitude of the correction turned out to be temperature dependent being larger for higher temperatures. A linear model of the correction as a function of the instrument's internal temperature has been derived from the experimental data. Case studies and a statistical analysis of the strongest gradient derived from corrected signals reveal that the temperature model is capable to correct overlap artefacts with high quality, in particular such due to diurnal variations. The presented correction method has the potential to significantly improve the detection of the boundary layer with gradient based methods because it removes false candidates and hence simplifies the attribution of the detected gradients to the planetary boundary layer. A particularly high benefit can be

  14. MSTor: A program for calculating partition functions, free energies, enthalpies, entropies, and heat capacities of complex molecules including torsional anharmonicity

    NASA Astrophysics Data System (ADS)

    Zheng, Jingjing; Mielke, Steven L.; Clarkson, Kenneth L.; Truhlar, Donald G.

    2012-08-01

    We present a Fortran program package, MSTor, which calculates partition functions and thermodynamic functions of complex molecules involving multiple torsional motions by the recently proposed MS-T method. This method interpolates between the local harmonic approximation in the low-temperature limit, and the limit of free internal rotation of all torsions at high temperature. The program can also carry out calculations in the multiple-structure local harmonic approximation. The program package also includes six utility codes that can be used as stand-alone programs to calculate reduced moment of inertia matrices by the method of Kilpatrick and Pitzer, to generate conformational structures, to calculate, either analytically or by Monte Carlo sampling, volumes for torsional subdomains defined by Voronoi tessellation of the conformational subspace, to generate template input files, and to calculate one-dimensional torsional partition functions using the torsional eigenvalue summation method. Catalogue identifier: AEMF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMF_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 77 434 No. of bytes in distributed program, including test data, etc.: 3 264 737 Distribution format: tar.gz Programming language: Fortran 90, C, and Perl Computer: Itasca (HP Linux cluster, each node has two-socket, quad-core 2.8 GHz Intel Xeon X5560 “Nehalem EP” processors), Calhoun (SGI Altix XE 1300 cluster, each node containing two quad-core 2.66 GHz Intel Xeon “Clovertown”-class processors sharing 16 GB of main memory), Koronis (Altix UV 1000 server with 190 6-core Intel Xeon X7542 “Westmere” processors at 2.66 GHz), Elmo (Sun Fire X4600 Linux cluster with AMD Opteron cores), and Mac Pro (two 2.8 GHz Quad-core Intel Xeon

  15. Active stable maintenance functions in low copy-number plasmids of Gram-positive bacteria I. Partition systems.

    PubMed

    Dmowski, Michał; Jagura-Burdzy, Grazyna

    2013-01-01

    Low copy number plasmids cannot rely on the random segregation during bacterial cell division. To be stably maintained in the population they evolved two types of mechanisms (i) partition systems (PAR) that actively separate replicated plasmid molecules to the daughter cells and (ii) toxin-andidote systems (TA) that act after cell division to kill plasmid-less cells. Our knowledge of partition systems has been based mainly on analysis of plasmids from Gram-negative bacteria. Now, numerous partition systems of plasmids from Gram-positive bacteria have also been characterized and make significant contribution to our understanding of these mechanisms.

  16. Once More on the Radiative Corrections to the Nucleon Structure Functions in QCD

    NASA Astrophysics Data System (ADS)

    Stamenov, D. B.

    A new representation of the next-to-leading QCD corrections to the nucleon structure functions is given in terms of parton distributions. All O(αs) corrections to the leading logarithmic approximation (LLA) are included. In contrast to the similar representations in the literature terms of order O (α s2) do not appear in our expressions for the nucleon structure functions taken in the next-to-leading logarithmic approximation. This result is generalized for any order in αs beyond the LLA. Terms of order O(α sn) which belong only to the approximation considered are present in such a representation for the structure functions.

  17. Ions in solution: Density corrected density functional theory (DC-DFT)

    SciTech Connect

    Kim, Min-Cheol; Sim, Eunji; Burke, Kieron

    2014-05-14

    Standard density functional approximations often give questionable results for odd-electron radical complexes, with the error typically attributed to self-interaction. In density corrected density functional theory (DC-DFT), certain classes of density functional theory calculations are significantly improved by using densities more accurate than the self-consistent densities. We discuss how to identify such cases, and how DC-DFT applies more generally. To illustrate, we calculate potential energy surfaces of HO·Cl{sup −} and HO·H{sub 2}O complexes using various common approximate functionals, with and without this density correction. Commonly used approximations yield wrongly shaped surfaces and/or incorrect minima when calculated self consistently, while yielding almost identical shapes and minima when density corrected. This improvement is retained even in the presence of implicit solvent.

  18. Generalized gradient approximation exchange energy functional with correct asymptotic behavior of the corresponding potential.

    PubMed

    Carmona-Espíndola, Javier; Gázquez, José L; Vela, Alberto; Trickey, S B

    2015-02-01

    A new non-empirical exchange energy functional of the generalized gradient approximation (GGA) type, which gives an exchange potential with the correct asymptotic behavior, is developed and explored. In combination with the Perdew-Burke-Ernzerhof (PBE) correlation energy functional, the new CAP-PBE (CAP stands for correct asymptotic potential) exchange-correlation functional gives heats of formation, ionization potentials, electron affinities, proton affinities, binding energies of weakly interacting systems, barrier heights for hydrogen and non-hydrogen transfer reactions, bond distances, and harmonic frequencies on standard test sets that are fully competitive with those obtained from other GGA-type functionals that do not have the correct asymptotic exchange potential behavior. Distinct from them, the new functional provides important improvements in quantities dependent upon response functions, e.g., static and dynamic polarizabilities and hyperpolarizabilities. CAP combined with the Lee-Yang-Parr correlation functional gives roughly equivalent results. Consideration of the computed dynamical polarizabilities in the context of the broad spectrum of other properties considered tips the balance to the non-empirical CAP-PBE combination. Intriguingly, these improvements arise primarily from improvements in the highest occupied and lowest unoccupied molecular orbitals, and not from shifts in the associated eigenvalues. Those eigenvalues do not change dramatically with respect to eigenvalues from other GGA-type functionals that do not provide the correct asymptotic behavior of the potential. Unexpected behavior of the potential at intermediate distances from the nucleus explains this unexpected result and indicates a clear route for improvement.

  19. Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea, Antarctica

    PubMed Central

    Delmont, Tom O.; Eren, A. Murat; Vineis, Joseph H.; Post, Anton F.

    2015-01-01

    Antarctica polynyas support intense phytoplankton blooms, impacting their environment by a substantial depletion of inorganic carbon and nutrients. These blooms are dominated by the colony-forming haptophyte Phaeocystis antarctica and they are accompanied by a distinct bacterial population. Yet, the ecological role these bacteria may play in P. antarctica blooms awaits elucidation of their functional gene pool and of the geochemical activities they support. Here, we report on a metagenome (~160 million reads) analysis of the microbial community associated with a P. antarctica bloom event in the Amundsen Sea polynya (West Antarctica). Genomes of the most abundant Bacteroidetes and Proteobacteria populations have been reconstructed and a network analysis indicates a strong functional partitioning of these bacterial taxa. Three of them (SAR92, and members of the Oceanospirillaceae and Cryomorphaceae) are found in close association with P. antarctica colonies. Distinct features of their carbohydrate, nitrogen, sulfur and iron metabolisms may serve to support mutualistic relationships with P. antarctica. The SAR92 genome indicates a specialization in the degradation of fatty acids and dimethylsulfoniopropionate (compounds released by P. antarctica) into dimethyl sulfide, an aerosol precursor. The Oceanospirillaceae genome carries genes that may enhance algal physiology (cobalamin synthesis). Finally, the Cryomorphaceae genome is enriched in genes that function in cell or colony invasion. A novel pico-eukaryote, Micromonas related genome (19.6 Mb, ~94% completion) was also recovered. It contains the gene for an anti-freeze protein, which is lacking in Micromonas at lower latitudes. These draft genomes are representative for abundant microbial taxa across the Southern Ocean surface. PMID:26579075

  20. Moduli spaces of framed symplectic and orthogonal bundles on P2 and the K-theoretic Nekrasov partition functions

    NASA Astrophysics Data System (ADS)

    Choy, Jaeyoo

    2016-08-01

    Let K be the compact Lie group USp(N / 2) or SO(N , R) . Let MnK be the moduli space of framed K-instantons over S4 with the instanton number n. By Donaldson (1984), MnK is endowed with a natural scheme structure. It is a Zariski open subset of a GIT quotient of μ-1(0) , where μ is a holomorphic moment map such that μ-1(0) consists of the ADHM data. The purpose of the paper is to study the geometric properties of μ-1(0) and its GIT quotient, such as complete intersection, irreducibility, reducedness and normality. If K = USp(N / 2) then μ is flat and μ-1(0) is an irreducible normal variety for any n and even N. If K = SO(N , R) the similar results are proven for low n and N. As an application one can obtain a mathematical interpretation of the K-theoretic Nekrasov partition function of Nekrasov and Shadchin (2004).

  1. Partition coefficients for iron between plagioclase and basalt as a function of oxygen fugacity - Implications for Archean and lunar anorthosites

    NASA Technical Reports Server (NTRS)

    Phinney, W. C.

    1992-01-01

    As a prelude to determinations of the content of total iron as FeO(T) in melts in equilibrium with calcic anorthosites, the partition coefficients (Ds) for FeO(T) between calcic plagioclase and basaltic melt were determined, as a function of oxygen fugacity (f(O2)), for a basaltic composition that occurs as matrices for plagioclase megacrysts. Results showed that, at the liquidus conditions, the value of D for FeO(T) between calcic plagioclase and tholeiitic basalt changed little (from 0.030 to 0.044) between the very low f(O2) of the iron-wustite buffer and that of the quartz-fayalite-magnetite (QFM) buffer. At fugacities above QFM, the value for D increased rapidly to 0.14 at the magnetite-hematite buffer and to 0.33 in air. The increase in D results from the fact that, at f(O2) below QFM, nearly all of the Fe is in the Fe(2+) state; above QFM, the Fe(3+)/Fe(2+) ratio in the melt increases rapidly, causing more Fe to enter the plagioclase which accepts Fe(3+) more readily than Fe(2+).

  2. A single 43-bp sopC repeat of plasmid mini-F is sufficient to allow assembly of a functional nucleoprotein partition complex.

    PubMed

    Biek, D P; Shi, J

    1994-08-16

    Stable maintenance of the low-copy-number mini-F plasmid in Escherichia coli is dependent on a functional partition system. The sop partition region encodes proteins SopA and SopB and a cis-acting element sopC, which contains multiple sites to which SopB binds. We have found that SopB protein acting at sopC in vivo is associated with a marked effect on plasmid DNA supercoiling, which may reflect the formation of a wrapped nucleoprotein complex. In this study, we demonstrate that a functional partition complex can form with a single 43-bp SopB binding site. Our experiments suggest that SopB bound at a single site nucleates the binding of additional SopB protein and wrapping of adjacent DNA sequences, such that approximately equal numbers of supercoils are restrained regardless of the number of tandem sopC repeats present. It is likely that this unusual nucleoprotein complex allows interaction of the plasmid with the partition apparatus.

  3. Benchmark tests of a strongly constrained semilocal functional with a long-range dispersion correction

    NASA Astrophysics Data System (ADS)

    Brandenburg, J. G.; Bates, J. E.; Sun, J.; Perdew, J. P.

    2016-09-01

    The strongly constrained and appropriately normed (SCAN) semilocal density functional [J. Sun, A. Ruzsinszky, and J. P. Perdew, Phys. Rev. Lett. 115, 036402 (2015), 10.1103/PhysRevLett.115.036402] obeys all 17 known exact constraints for meta-generalized-gradient approximations (meta-GGAs), and it includes some medium-range correlation effects. Long-range London dispersion interactions are still missing, but they can be accounted for via an appropriate correction scheme. In this study, we combine SCAN with an efficient London dispersion correction and show that lattice energies of simple organic crystals can be improved with the applied correction by 50%. The London-dispersion corrected SCAN meta-GGA outperforms all other tested London-dispersion corrected meta-GGAs for molecular geometries. Our method yields mean absolute deviations (MADs) for main group bond lengths that are consistently below 1 pm, rotational constants with MADs of 0.2%, and noncovalent distances with MADs below 1%. For a large database of general main group thermochemistry and kinetics (˜800 chemical species), one of the lowest weighted mean absolute deviations for long-range corrected meta-GGA functionals is achieved. Noncovalent interactions are of average quality, and hydrogen bonded systems in particular seem to suffer from overestimated polarization related to the self-interaction error of SCAN. We also discuss some consequences of numerical sensitivity encountered for meta-GGAs.

  4. Next-to leading order analysis of target mass corrections to structure functions and asymmetries

    SciTech Connect

    L. T. Brady, A. Accardi, T. J. Hobbs, W. Melnitchouk

    2011-10-01

    We perform a comprehensive analysis of target mass corrections (TMCs) to spin-averaged structure functions and asymmetries at next-to-leading order. Several different prescriptions for TMCs are considered, including the operator product expansion, and various approximations to it, collinear factorization, and xi-scaling. We assess the impact of each of these on a number of observables, such as the neutron to proton F{sub 2} structure function ratio, and parity-violating electron scattering asymmetries for protons and deuterons which are sensitive to gamma-Z interference effects. The corrections from higher order radiative and nuclear effects on the parity-violating deuteron asymmetry are also quantified.

  5. Communication: Self-interaction correction with unitary invariance in density functional theory

    SciTech Connect

    Pederson, Mark R.; Ruzsinszky, Adrienn; Perdew, John P.

    2014-03-28

    Standard spin-density functionals for the exchange-correlation energy of a many-electron ground state make serious self-interaction errors which can be corrected by the Perdew-Zunger self-interaction correction (SIC). We propose a size-extensive construction of SIC orbitals which, unlike earlier constructions, makes SIC computationally efficient, and a true spin-density functional. The SIC orbitals are constructed from a unitary transformation that is explicitly dependent on the non-interacting one-particle density matrix. When this SIC is applied to the local spin-density approximation, improvements are found for the atomization energies of molecules.

  6. Alkyl nitrate formation from the reactions of C8-C14 n-alkanes with OH radicals in the presence of NO(x): measured yields with essential corrections for gas-wall partitioning.

    PubMed

    Yeh, Geoffrey K; Ziemann, Paul J

    2014-09-18

    In this study, C8-C14 n-alkanes were reacted with OH radicals in the presence of NO(x) in a Teflon film environmental chamber and isomer-specific yields of alkyl nitrates were determined using gas chromatography. Because results indicated significant losses of alkyl nitrates to chamber walls, gas-wall partitioning was investigated by monitoring the concentrations of a suite of synthesized alkyl nitrates added to the chamber. Gas-to-wall partitioning increased with increasing carbon number and with proximity of the nitrooxy group to the terminal carbon, with losses as high as 86%. The results were used to develop a structure-activity model to predict the effects of carbon number and isomer structure on gas-wall partitioning, which was used to correct the measured yields of alkyl nitrate isomers formed in chamber reactions. The resulting branching ratios for formation of secondary alkyl nitrates were similar for all isomers of a particular carbon number, and average values, which were almost identical to alkyl nitrate yields, were 0.219, 0.206, 0.254, 0.291, and 0.315 for reactions of n-octane, n-decane, n-dodecane, n-tridecane, and n-tetradecane, respectively. The increase in average branching ratios and alkyl nitrate yields with increasing carbon number to a plateau value of ∼0.30 at about C13-C14 is consistent with predictions of a previously developed model, indicating that the model is valid for alkane carbon numbers ≥C3.

  7. Alkyl nitrate formation from the reactions of C8-C14 n-alkanes with OH radicals in the presence of NO(x): measured yields with essential corrections for gas-wall partitioning.

    PubMed

    Yeh, Geoffrey K; Ziemann, Paul J

    2014-09-18

    In this study, C8-C14 n-alkanes were reacted with OH radicals in the presence of NO(x) in a Teflon film environmental chamber and isomer-specific yields of alkyl nitrates were determined using gas chromatography. Because results indicated significant losses of alkyl nitrates to chamber walls, gas-wall partitioning was investigated by monitoring the concentrations of a suite of synthesized alkyl nitrates added to the chamber. Gas-to-wall partitioning increased with increasing carbon number and with proximity of the nitrooxy group to the terminal carbon, with losses as high as 86%. The results were used to develop a structure-activity model to predict the effects of carbon number and isomer structure on gas-wall partitioning, which was used to correct the measured yields of alkyl nitrate isomers formed in chamber reactions. The resulting branching ratios for formation of secondary alkyl nitrates were similar for all isomers of a particular carbon number, and average values, which were almost identical to alkyl nitrate yields, were 0.219, 0.206, 0.254, 0.291, and 0.315 for reactions of n-octane, n-decane, n-dodecane, n-tridecane, and n-tetradecane, respectively. The increase in average branching ratios and alkyl nitrate yields with increasing carbon number to a plateau value of ∼0.30 at about C13-C14 is consistent with predictions of a previously developed model, indicating that the model is valid for alkane carbon numbers ≥C3. PMID:24654572

  8. Ensemble density variational methods with self- and ghost-interaction-corrected functionals

    SciTech Connect

    Pastorczak, Ewa; Pernal, Katarzyna

    2014-05-14

    Ensemble density functional theory (DFT) offers a way of predicting excited-states energies of atomic and molecular systems without referring to a density response function. Despite a significant theoretical work, practical applications of the proposed approximations have been scarce and they do not allow for a fair judgement of the potential usefulness of ensemble DFT with available functionals. In the paper, we investigate two forms of ensemble density functionals formulated within ensemble DFT framework: the Gross, Oliveira, and Kohn (GOK) functional proposed by Gross et al. [Phys. Rev. A 37, 2809 (1988)] alongside the orbital-dependent eDFT form of the functional introduced by Nagy [J. Phys. B 34, 2363 (2001)] (the acronym eDFT proposed in analogy to eHF – ensemble Hartree-Fock method). Local and semi-local ground-state density functionals are employed in both approaches. Approximate ensemble density functionals contain not only spurious self-interaction but also the so-called ghost-interaction which has no counterpart in the ground-state DFT. We propose how to correct the GOK functional for both kinds of interactions in approximations that go beyond the exact-exchange functional. Numerical applications lead to a conclusion that functionals free of the ghost-interaction by construction, i.e., eDFT, yield much more reliable results than approximate self- and ghost-interaction-corrected GOK functional. Additionally, local density functional corrected for self-interaction employed in the eDFT framework yields excitations energies of the accuracy comparable to that of the uncorrected semi-local eDFT functional.

  9. Improved methods for Feynman path integral calculations and their application to calculate converged vibrational–rotational partition functions, free energies, enthalpies, entropies, and heat capacities for methane

    SciTech Connect

    Mielke, Steven L. E-mail: truhlar@umn.edu; Truhlar, Donald G. E-mail: truhlar@umn.edu

    2015-01-28

    We present an improved version of our “path-by-path” enhanced same path extrapolation scheme for Feynman path integral (FPI) calculations that permits rapid convergence with discretization errors ranging from O(P{sup −6}) to O(P{sup −12}), where P is the number of path discretization points. We also present two extensions of our importance sampling and stratified sampling schemes for calculating vibrational–rotational partition functions by the FPI method. The first is the use of importance functions for dihedral angles between sets of generalized Jacobi coordinate vectors. The second is an extension of our stratification scheme to allow some strata to be defined based only on coordinate information while other strata are defined based on both the geometry and the energy of the centroid of the Feynman path. These enhanced methods are applied to calculate converged partition functions by FPI methods, and these results are compared to ones obtained earlier by vibrational configuration interaction (VCI) calculations, both calculations being for the Jordan–Gilbert potential energy surface. The earlier VCI calculations are found to agree well (within ∼1.5%) with the new benchmarks. The FPI partition functions presented here are estimated to be converged to within a 2σ statistical uncertainty of between 0.04% and 0.07% for the given potential energy surface for temperatures in the range 300–3000 K and are the most accurately converged partition functions for a given potential energy surface for any molecule with five or more atoms. We also tabulate free energies, enthalpies, entropies, and heat capacities.

  10. Improved methods for Feynman path integral calculations and their application to calculate converged vibrational-rotational partition functions, free energies, enthalpies, entropies, and heat capacities for methane.

    PubMed

    Mielke, Steven L; Truhlar, Donald G

    2015-01-28

    We present an improved version of our "path-by-path" enhanced same path extrapolation scheme for Feynman path integral (FPI) calculations that permits rapid convergence with discretization errors ranging from O(P(-6)) to O(P(-12)), where P is the number of path discretization points. We also present two extensions of our importance sampling and stratified sampling schemes for calculating vibrational-rotational partition functions by the FPI method. The first is the use of importance functions for dihedral angles between sets of generalized Jacobi coordinate vectors. The second is an extension of our stratification scheme to allow some strata to be defined based only on coordinate information while other strata are defined based on both the geometry and the energy of the centroid of the Feynman path. These enhanced methods are applied to calculate converged partition functions by FPI methods, and these results are compared to ones obtained earlier by vibrational configuration interaction (VCI) calculations, both calculations being for the Jordan-Gilbert potential energy surface. The earlier VCI calculations are found to agree well (within ∼1.5%) with the new benchmarks. The FPI partition functions presented here are estimated to be converged to within a 2σ statistical uncertainty of between 0.04% and 0.07% for the given potential energy surface for temperatures in the range 300-3000 K and are the most accurately converged partition functions for a given potential energy surface for any molecule with five or more atoms. We also tabulate free energies, enthalpies, entropies, and heat capacities.

  11. Improved methods for Feynman path integral calculations and their application to calculate converged vibrational-rotational partition functions, free energies, enthalpies, entropies, and heat capacities for methane.

    PubMed

    Mielke, Steven L; Truhlar, Donald G

    2015-01-28

    We present an improved version of our "path-by-path" enhanced same path extrapolation scheme for Feynman path integral (FPI) calculations that permits rapid convergence with discretization errors ranging from O(P(-6)) to O(P(-12)), where P is the number of path discretization points. We also present two extensions of our importance sampling and stratified sampling schemes for calculating vibrational-rotational partition functions by the FPI method. The first is the use of importance functions for dihedral angles between sets of generalized Jacobi coordinate vectors. The second is an extension of our stratification scheme to allow some strata to be defined based only on coordinate information while other strata are defined based on both the geometry and the energy of the centroid of the Feynman path. These enhanced methods are applied to calculate converged partition functions by FPI methods, and these results are compared to ones obtained earlier by vibrational configuration interaction (VCI) calculations, both calculations being for the Jordan-Gilbert potential energy surface. The earlier VCI calculations are found to agree well (within ∼1.5%) with the new benchmarks. The FPI partition functions presented here are estimated to be converged to within a 2σ statistical uncertainty of between 0.04% and 0.07% for the given potential energy surface for temperatures in the range 300-3000 K and are the most accurately converged partition functions for a given potential energy surface for any molecule with five or more atoms. We also tabulate free energies, enthalpies, entropies, and heat capacities. PMID:25637967

  12. Dispersion correction derived from first principles for density functional theory and Hartree-Fock theory.

    PubMed

    Guidez, Emilie B; Gordon, Mark S

    2015-03-12

    The modeling of dispersion interactions in density functional theory (DFT) is commonly performed using an energy correction that involves empirically fitted parameters for all atom pairs of the system investigated. In this study, the first-principles-derived dispersion energy from the effective fragment potential (EFP) method is implemented for the density functional theory (DFT-D(EFP)) and Hartree-Fock (HF-D(EFP)) energies. Overall, DFT-D(EFP) performs similarly to the semiempirical DFT-D corrections for the test cases investigated in this work. HF-D(EFP) tends to underestimate binding energies and overestimate intermolecular equilibrium distances, relative to coupled cluster theory, most likely due to incomplete accounting for electron correlation. Overall, this first-principles dispersion correction yields results that are in good agreement with coupled-cluster calculations at a low computational cost.

  13. Second-order corrections to the wave function at the origin in muonic hydrogen and pionium

    SciTech Connect

    Ivanov, Vladimir G.; Korzinin, Evgeny Yu.; Karshenboim, Savely G.

    2009-07-15

    Nonrelativistic second-order corrections to the wave function at the origin in muonic and exotic atoms are considered. The corrections are due to the electronic vacuum polarization. Such corrections are of interest due to various effective approaches, which take into account QED and hadronic effects. The wave function at the origin plays a key role in the calculation of the pionium lifetime, various finite nuclear size effects, and the hyperfine splitting. The results are obtained for the 1s and 2s states in pionic and muonic hydrogen and deuterium and in pionium, a bound system of {pi}{sup +} and {pi}{sup -}. Applications to the hyperfine structure and the Lamb shift in muonic hydrogen are also considered.

  14. State of some peripheral organs during laser puncture correction of ovarian functional deficiency

    NASA Astrophysics Data System (ADS)

    Vylegzhanina, T. A.; Kuznetsova, Tatiana I.; Maneeva, O.; Ryzhkovskaya, E. L.; Yemelianova, A.

    2001-01-01

    The findings from studies on structural and functional parameters of the adrenal, thyroid, and pineal glands in conditions of ovarian hypofunction and after its correction by laser puncture are presented. An experimentally induced hypofunction of the ovaries was shown to be accompanied by a decreased hormonal synthesis in the cortical fascicular zone. The epiphysis showed ultra structural signs of increased functional activity. Application of a helium-neon laser to biologically active points of the ovarian reflexogenic zone induced normalization of the ovarian cycle, potentiating of the adrenal functional state, and a decreased thyroid hormone production and abolished the activatory effect of the dark regime on the functional state of the pineal gland.

  15. A partition function-based weighting scheme in force field parameter development using ab initio calculation results in global configurational space.

    PubMed

    Wu, Yao; Dai, Xiaodong; Huang, Niu; Zhao, Lifeng

    2013-06-01

    In force field parameter development using ab initio potential energy surfaces (PES) as target data, an important but often neglected matter is the lack of a weighting scheme with optimal discrimination power to fit the target data. Here, we developed a novel partition function-based weighting scheme, which not only fits the target potential energies exponentially like the general Boltzmann weighting method, but also reduces the effect of fitting errors leading to overfitting. The van der Waals (vdW) parameters of benzene and propane were reparameterized by using the new weighting scheme to fit the high-level ab initio PESs probed by a water molecule in global configurational space. The molecular simulation results indicate that the newly derived parameters are capable of reproducing experimental properties in a broader range of temperatures, which supports the partition function-based weighting scheme. Our simulation results also suggest that structural properties are more sensitive to vdW parameters than partial atomic charge parameters in these systems although the electrostatic interactions are still important in energetic properties. As no prerequisite conditions are required, the partition function-based weighting method may be applied in developing any types of force field parameters.

  16. Implementation and benchmark of a long-range corrected functional in the density functional based tight-binding method.

    PubMed

    Lutsker, V; Aradi, B; Niehaus, T A

    2015-11-14

    Bridging the gap between first principles methods and empirical schemes, the density functional based tight-binding method (DFTB) has become a versatile tool in predictive atomistic simulations over the past years. One of the major restrictions of this method is the limitation to local or gradient corrected exchange-correlation functionals. This excludes the important class of hybrid or long-range corrected functionals, which are advantageous in thermochemistry, as well as in the computation of vibrational, photoelectron, and optical spectra. The present work provides a detailed account of the implementation of DFTB for a long-range corrected functional in generalized Kohn-Sham theory. We apply the method to a set of organic molecules and compare ionization potentials and electron affinities with the original DFTB method and higher level theory. The new scheme cures the significant overpolarization in electric fields found for local DFTB, which parallels the functional dependence in first principles density functional theory (DFT). At the same time, the computational savings with respect to full DFT calculations are not compromised as evidenced by numerical benchmark data. PMID:26567646

  17. Implementation and benchmark of a long-range corrected functional in the density functional based tight-binding method

    SciTech Connect

    Lutsker, V.; Niehaus, T. A.; Aradi, B.

    2015-11-14

    Bridging the gap between first principles methods and empirical schemes, the density functional based tight-binding method (DFTB) has become a versatile tool in predictive atomistic simulations over the past years. One of the major restrictions of this method is the limitation to local or gradient corrected exchange-correlation functionals. This excludes the important class of hybrid or long-range corrected functionals, which are advantageous in thermochemistry, as well as in the computation of vibrational, photoelectron, and optical spectra. The present work provides a detailed account of the implementation of DFTB for a long-range corrected functional in generalized Kohn-Sham theory. We apply the method to a set of organic molecules and compare ionization potentials and electron affinities with the original DFTB method and higher level theory. The new scheme cures the significant overpolarization in electric fields found for local DFTB, which parallels the functional dependence in first principles density functional theory (DFT). At the same time, the computational savings with respect to full DFT calculations are not compromised as evidenced by numerical benchmark data.

  18. Implementation and benchmark of a long-range corrected functional in the density functional based tight-binding method

    NASA Astrophysics Data System (ADS)

    Lutsker, V.; Aradi, B.; Niehaus, T. A.

    2015-11-01

    Bridging the gap between first principles methods and empirical schemes, the density functional based tight-binding method (DFTB) has become a versatile tool in predictive atomistic simulations over the past years. One of the major restrictions of this method is the limitation to local or gradient corrected exchange-correlation functionals. This excludes the important class of hybrid or long-range corrected functionals, which are advantageous in thermochemistry, as well as in the computation of vibrational, photoelectron, and optical spectra. The present work provides a detailed account of the implementation of DFTB for a long-range corrected functional in generalized Kohn-Sham theory. We apply the method to a set of organic molecules and compare ionization potentials and electron affinities with the original DFTB method and higher level theory. The new scheme cures the significant overpolarization in electric fields found for local DFTB, which parallels the functional dependence in first principles density functional theory (DFT). At the same time, the computational savings with respect to full DFT calculations are not compromised as evidenced by numerical benchmark data.

  19. Vapor Liquid Equilibria of Hydrofluorocarbons Using Dispersion-Corrected and Nonlocal Density Functionals.

    PubMed

    Goel, Himanshu; Butler, Charles L; Windom, Zachary W; Rai, Neeraj

    2016-07-12

    Recent developments in dispersion corrected and nonlocal density functionals are aimed at accurately capturing dispersion interactions, a key shortcoming of local and semilocal approximations of density functional theory. These functionals have shown significant promise for dimers and small clusters of molecules as well as crystalline materials. However, their efficacy for predicting vapor liquid equilibria is largely unexplored. In this work, we examine the accuracy of dispersion-corrected and nonlocal van der Waals functionals by computing the vapor liquid coexistence curves (VLCCs) of hydrofluoromethanes. Our results indicate that the PBE-D3 functional performs significantly better in predicting saturated liquid densities than the rVV10 functional. With the PBE-D3 functional, we also find that as the number of fluorine atoms increase in the molecule, the accuracy of saturated liquid density prediction improves as well. All the functionals significantly underpredict the saturated vapor densities, which also result in an underprediction of saturated vapor pressure of all compounds. Despite the differences in the bulk liquid densities, the local microstructures of the liquid CFH3 and CF2H2 are relatively insensitive to the density functional employed. For CF3H, however, rVV10 predicts slightly more structured liquid than the PBE-D3 functional.

  20. Vapor Liquid Equilibria of Hydrofluorocarbons Using Dispersion-Corrected and Nonlocal Density Functionals.

    PubMed

    Goel, Himanshu; Butler, Charles L; Windom, Zachary W; Rai, Neeraj

    2016-07-12

    Recent developments in dispersion corrected and nonlocal density functionals are aimed at accurately capturing dispersion interactions, a key shortcoming of local and semilocal approximations of density functional theory. These functionals have shown significant promise for dimers and small clusters of molecules as well as crystalline materials. However, their efficacy for predicting vapor liquid equilibria is largely unexplored. In this work, we examine the accuracy of dispersion-corrected and nonlocal van der Waals functionals by computing the vapor liquid coexistence curves (VLCCs) of hydrofluoromethanes. Our results indicate that the PBE-D3 functional performs significantly better in predicting saturated liquid densities than the rVV10 functional. With the PBE-D3 functional, we also find that as the number of fluorine atoms increase in the molecule, the accuracy of saturated liquid density prediction improves as well. All the functionals significantly underpredict the saturated vapor densities, which also result in an underprediction of saturated vapor pressure of all compounds. Despite the differences in the bulk liquid densities, the local microstructures of the liquid CFH3 and CF2H2 are relatively insensitive to the density functional employed. For CF3H, however, rVV10 predicts slightly more structured liquid than the PBE-D3 functional. PMID:27295451

  1. Esthetics built to last: treatment of functional anomalies may need to precede esthetic corrections.

    PubMed

    Bassett, Joyce L

    2014-02-01

    In this case of a 33 year-old male patient seeking a more esthetically pleasing smile, comprehensive restorative treatment planning included recognition of the patient's incisor position and morphology, dentofacial requirements, and appropriate vertical dimension. The accepted treatment plan consisted of orthodontic correction of the patient's anterior constriction, followed by placement of eight maxillary veneers and composite augmentation on the mandibular incisors and canines. Keys to achieving a successful outcome included knowledge of smile design, material selection, and preparation techniques. The case demonstrates how functional problems oftentimes must be addressed before esthetic correction can be made.

  2. Comparison of the spending function method and the Christmas tree correction for group sequential trials.

    PubMed

    Stallard, N; Facey, K M

    1996-07-01

    Sequential designs for continuous monitoring can be derived from the theory of a Brownian motion process. In practice, infrequent analyses lead to a discrete monitoring process. In this paper, two methods proposed to correct for discrete monitoring are compared. The methods are used to create procedures similar to both the O'Brien and Fleming test and the triangular test and are compared in terms of the error rates. For the O'Brien and Fleming test, the spending function method is found to achieve the required error rates more accurately than the Christmas tree correction, while for the triangular test, both methods perform as planned.

  3. Exploiting on-node heterogeneity for in-situ analytics of climate simulations via a functional partitioning framework

    NASA Astrophysics Data System (ADS)

    Sapra, Karan; Gupta, Saurabh; Atchley, Scott; Anantharaj, Valentine; Miller, Ross; Vazhkudai, Sudharshan

    2016-04-01

    Efficient resource utilization is critical for improved end-to-end computing and workflow of scientific applications. Heterogeneous node architectures, such as the GPU-enabled Titan supercomputer at the Oak Ridge Leadership Computing Facility (OLCF), present us with further challenges. In many HPC applications on Titan, the accelerators are the primary compute engines while the CPUs orchestrate the offloading of work onto the accelerators, and moving the output back to the main memory. On the other hand, applications that do not exploit GPUs, the CPU usage is dominant while the GPUs idle. We utilized Heterogenous Functional Partitioning (HFP) runtime framework that can optimize usage of resources on a compute node to expedite an application's end-to-end workflow. This approach is different from existing techniques for in-situ analyses in that it provides a framework for on-the-fly analysis on-node by dynamically exploiting under-utilized resources therein. We have implemented in the Community Earth System Model (CESM) a new concurrent diagnostic processing capability enabled by the HFP framework. Various single variate statistics, such as means and distributions, are computed in-situ by launching HFP tasks on the GPU via the node local HFP daemon. Since our current configuration of CESM does not use GPU resources heavily, we can move these tasks to GPU using the HFP framework. Each rank running the atmospheric model in CESM pushes the variables of of interest via HFP function calls to the HFP daemon. This node local daemon is responsible for receiving the data from main program and launching the designated analytics tasks on the GPU. We have implemented these analytics tasks in C and use OpenACC directives to enable GPU acceleration. This methodology is also advantageous while executing GPU-enabled configurations of CESM when the CPUs will be idle during portions of the runtime. In our implementation results, we demonstrate that it is more efficient to use HFP

  4. Correction of an adult Class II division 2 individual using fixed functional appliance: A noncompliance approach.

    PubMed

    Basavaraddi, Shrinivas; Gandedkar, Narayan H; Belludi, Anup; Patil, Anand

    2016-01-01

    This case report describes the application of fixed functional appliance in the treatment of an adult female having Class II division 2 malocclusion with retroclination of upper incisors. Fixed functional appliance was used to correct the overjet after the uprighting of upper incisors. Fixed functional appliance was fitted on a rigid rectangular arch wire. Application of fixed functional appliance achieved a good Class I molar relationship along with Class I canine relationship with normal overjet and overbite. Fixed functional appliance is effective in the treatment of Class II malocclusions, even in adult patients, and can serve as an alternate choice of treatment instead of orthognathic surgery. This is a case; wherein, fixed functional appliance was successfully used to relieve deep bite and overjet that was ensued after leveling and aligning. We demonstrate that fixed functional appliance can act as a "noncompliant corrector" and use of Class II elastics can be avoided.

  5. Correction of an adult Class II division 2 individual using fixed functional appliance: A noncompliance approach

    PubMed Central

    Basavaraddi, Shrinivas; Gandedkar, Narayan H.; Belludi, Anup; Patil, Anand

    2016-01-01

    This case report describes the application of fixed functional appliance in the treatment of an adult female having Class II division 2 malocclusion with retroclination of upper incisors. Fixed functional appliance was used to correct the overjet after the uprighting of upper incisors. Fixed functional appliance was fitted on a rigid rectangular arch wire. Application of fixed functional appliance achieved a good Class I molar relationship along with Class I canine relationship with normal overjet and overbite. Fixed functional appliance is effective in the treatment of Class II malocclusions, even in adult patients, and can serve as an alternate choice of treatment instead of orthognathic surgery. This is a case; wherein, fixed functional appliance was successfully used to relieve deep bite and overjet that was ensued after leveling and aligning. We demonstrate that fixed functional appliance can act as a “noncompliant corrector” and use of Class II elastics can be avoided. PMID:27041908

  6. A paper form processing system with an error correcting function for reading handwritten Kanji strings

    SciTech Connect

    Katsumi Marukawa; Kazuki Nakashima; Masashi Koga; Yoshihiro Shima; Hiromichi Fujisawa

    1994-12-31

    This paper presents a paper form processing system with an error correcting function for reading handwritten kanji strings. In the paper form processing system, names and addresses are important key data, and especially this paper takes up an error correcting method for name and address recognition. The method automatically corrects errors of the kanji OCR (Optical Character Reader) with the help of word dictionaries and other knowledge. Moreover, it allows names and addresses to be written in any style. The method consists of word matching {open_quotes}furigana{close_quotes} verification for name strings, and address approval for address strings. For word matching, kanji name candidates are extracted by automaton-type word matching. In {open_quotes}furigana{close_quotes} verification, kana candidate characters recognized by the kana OCR are compared with kana`s searched from the name dictionary based on kanji name candidates, given by the word matching. The correct name is selected from the results of word matching and furigana verification. Also, the address approval efficiently searches for the right address based on a bottom-up procedure which follows hierarchical relations from a lower placename to a upper one by using the positional condition among the placenames. We ascertained that the error correcting method substantially improves the recognition rate and processing speed in experiments on 5,032 forms.

  7. The impact of "physiological correction" on functional connectivity analysis of pharmacological resting state fMRI.

    PubMed

    Khalili-Mahani, Najmeh; Chang, Catie; van Osch, Matthias J; Veer, Ilya M; van Buchem, Mark A; Dahan, Albert; Beckmann, Christian F; van Gerven, Joop M A; Rombouts, Serge A R B

    2013-01-15

    Growing interest in pharmacological resting state fMRI (RSfMRI) necessitates developing standardized and robust analytical approaches that are insensitive to spurious correlated physiological signals. However, in pharmacological experiments physiological variations constitute an important aspect of the pharmacodynamic/pharmacokinetic profile of drug action; therefore retrospective corrective methods that discard physiological signals as noise may not be suitable. Previously, we have shown that template-based dual regression analysis is a sensitive method for model-free and objective detection of drug-specific effects on functional brain connectivity. In the current study, the robustness of this standard approach to physiological variations in a placebo controlled, repeated measures pharmacological RSfMRI study of morphine and alcohol in 12 healthy young men is tested. The impact of physiology-related variations on statistical inferences has been studied by: 1) modeling average physiological rates in higher level group analysis; 2) Regressing out the instantaneous respiration variation (RV); 3) applying retrospective image correction (RETROICOR) in the preprocessing stage; and 4) performing combined RV and heart rate correction (RVHRCOR) by regressing out physiological pulses convolved with canonical respiratory and cardiac hemodynamic response functions. Results indicate regional sensitivity of the BOLD signal to physiological variations, especially in the vicinity of large vessels, plus certain brain structures that are reported to be involved in physiological regulation, such as posterior cingulate, precuneus, medial prefrontal and insular cortices, as well as the thalamus, cerebellum and the brainstem. The largest impact of "correction" on final statistical test outcomes resulted from including the average respiration frequency and heart rate in the higher-level group analysis. Overall, the template-based dual regression method seems robust against physical

  8. Fermi orbital derivatives in self-interaction corrected density functional theory: Applications to closed shell atoms

    SciTech Connect

    Pederson, Mark R.

    2015-02-14

    A recent modification of the Perdew-Zunger self-interaction-correction to the density-functional formalism has provided a framework for explicitly restoring unitary invariance to the expression for the total energy. The formalism depends upon construction of Löwdin orthonormalized Fermi-orbitals which parametrically depend on variational quasi-classical electronic positions. Derivatives of these quasi-classical electronic positions, required for efficient minimization of the self-interaction corrected energy, are derived and tested, here, on atoms. Total energies and ionization energies in closed-shell singlet atoms, where correlation is less important, using the Perdew-Wang 1992 Local Density Approximation (PW92) functional, are in good agreement with experiment and non-relativistic quantum-Monte-Carlo results albeit slightly too low.

  9. Molecular density functional theory for water with liquid-gas coexistence and correct pressure

    SciTech Connect

    Jeanmairet, Guillaume Levesque, Maximilien; Sergiievskyi, Volodymyr; Borgis, Daniel

    2015-04-21

    The solvation of hydrophobic solutes in water is special because liquid and gas are almost at coexistence. In the common hypernetted chain approximation to integral equations, or equivalently in the homogenous reference fluid of molecular density functional theory, coexistence is not taken into account. Hydration structures and energies of nanometer-scale hydrophobic solutes are thus incorrect. In this article, we propose a bridge functional that corrects this thermodynamic inconsistency by introducing a metastable gas phase for the homogeneous solvent. We show how this can be done by a third order expansion of the functional around the bulk liquid density that imposes the right pressure and the correct second order derivatives. Although this theory is not limited to water, we apply it to study hydrophobic solvation in water at room temperature and pressure and compare the results to all-atom simulations. The solvation free energy of small molecular solutes like n-alkanes and hard sphere solutes whose radii range from angstroms to nanometers is now in quantitative agreement with reference all atom simulations. The macroscopic liquid-gas surface tension predicted by the theory is comparable to experiments. This theory gives an alternative to the empirical hard sphere bridge correction used so far by several authors.

  10. Molecular density functional theory for water with liquid-gas coexistence and correct pressure.

    PubMed

    Jeanmairet, Guillaume; Levesque, Maximilien; Sergiievskyi, Volodymyr; Borgis, Daniel

    2015-04-21

    The solvation of hydrophobic solutes in water is special because liquid and gas are almost at coexistence. In the common hypernetted chain approximation to integral equations, or equivalently in the homogenous reference fluid of molecular density functional theory, coexistence is not taken into account. Hydration structures and energies of nanometer-scale hydrophobic solutes are thus incorrect. In this article, we propose a bridge functional that corrects this thermodynamic inconsistency by introducing a metastable gas phase for the homogeneous solvent. We show how this can be done by a third order expansion of the functional around the bulk liquid density that imposes the right pressure and the correct second order derivatives. Although this theory is not limited to water, we apply it to study hydrophobic solvation in water at room temperature and pressure and compare the results to all-atom simulations. The solvation free energy of small molecular solutes like n-alkanes and hard sphere solutes whose radii range from angstroms to nanometers is now in quantitative agreement with reference all atom simulations. The macroscopic liquid-gas surface tension predicted by the theory is comparable to experiments. This theory gives an alternative to the empirical hard sphere bridge correction used so far by several authors.

  11. Vapor-liquid Coexistence Curves for Methanol and Methane using Dispersion-Corrected Density Functional Theory

    SciTech Connect

    McGrath, Matthew J.; Kuo, I-F W.; Ghogomu, Julius N.; Mundy, Christopher J.; Siepmann, Joern I.

    2011-10-13

    First principles Monte Carlo simulations in the Gibbs and isobaric-isothermal ensembles were performed to map the vapor-liquid coexistence curves (VLCC) of methanol and methane described by Kohn-Sham density functional theory using the Becke-Lee-Yang-Parr (BLYP) exchange and correlation functionals with the Grimme correction term for dispersive (D2) interactions. The simulations indicate that the BLYP-D2 description underpredicts the saturated vapor densities and overpredicts the saturated liquid densities and critical and boiling temperatures for both compounds. Although the deviations are quite large, these results present a significant improvement over the BLYP functional without the correction term which misses the experimental results by a larger extent in the opposite direction. With the D2 correction, an increase in the basis set does not lead to significant changes in the VLCC properties. This work was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

  12. Efficient on-line setup correction strategies using plan-intent functions

    SciTech Connect

    Keller, Harry; Jaffray, David A.; Rosewall, Tara; White, Elizabeth

    2006-05-15

    With the introduction of image-guided radiation therapy (IGRT) delivery systems on-line set-up correction strategies have gained in popularity. Usually, the correction workload of these strategies is high compared to off-line strategies as daily setup corrections have to be performed based on a predefined action level. In this work, it is proposed that on-line strategies must not only be judged in terms of workload but also in terms of efficacy. While workload can be easily predicted for such strategies, the efficacy must ultimately reflect the efficiency with which the original treatment plan intent is met. The purpose of this work is to investigate the tradeoff between workload and efficacy of three different on-line set-up correction strategies: The common fixed action level strategy and two novel on-line setup correction strategies, i.e., a dose-volume histogram (DVH) constraint and an equivalent uniform dose (EUD) score strategy that aim directly for better compliance with original treatment plan intent. All strategies were reformulated in terms of a score function that reflected treatment plan intent. A retrospective study was conducted on 5 prostate patients (7-field conformal, 79.8 Gy, 42 fractions). PTV margins were 10 mm except in the posterior direction (7 mm). The original treatment plan intent for these patients was defined using a set of DVH constraints. The results show that the on-line setup correction strategy based on a fixed action level of 3 mm resulted in a considerable correction workload. For larger action levels, a dose benefit (in terms of EUD) in the rectum and bladder was observed for all patients which is clinically ''fortuitous'' but difficult to take advantage of. In contrast, the application of the two novel strategies generally resulted in a controlled decrease of the dose to the rectum and the bladder with a smaller workload. It is concluded that using information about target anatomy and the planned dose distribution allows the

  13. Long-range corrected density functional theory with linearly-scaled HF exchange

    SciTech Connect

    Song, Jong-Won; Hirao, Kimihiko

    2015-12-31

    Long-range corrected density functional theory (LC-DFT) attracts many chemists’ attentions as a quantum chemical method to be applied to large molecular system and its property calculations. However, the expensive time cost to evaluate the long-range HF exchange is a big obstacle to be overcome to be applied to the large molecular systems and the solid state materials. Upon this problem, we propose a linear-scaling method of the HF exchange integration, in particular, for the LC-DFT hybrid functional.

  14. Optimization of choline administration regimen for correction of cognitive functions in rats after brain injury.

    PubMed

    Guseva, M V; Kamenskii, A A; Gusev, V B

    2013-06-01

    Choline diet promotes improvement of the brain cognitive functions in rats with moderate-to-severe traumatic brain injury. In previous studies, the rats received choline being standard (0.2%) or choline-supplemented (2%) diet for 2 weeks prior to and 2 weeks after experimental brain injury. To the end of the experiments (in 4 weeks), the post-traumatic disturbances in the cognitive functions were observed in both groups, although they were less pronounced than in the rats kept on the choline-supplemented diet. Based on original mathematical model, this paper proposes a method to calculate the most efficient use of choline to correct the brain cognitive functions. In addition to evaluating the cognitive functions, the study assessed expression of α7 nicotinic acetylcholine receptors, the amount of consumed food and water, and the dynamics of body weight.

  15. Unraveling the structure of membrane proteins in situ by transfer function corrected cryo-electron tomography.

    PubMed

    Eibauer, Matthias; Hoffmann, Christian; Plitzko, Jürgen M; Baumeister, Wolfgang; Nickell, Stephan; Engelhardt, Harald

    2012-12-01

    Cryo-electron tomography in combination with subtomogram averaging allows to investigate the structure of protein assemblies in their natural environment in a close to live state. To make full use of the structural information contained in tomograms it is necessary to analyze the contrast transfer function (CTF) of projections and to restore the phases of higher spatial frequencies. CTF correction is however hampered by the difficulty of determining the actual defocus values from tilt series data, which is due to the low signal-to-noise ratio of electron micrographs. In this study, an extended acquisition scheme is introduced that enables an independent CTF determination. Two high-dose images are recorded along the tilt axis on both sides of each projection, which allow an accurate determination of the defocus values of these images. These values are used to calculate the CTF for each image of the tilt series. We applied this scheme to the mycobacterial outer membrane protein MspA reconstituted in lipid vesicles and tested several variants of CTF estimation in combination with subtomogram averaging and correction of the modulation transfer function (MTF). The 3D electron density map of MspA was compared with a structure previously determined by X-ray crystallography. We were able to demonstrate that structural information up to a resolution of 16.8Å can be recovered using our CTF correction approach, whereas the uncorrected 3D map had a resolution of only 26.2Å.

  16. Partial volume correction using structural-functional synergistic resolution recovery: comparison with geometric transfer matrix method.

    PubMed

    Kim, Euitae; Shidahara, Miho; Tsoumpas, Charalampos; McGinnity, Colm J; Kwon, Jun Soo; Howes, Oliver D; Turkheimer, Federico E

    2013-06-01

    We validated the use of a novel image-based method for partial volume correction (PVC), structural-functional synergistic resolution recovery (SFS-RR) for the accurate quantification of dopamine synthesis capacity measured using [(18)F]DOPA positron emission tomography. The bias and reliability of SFS-RR were compared with the geometric transfer matrix (GTM) method. Both methodologies were applied to the parametric maps of [(18)F]DOPA utilization rates (ki(cer)). Validation was first performed by measuring repeatability on test-retest scans. The precision of the methodologies instead was quantified using simulated [(18)F]DOPA images. The sensitivity to the misspecification of the full-width-half-maximum (FWHM) of the scanner point-spread-function on both approaches was also assessed. In the in-vivo data, the ki(cer) was significantly increased by application of both PVC procedures while the reliability remained high (intraclass correlation coefficients >0.85). The variability was not significantly affected by either PVC approach (<10% variability in both cases). The corrected ki(cer) was significantly influenced by the FWHM applied in both the acquired and simulated data. This study shows that SFS-RR can effectively correct for partial volume effects to a comparable degree to GTM but with the added advantage that it enables voxelwise analyses, and that the FWHM used can affect the PVC result indicating the importance of accurately calibrating the FWHM used in the recovery model.

  17. Tie-dyed1 Encodes a Novel, Phloem-Expressed Transmembrane Protein That Functions in Carbohydrate Partitioning1[C][W][OA

    PubMed Central

    Ma, Yi; Slewinski, Thomas L.; Baker, R. Frank; Braun, David M.

    2009-01-01

    Carbon is partitioned between export from the leaf and retention within the leaf, and this process is essential for all aspects of plant growth and development. In most plants, sucrose is loaded into the phloem of carbon-exporting leaves (sources), transported through the veins, and unloaded into carbon-importing tissues (sinks). We have taken a genetic approach to identify genes regulating carbon partitioning in maize (Zea mays). We identified a collection of mutants, called the tie-dyed (tdy) loci, that hyperaccumulate carbohydrates in regions of their leaves. To understand the molecular function of Tdy1, we cloned the gene. Tdy1 encodes a novel transmembrane protein present only in grasses, although two protein domains are conserved across angiosperms. We found that Tdy1 is expressed exclusively in phloem cells of both source and sink tissues, suggesting that Tdy1 may play a role in phloem loading and unloading processes. In addition, Tdy1 RNA accumulates in protophloem cells upon differentiation, suggesting that Tdy1 may function as soon as phloem cells become competent to transport assimilates. Monitoring the movement of a fluorescent, soluble dye showed that tdy1 leaves have retarded phloem loading. However, once the dye entered into the phloem, solute transport appeared equal in wild-type and tdy1 mutant plants, suggesting that tdy1 plants are not defective in phloem unloading. Therefore, even though Tdy1 RNA accumulates in source and sink tissues, we propose that TDY1 functions in carbon partitioning by promoting phloem loading. Possible roles for TDY1 are discussed. PMID:18923021

  18. Long-term surgical versus functional Class II correction: a comparison of identical twins.

    PubMed

    Chhibber, Aditya; Upadhyay, Madhur; Uribe, Flavio; Nanda, Ravindra

    2015-01-01

    The purpose of this twin case comparison was to assess the short- and long-term effects of nonsurgical treatment vs orthognathic surgical treatment for Class II correction. Two identical twins (age 13 years 3 months) were treated for Class II correction where one patient was treated nonsurgically using a fixed functional appliance, while the other was treated using orthognathic mandibular advancement surgery. The patients were recalled and evaluated 5 years in retention. Comparing changes in the short and long term, surgical treatment led to superior skeletal results compared to the nonsurgical twin. However, the soft tissue profile was remarkably similar for both patients suggesting that soft tissue profile changes may not necessarily follow similar changes in the bony skeletal structures. PMID:25075777

  19. Cardiac function assessed by attenuation-corrected radionuclide pressure-volume indices

    SciTech Connect

    Maurer, A.H.; Siegel, J.A.; Blasius, K.M.; Deneberg, B.S.; Spann, J.F.; Malmud, L.S.

    1985-07-01

    Using attenuation-corrected radionuclide volumes and arm-cuff peak systolic pressures, the authors established the mean value for the ratio of left ventricular (LV) peak systolic pressure/end systolic volume at rest for 15 healthy persons. In 43 patients with coronary disease, this ratio was more sensitive as an indicator of abnormal LV function and for predicting coronary artery disease than the resting ejection fraction. The slope of an end systolic pressure-volume line was also calculated from data obtained under three loading conditions: at rest, during isometric handgrip testing, and after the sublingual administration of nitroglycerin. These results represent an improvement over previous radionuclide pressure-volume measurements that have not used attenuation correction and show the need for accurate, nongeometric measurements of the LV end systolic volume.

  20. Determinant representation of the domain-wall boundary condition partition function of a Richardson-Gaudin model containing one arbitrary spin

    NASA Astrophysics Data System (ADS)

    Faribault, Alexandre; Tschirhart, Hugo; Muller, Nicolas

    2016-05-01

    In this work we present a determinant expression for the domain-wall boundary condition partition function of rational (XXX) Richardson-Gaudin models which, in addition to N-1 spins \\frac{1}{2}, contains one arbitrarily large spin S. The proposed determinant representation is written in terms of a set of variables which, from previous work, are known to define eigenstates of the quantum integrable models belonging to this class as solutions to quadratic Bethe equations. Such a determinant can be useful numerically since systems of quadratic equations are much simpler to solve than the usual highly nonlinear Bethe equations. It can therefore offer significant gains in stability and computation speed.

  1. Motion corrected LV quantification based on 3D modelling for improved functional assessment in cardiac MRI

    NASA Astrophysics Data System (ADS)

    Liew, Y. M.; McLaughlin, R. A.; Chan, B. T.; Aziz, Y. F. Abdul; Chee, K. H.; Ung, N. M.; Tan, L. K.; Lai, K. W.; Ng, S.; Lim, E.

    2015-04-01

    Cine MRI is a clinical reference standard for the quantitative assessment of cardiac function, but reproducibility is confounded by motion artefacts. We explore the feasibility of a motion corrected 3D left ventricle (LV) quantification method, incorporating multislice image registration into the 3D model reconstruction, to improve reproducibility of 3D LV functional quantification. Multi-breath-hold short-axis and radial long-axis images were acquired from 10 patients and 10 healthy subjects. The proposed framework reduced misalignment between slices to subpixel accuracy (2.88 to 1.21 mm), and improved interstudy reproducibility for 5 important clinical functional measures, i.e. end-diastolic volume, end-systolic volume, ejection fraction, myocardial mass and 3D-sphericity index, as reflected in a reduction in the sample size required to detect statistically significant cardiac changes: a reduction of 21-66%. Our investigation on the optimum registration parameters, including both cardiac time frames and number of long-axis (LA) slices, suggested that a single time frame is adequate for motion correction whereas integrating more LA slices can improve registration and model reconstruction accuracy for improved functional quantification especially on datasets with severe motion artefacts.

  2. FUNCTIONAL AND RADIOGRAPHIC COMPARISON OF ANTERIOR AND POSTERIOR INSTRUMENTATION FOR THE CORRECTION OF ADOLESCENT IDIOPATHIC SCOLIOSIS

    PubMed Central

    Vieira, Juliano Silveira; da Silva Herrero, Carlos Fernando Pereira; Porto, Maximiliano Aguiar; Arlet, Vincent; Defino, Helton Luiz Aparecido

    2015-01-01

    Objective: This was a retrospective study to compare the anterior instrumentation (AI) and posterior instrumentation (PI) results among patients diagnosed with adolescent idiopathic scoliosis (Lenke type I) who were treated surgically. Methods: The results from 24 patients aged 11 to 18 years with Lenke type I idiopathic scoliosis who underwent surgery with AI (12 patients) or PI (12 patients) were compared. All the patients were operated by the same surgeon and were followed up for a minimum period of five years. The variables for comparison included: coronal and sagittal correction, distance from apical vertebra to midline, apical vertebral rotation, number of instrumented vertebrae and functional variables (by means of the SRS-22 questionnaire). The data obtained were analyzed using the SAS software, version 9. The two groups were compared using Student's t-test with a significance level of 5% (0.05). Results: The correction of the curve in the frontal plane was higher in the group of patients with the anterior approach, in the immediate (p=0.031) and late (p=0.043) postoperative periods, as was the apical vertebral rotation during the immediate (p=0.002) and late (p=0.019) evaluations. The number of instrumented vertebrae was 7.69 ± 1.38 in the AI group and 11.38 ± 2.92 in the PI group (p = 0.021). Functional assessment (SRS-22) did not show any significant difference (p > 0.05) between the groups. Conclusion: The patients who underwent scoliosis correction with AI presented greater correction in the frontal plane, greater derotation of apical vertebrae and a smaller number of fused vertebrae. PMID:27026964

  3. Importance of renal depth correction for quantitation of differential renal function

    SciTech Connect

    Choi, H.; Kirchner, P.T.

    1985-05-01

    To assess the frequency and magnitude of errors caused by asymmetries in renal depth, when estimates of differential function are based only posterior projections (as in DTPA studies). The authors compared ratios of right-to-left (R/L) DMSA localization derived from posterior camera images with R/L ratios based on geometric mean of posterior and anterior counts of each kidney. The factor (X) required to convert the ratio of R/L posterior counts to the more accurate R/L geometric counts (Rp/Lp.X = Rg/Lg) was determined in 55 randomly selected patients referred for DMSA studies. Frequency distributions for X and l/X reveal that the use of posterior counts alone is likely to produce differential flow/function estimates with errors greater than 30% in 5% of patients, greater than 20% in 16 of patients. Lack of depth correction also widens the normal range derived from normal controls, thus reducing sensitivity and specificity of quantitative renal studies by two different mechanisms. The authors recommend routine application of depth correction by conjugate counting or ultrasound techniques for all quantitations of renal function.

  4. Partition Theory for Periodic and Semi-Infinite Systems

    NASA Astrophysics Data System (ADS)

    Niffenegger, Kelsie; Wasserman, Adam

    Standard approximations to the exchange-correlation (XC) functional of Kohn-Sham Density-Functional Theory are insufficiently accurate to describe charge transfer at metal-atom interfaces and other systems requiring proper treatment of fractional electron charges. The root of the problem is connected to the lack of derivative discontinuities in the approximate XC functionals at integer numbers of electrons. Partition Theory (PT) is a promising, formally exact method to correct this issue. We study the simplest model for an atom adsorbed at a metal surface: A one-dimensional step potential separated a fixed distance from an attractive well that admits only one bound state when isolated. The semi-infinite metal is populated with non-interacting electrons up to the Fermi energy. We derive the PT-equations for this problem and indicate how the associated partition potential can be calculated. PT is also a promising method for improving the computational scaling of other large and/or periodic systems. We study the partition potential for periodic 1-D chains of identical attractive wells and comment on the uniqueness of the partition potential when going from finite to periodic systems.

  5. Phase correction-based singularity function analysis for partial k-space reconstruction.

    PubMed

    Luo, Jianhua; Zhu, Yuemin; Magnin, Isabelle

    2008-07-01

    Partial k-space acquisition is a conventional method in magnetic resonance imaging (MRI) for reducing imaging time while maintaining image quality. In this field, image reconstruction from partial k-space is a key issue. This paper proposes an approach fundamentally different from traditional techniques for reconstructing magnetic resonance (MR) images from partial k-space. It uses a so-called singularity function analysis (SFA) model based on phase correction. With such a reconstruction approach, some nonacquired negative spatial frequencies are first recovered by means of phase correction and Hermitian symmetry property, and then the other nonacquired negative and/or positive spatial frequencies are estimated using the mathematical SFA model. The method is particularly suitable for asymmetrical partial k-space acquisition owing to its ability of overcoming reconstruction limitations due to k-space truncations. The performance of this approach is evaluated using both simulated and real MR brain images, and compared with existing techniques. The results demonstrate that the proposed SFA based on phase correction achieves higher image quality than the initial SFA or the projection-onto-convex sets (POCS) method.

  6. Measurement and analysis of the point spread function with regard to straylight correction

    NASA Astrophysics Data System (ADS)

    Achatzi, Julian; Fischer, Gregor; Zimmer, Volker; Paulus, Dietrich; Bonnet, Gerhard

    2015-02-01

    Stray light is the part of an image that is formed by misdirected light. I.e. an ideal optic would map a point of the scene onto a point of the image. With real optics however, some parts of the light get misdirected. This is due to effects like scattering at edges, Fresnel reflections at optical surfaces, scattering at parts of the housing, scattering from dust and imperfections - on and inside of the lenses - and further reasons. These effects lead to errors in colour-measurements using spectral radiometers and other systems like scanners. Stray light is further limiting the dynamic range that can be achieved with High-Dynamic-Range-Technologies (HDR) and can lead to the rejection of cameras due to quality considerations. Therefore it is of interest, to measure, quantify and correct these effects. Our work aims at measuring the stray light point spread function (stray light PSF) of a system which is composed of a lens and an imaging sensor. In this paper we present a framework for the evaluation of PSF-models which can be used for the correction of straylight. We investigate if and how our evaluation framework can point out errors of these models and how these errors influence straylight correction.

  7. Comparison of motion correction techniques applied to functional near-infrared spectroscopy data from children.

    PubMed

    Hu, Xiao-Su; Arredondo, Maria M; Gomba, Megan; Confer, Nicole; DaSilva, Alexandre F; Johnson, Timothy D; Shalinsky, Mark; Kovelman, Ioulia

    2015-01-01

    Motion artifacts are the most significant sources of noise in the context of pediatric brain imaging designs and data analyses, especially in applications of functional near-infrared spectroscopy (fNIRS), in which it can completely affect the quality of the data acquired. Different methods have been developed to correct motion artifacts in fNIRS data, but the relative effectiveness of these methods for data from child and infant subjects (which is often found to be significantly noisier than adult data) remains largely unexplored. The issue is further complicated by the heterogeneity of fNIRS data artifacts. We compared the efficacy of the six most prevalent motion artifact correction techniques with fNIRS data acquired from children participating in a language acquisition task, including wavelet, spline interpolation, principal component analysis, moving average (MA), correlation-based signal improvement, and combination of wavelet and MA. The evaluation of five predefined metrics suggests that the MA and wavelet methods yield the best outcomes. These findings elucidate the varied nature of fNIRS data artifacts and the efficacy of artifact correction methods with pediatric populations, as well as help inform both the theory and practice of optical brain imaging analysis.

  8. Comparison of motion correction techniques applied to functional near-infrared spectroscopy data from children

    NASA Astrophysics Data System (ADS)

    Hu, Xiao-Su; Arredondo, Maria M.; Gomba, Megan; Confer, Nicole; DaSilva, Alexandre F.; Johnson, Timothy D.; Shalinsky, Mark; Kovelman, Ioulia

    2015-12-01

    Motion artifacts are the most significant sources of noise in the context of pediatric brain imaging designs and data analyses, especially in applications of functional near-infrared spectroscopy (fNIRS), in which it can completely affect the quality of the data acquired. Different methods have been developed to correct motion artifacts in fNIRS data, but the relative effectiveness of these methods for data from child and infant subjects (which is often found to be significantly noisier than adult data) remains largely unexplored. The issue is further complicated by the heterogeneity of fNIRS data artifacts. We compared the efficacy of the six most prevalent motion artifact correction techniques with fNIRS data acquired from children participating in a language acquisition task, including wavelet, spline interpolation, principal component analysis, moving average (MA), correlation-based signal improvement, and combination of wavelet and MA. The evaluation of five predefined metrics suggests that the MA and wavelet methods yield the best outcomes. These findings elucidate the varied nature of fNIRS data artifacts and the efficacy of artifact correction methods with pediatric populations, as well as help inform both the theory and practice of optical brain imaging analysis.

  9. Adsorption of imidazole on Au(111) surface: Dispersion corrected density functional study

    NASA Astrophysics Data System (ADS)

    Izzaouihda, Safia; Mahjoubi, Khaled; Abou El Makarim, Hassna; Komiha, Najia; Benoit, David M.

    2016-10-01

    We use density functional theory in the generalized gradient approximation to study the adsorption of imidazole on the Au(111) surface and account for dispersion effect using Grimme's empirical dispersion correction technique. Our results show that the adsorption energy of imidazole depends on the slab size and on the adsorption site. In agreement with other studies, we find the largest adsorption energy for imidazole on a top site of Au(111). However, we also note that the adsorption energy at other sites is substantial.

  10. Convergent conductivity corrections to the Casimir force via exponential basis functions

    SciTech Connect

    Cui, Song; Soh, Yeng Chai

    2010-12-15

    A closed-form finite conductivity correction factor for the ideal Casimir force is proposed, based on exponential basis functions. Our method can facilitate experimental verifications of theories in the study of the Casimir force. A theoretical analysis is given to explain why our method is accurate at both large and small separation gaps. Numerical computations have been performed to confirm that our method is accurate in various experimental configurations. Our approach is widely applicable to various Casimir force interactions between metals and dielectrics. Our study can be extended to the study of the repulsive Casimir force as well.

  11. Bidirectional scattering distribution function measurements from volume diffusers: correction factors and associated uncertainties.

    PubMed

    Germer, Thomas A

    2016-09-01

    We consider the effect of volume diffusion on measurements of the bidirectional scattering distribution function when a finite distance is used for the solid angle defining aperture. We derive expressions for correction factors that can be used when the reduced scattering coefficients and the index of refraction are known. When these quantities are not known, the expressions can be used to guide the assessment of measurement uncertainty. We find that some measurement geometries reduce the effect of volume diffusion compared to their reciprocal geometries. PMID:27607273

  12. [Music-Acoustic Signals Controlled by Subject's Brain Potentials in the Correction of Unfavorable Functional States].

    PubMed

    Fedotchev, A I; Bondar, A T; Bakhchina, A V; Parin, S B; Polevaya, S A; Radchenko, G S

    2016-01-01

    Literature review and the results of own studies on the development and experimental testing of musical EEG neurofeedback technology are presented. The technology is based on exposure of subjects to music or music-like signals that are organized in strict accordance with the current values of brain potentials of the patient. The main attention is paid to the analysis of the effectiveness of several versions of the technology, using specific and meaningful for the individual narrow-frequency EEG oscillators during the correction of unfavorable changes of the functional state. PMID:27149824

  13. Line-ratio based ring artifact correction method using transfer function

    NASA Astrophysics Data System (ADS)

    Oh, Daejoong; Hwang, Dosik; Kim, Younguk

    2016-03-01

    Computed tomography (CT) has been used for medical purposes. However there are many artifacts at CT images and that makes distorted image. Ring artifact is caused by non-uniform sensitivity of detectors and makes ring shape artifact. Line-ratio method was proposed to solve the problem however there are some problem at specific case. Therefore we propose advanced method to correct ring artifact using transfer function. As a result, ring artifacts can be removed at more global cases. Simulation data shows the proposed method outperforms the conventional line-ratio method.

  14. [Music-Acoustic Signals Controlled by Subject's Brain Potentials in the Correction of Unfavorable Functional States].

    PubMed

    Fedotchev, A I; Bondar, A T; Bakhchina, A V; Parin, S B; Polevaya, S A; Radchenko, G S

    2016-01-01

    Literature review and the results of own studies on the development and experimental testing of musical EEG neurofeedback technology are presented. The technology is based on exposure of subjects to music or music-like signals that are organized in strict accordance with the current values of brain potentials of the patient. The main attention is paid to the analysis of the effectiveness of several versions of the technology, using specific and meaningful for the individual narrow-frequency EEG oscillators during the correction of unfavorable changes of the functional state.

  15. A New Spinel-Olivine Oxybarometer: Near-Liquidus Partitioning of V between Olivine-Melt, Spinel-Melt, and Spinel-Olivine in Martian Basalt Composition Y980459 as a Function of Oxygen Fugacity

    NASA Technical Reports Server (NTRS)

    Papike, J. J.; Le, L.; Burger, P. V.; Shearer, C. K.; Bell, A. S.; Jones, J.

    2013-01-01

    Our research on valence state partitioning began in 2005 with a review of Cr, Fe, Ti, and V partitioning among crystallographic sites in olivine, pyroxene, and spinel [1]. That paper was followed by several on QUE94201 melt composition and specifically on Cr, V, and Eu partitioning between pyroxene and melt [2-5]. This paper represents the continuation of our examination of the partitioning of multivalent V between olivine, spinel, and melt in martian olivine-phyric basalts of Y980459 composition [6, 7]. Here we introduce a new, potentially powerful oxybarometer, V partitioning between spinel and olivine, which can be used when no melt is preserved in the meteorite. The bulk composition of QUE94201 was ideal for our study of martian pyroxene-phyric basalts and specifically the partitioning between pyroxene-melt for Cr, V, and Eu. Likewise, bulk composition Y980459 is ideal for the study of martian olivine-phyric basalts and specifically for olivine-melt, spinel-melt, and spinel-olivine partitioning of V as a function of oxygen fugacity.

  16. Robust and automated solution for correcting hotspots locally using cost-function based OPC solver

    NASA Astrophysics Data System (ADS)

    Babcock, Carl; Yang, Dongok; McGowan, Sarah; Ye, Jun; Yan, Bo; Qiu, Jianhong; Baron, Stanislas; Pandey, Taksh; Kapasi, Sanjay; Aquino, Chris

    2014-03-01

    In previous work1, we introduced a new technology called Flexible Mask Optimization (FMO) that was successfully used for localized OPC correction. OPC/RET techniques such as model-based assist feature and process-window-based OPC solvers have become essential for addressing critical patterning issues at 2× and lower technology nodes. With an FMO flow, critical patterns were identified, classified and corrected in localized areas only, using advanced techniques. One challenge with this flow is that once the hotspots are identified, a user still has to come up with OPC solutions to address the hotspots. This process can be cumbersome and time consuming as different types of hotspots with new designs may require different recipes, causing delays to tapeout. What is required is a robust, powerful and automated OPC technique that can handle various types of hotspots, so an automatic hotspot correction flow can be established. In this work, we introduce a new cost-function-based OPC technique called Co-optimization OPC that can be used to correct various types of hotspots with minimum tuning effort. In this approach, the OPC solver simultaneously solves for all the segments in a patch including main and sub-resolution assist features (SRAF), applying additional user-defined cost function constraints such as MEEF, PV band, MRC and SRAF printability. Unlike conventional OPC solvers, Cooptimization solvers can also move and grow SRAFs, which further improves the process window. The key benefit of the Co-optimization OPC solution is that it can be used in a standard recipe to resolve many different hotspots encountered across various designs for a given layer. In this study, we demonstrate that Co-optimization OPC can be successfully used to address various types of hotspots across designs for selected 2× nm node line/space layers, as an example. These layers have been particularly challenging as they use single-exposure lithography with k1 around 0.3. Aggressive RET

  17. Ionic partitioning and stomatal regulation: dissecting functional elements of the genotypic basis of salt stress adaptation in grafted melon.

    PubMed

    Sanoubar, Rabab; Orsini, Francesco; Gianquinto, Giorgio

    2013-11-01

    Vegetable grafting is commonly claimed to improve crop's tolerance to biotic and abiotic stresses, including salinity. Although the use of inter-specific graftings is relatively common, whether the improved salt tolerance should be attributed to the genotypic background rather than the grafting per se is a matter of discussion among scientists. It is clear that most of published research has to date overlooked the issue, with the mutual presence of self-grafted and non-grafted controls resulting to be quite rare within experimental evidences. It was recently demonstrated that the genotype of the rootstock and grafting per se are responsible respectively for the differential ion accumulation and partitioning as well as to the stomatal adaptation to the stress. The present paper contributes to the ongoing discussion with further data on the differences associated to salinity response in a range of grafted melon combinations.

  18. Self-Interaction Corrected Density Functional Approximations with Unitary Invariance: Applications to Molecules

    NASA Astrophysics Data System (ADS)

    Pederson, Mark

    For a system of 2N electrons, the Fermi-hole may be interpreted as the square of a normalized ''Fermi orbital'', F (a) ≡ρσ (a , r) /√{ρσ (a) } . This normalized orbital captures all of the spin density at its position of definition, or descriptor, (a) . Given a set of N quasi-classical electronic positions (ai) and a spin density-matrix composed of N Kohn-Sham orbitals, the resulting set of Fermi orbitals may then be used to construct a set of localized Loewdin-orthonormalized orbitals. These orbitals are explicitly a functional of the spin density and are related to the Kohn-Sham orbitals by a unitary transformation that is parametrically dependent on the set quasi-classical electronic descriptors. The construction of such localized orbitals allows for the restoration of unitary invariance into the original Perdew-Zunger self-interaction correction and provides a possible simplification compared to the localization-equation based solution of self-interaction corrected functionals. This talk will discuss the construction of this Fermi-orbital-based self-interaction corrected method and the minimization algorithm that relies upon analytical derivatives of the self-interaction energy with respect to the Fermi-orbital descriptors. Recent applications to a large set of molecules including aromatic molecules, molecules with open transition-metal centers, and molecules with frustrated Kekule' structures will be discussed. Initial applications indicate improvements in atomization energies of pi-bonded systems and demonstrate the desired downward shift of orbital energies relative to their Kohn-Sham counterparts.

  19. Experimental determination of Pb partitioning between sulfide melt and basalt melt as a function of P, T and X

    NASA Astrophysics Data System (ADS)

    Hart, Stanley R.; Gaetani, Glenn A.

    2016-07-01

    We have measured the partition coefficient of Pb (KdPb) between FeS melt and basalt melt at temperatures of 1250-1523 °C, pressures of 1.0-3.5 GPa and oxygen fugacities at iron-wustite and wustite-magnetite. The total observed range of KdPb is 4.0-66.6, with a strong negative dependence on pressure and a strong negative dependence on FeO of the silicate melt (Fe+2 only). The FeO control was constrained over a wide range of FeO (4.2-39.5%). We found that the effect of oxygen fugacity can be subsumed under the FeO control parameter. Prior work has established the lack of a significant effect of temperature (Kiseeva and Wood, 2015; Li and Audétat, 2015). Our data are parameterized as: KdPb = 4.8 + (512 - 119*P in GPa)*(1/FeO - 0.021). We also measured a single value of KdPb between clinopyroxene and basalt melt at 2.0 GPa of 0.020 ± 0.001. This experimental data supports the "natural" partitioning of Pb measured on sulfide globules in MORB (Patten et al., 2013), but not the low KdPb of ∼3 inferred from sulfides in abyssal peridotites by Warren and Shirey (2012). It also quantitatively affirms the modeling of Hart and Gaetani (2006) with respect to using sulfide to buffer the canonical Nd/Pb ratio for MORB and OIB (Hofmann, 2003). For the low FeO and pressure of segregation typical of MORB, KdPb ∼ 45, and the Nd/Pb ratio of erupted basalts will be the same as the Nd/Pb ratio of the mantle source. The remaining puzzle is why MORB and OIB have the same Nd/Pb when they clearly have different FeO and pressure of melt segregation.

  20. Using the electron localization function to correct for confinement physics in semi-local density functional theory

    SciTech Connect

    Hao, Feng Mattsson, Ann E.; Armiento, Rickard

    2014-05-14

    We have previously proposed that further improved functionals for density functional theory can be constructed based on the Armiento-Mattsson subsystem functional scheme if, in addition to the uniform electron gas and surface models used in the Armiento-Mattsson 2005 functional, a model for the strongly confined electron gas is also added. However, of central importance for this scheme is an index that identifies regions in space where the correction provided by the confined electron gas should be applied. The electron localization function (ELF) is a well-known indicator of strongly localized electrons. We use a model of a confined electron gas based on the harmonic oscillator to show that regions with high ELF directly coincide with regions where common exchange energy functionals have large errors. This suggests that the harmonic oscillator model together with an index based on the ELF provides the crucial ingredients for future improved semi-local functionals. For a practical illustration of how the proposed scheme is intended to work for a physical system we discuss monoclinic cupric oxide, CuO. A thorough discussion of this system leads us to promote the cell geometry of CuO as a useful benchmark for future semi-local functionals. Very high ELF values are found in a shell around the O ions, and take its maximum value along the Cu–O directions. An estimate of the exchange functional error from the effect of electron confinement in these regions suggests a magnitude and sign that could account for the error in cell geometry.

  1. Kinetic corrections from analytic non-Maxwellian distribution functions in magnetized plasmas

    NASA Astrophysics Data System (ADS)

    Izacard, Olivier

    2016-08-01

    In magnetized plasma physics, almost all developed analytic theories assume a Maxwellian distribution function (MDF) and in some cases small deviations are described using the perturbation theory. The deviations with respect to the Maxwellian equilibrium, called kinetic effects, are required to be taken into account especially for fusion reactor plasmas. Generally, because the perturbation theory is not consistent with observed steady-state non-Maxwellians, these kinetic effects are numerically evaluated by very central processing unit (CPU)-expensive codes, avoiding the analytic complexity of velocity phase space integrals. We develop here a new method based on analytic non-Maxwellian distribution functions constructed from non-orthogonal basis sets in order to (i) use as few parameters as possible, (ii) increase the efficiency to model numerical and experimental non-Maxwellians, (iii) help to understand unsolved problems such as diagnostics discrepancies from the physical interpretation of the parameters, and (iv) obtain analytic corrections due to kinetic effects given by a small number of terms and removing the numerical error of the evaluation of velocity phase space integrals. This work does not attempt to derive new physical effects even if it could be possible to discover one from the better understandings of some unsolved problems, but here we focus on the analytic prediction of kinetic corrections from analytic non-Maxwellians. As applications, examples of analytic kinetic corrections are shown for the secondary electron emission, the Langmuir probe characteristic curve, and the entropy. This is done by using three analytic representations of the distribution function: the Kappa distribution function, the bi-modal or a new interpreted non-Maxwellian distribution function (INMDF). The existence of INMDFs is proved by new understandings of the experimental discrepancy of the measured electron temperature between two diagnostics in JET. As main results, it

  2. Kinetic corrections from analytic non-Maxwellian distribution functions in magnetized plasmas

    DOE PAGES

    Izacard, Olivier

    2016-08-02

    In magnetized plasma physics, almost all developed analytic theories assume a Maxwellian distribution function (MDF) and in some cases small deviations are described using the perturbation theory. The deviations with respect to the Maxwellian equilibrium, called kinetic effects, are required to be taken into account especially for fusion reactor plasmas. Generally, because the perturbation theory is not consistent with observed steady-state non-Maxwellians, these kinetic effects are numerically evaluated by very central processing unit (CPU)-expensive codes, avoiding the analytic complexity of velocity phase space integrals. We develop here a new method based on analytic non-Maxwellian distribution functions constructed from non-orthogonal basismore » sets in order to (i) use as few parameters as possible, (ii) increase the efficiency to model numerical and experimental non-Maxwellians, (iii) help to understand unsolved problems such as diagnostics discrepancies from the physical interpretation of the parameters, and (iv) obtain analytic corrections due to kinetic effects given by a small number of terms and removing the numerical error of the evaluation of velocity phase space integrals. This work does not attempt to derive new physical effects even if it could be possible to discover one from the better understandings of some unsolved problems, but here we focus on the analytic prediction of kinetic corrections from analytic non-Maxwellians. As applications, examples of analytic kinetic corrections are shown for the secondary electron emission, the Langmuir probe characteristic curve, and the entropy. This is done by using three analytic representations of the distribution function: the Kappa distribution function, the bi-modal or a new interpreted non-Maxwellian distribution function (INMDF). The existence of INMDFs is proved by new understandings of the experimental discrepancy of the measured electron temperature between two diagnostics in JET. As main

  3. Ensemble density functional theory method correctly describes bond dissociation, excited state electron transfer, and double excitations

    SciTech Connect

    Filatov, Michael; Huix-Rotllant, Miquel; Burghardt, Irene

    2015-05-14

    State-averaged (SA) variants of the spin-restricted ensemble-referenced Kohn-Sham (REKS) method, SA-REKS and state-interaction (SI)-SA-REKS, implement ensemble density functional theory for variationally obtaining excitation energies of molecular systems. In this work, the currently existing version of the SA-REKS method, which included only one excited state into the ensemble averaging, is extended by adding more excited states to the averaged energy functional. A general strategy for extension of the REKS-type methods to larger ensembles of ground and excited states is outlined and implemented in extended versions of the SA-REKS and SI-SA-REKS methods. The newly developed methods are tested in the calculation of several excited states of ground-state multi-reference systems, such as dissociating hydrogen molecule, and excited states of donor–acceptor molecular systems. For hydrogen molecule, the new method correctly reproduces the distance dependence of the lowest excited state energies and describes an avoided crossing between the doubly excited and singly excited states. For bithiophene–perylenediimide stacked complex, the SI-SA-REKS method correctly describes crossing between the locally excited state and the charge transfer excited state and yields vertical excitation energies in good agreement with the ab initio wavefunction methods.

  4. Ensemble density functional theory method correctly describes bond dissociation, excited state electron transfer, and double excitations.

    PubMed

    Filatov, Michael; Huix-Rotllant, Miquel; Burghardt, Irene

    2015-05-14

    State-averaged (SA) variants of the spin-restricted ensemble-referenced Kohn-Sham (REKS) method, SA-REKS and state-interaction (SI)-SA-REKS, implement ensemble density functional theory for variationally obtaining excitation energies of molecular systems. In this work, the currently existing version of the SA-REKS method, which included only one excited state into the ensemble averaging, is extended by adding more excited states to the averaged energy functional. A general strategy for extension of the REKS-type methods to larger ensembles of ground and excited states is outlined and implemented in extended versions of the SA-REKS and SI-SA-REKS methods. The newly developed methods are tested in the calculation of several excited states of ground-state multi-reference systems, such as dissociating hydrogen molecule, and excited states of donor-acceptor molecular systems. For hydrogen molecule, the new method correctly reproduces the distance dependence of the lowest excited state energies and describes an avoided crossing between the doubly excited and singly excited states. For bithiophene-perylenediimide stacked complex, the SI-SA-REKS method correctly describes crossing between the locally excited state and the charge transfer excited state and yields vertical excitation energies in good agreement with the ab initio wavefunction methods.

  5. Vibrational and Thermal Properties of β-HMX and TATB from Dispersion Corrected Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Landerville, Aaron; Oleynik, Ivan

    2015-06-01

    Dispersion Corrected Density Functional Theory (DFT+vdW) calculations are performed to predict vibrational and thermal properties of the bulk energetic materials (EMs) β-octahydrocyclotetramethylene-tetranitramine (β-HMX) and triaminotrinitrobenzene (TATB). DFT+vdW calculations of optimized unit cells along the hydrostatic equation of state are followed by frozen-phonon calculations of their respective vibration spectra. These are then used under the quasi-harmonic approximation to obtain zero-point and thermal free energy contributions to the pressure, resulting in PVT equations of state for each material that is in excellent agreement with experiment. Further, heat capacities, thermal expansion coefficients, and Gruneissen parameters as functions of temperature are calculated and compared with experiment. The vibrational properties, including phonon densities of states and pressure dependencies of individual modes, are also analyzed and compared with experiment.

  6. Young Children's Partitioning Strategies.

    ERIC Educational Resources Information Center

    Charles, Kathy; Nason, Rod

    2000-01-01

    Studies knowledge of young children's partitioning strategies by setting out not only to identify new partitioning strategies, but also to develop taxonomy for classifying young children's partitioning strategies in terms of their abilities. Provides taxonomy utilizing children's informal partitioning strategies as the foundation upon which to…

  7. Combining MRI with PET for partial volume correction improves image-derived input functions in mice

    PubMed Central

    Evans, Eleanor; Buonincontri, Guido; Izquierdo, David; Methner, Carmen; Hawkes, Rob C.; Ansorge, Richard E.; Krieg, Thomas; Carpenter, T. Adrian; Sawiak, Stephen J.

    2015-01-01

    Accurate kinetic modelling using dynamic PET requires knowledge of the tracer concentration in plasma, known as the arterial input function (AIF). AIFs are usually determined by invasive blood sampling, but this is prohibitive in murine studies due to low total blood volumes. As a result of the low spatial resolution of PET, image-derived input functions (IDIFs) must be extracted from left ventricular blood pool (LVBP) ROIs of the mouse heart. This is challenging because of partial volume and spillover effects between the LVBP and myocardium, contaminating IDIFs with tissue signal. We have applied the geometric transfer matrix (GTM) method of partial volume correction (PVC) to 12 mice injected with 18F-FDG affected by a Myocardial Infarction (MI), of which 6 were treated with a drug which reduced infarction size [1]. We utilised high resolution MRI to assist in segmenting mouse hearts into 5 classes: LVBP, infarcted myocardium, healthy myocardium, lungs/body and background. The signal contribution from these 5 classes was convolved with the point spread function (PSF) of the Cambridge split magnet PET scanner and a non-linear fit was performed on the 5 measured signal components. The corrected IDIF was taken as the fitted LVBP component. It was found that the GTM PVC method could recover an IDIF with less contamination from spillover than an IDIF extracted from PET data alone. More realistic values of Ki were achieved using GTM IDIFs, which were shown to be significantly different (p<0.05) between the treated and untreated groups. PMID:26213413

  8. Hartree approximation to the one loop quantum gravitational correction to the graviton mode function on de Sitter

    SciTech Connect

    Mora, P.J.; Woodard, R.P.; Tsamis, N.C. E-mail: tsamis@physics.uoc.gr

    2013-10-01

    We use the Hartree approximation to the Einstein equation on de Sitter background to solve for the one loop correction to the graviton mode function. This should give a reasonable approximation to how the ensemble of inflationary gravitons affects a single external graviton. At late times we find that the one loop correction to the plane wave mode function u(η,k) goes like GH{sup 2}ln (a)/a{sup 2}, where a is the inflationary scale factor. One consequence is that the one loop corrections to the ''electric'' components of the linearized Weyl tensor grow compared to the tree order result.

  9. Theoretical study of the adsorption of aromatic units on carbon allotropes including explicit (empirical) DFT dispersion corrections and implicitly dispersion-corrected functionals: the pyridine case.

    PubMed

    Ramos-Berdullas, Nicolás; Pérez-Juste, Ignacio; Van Alsenoy, Christian; Mandado, Marcos

    2015-01-01

    The suitability of implicitly dispersion-corrected functionals, namely the M06-2X, for the determination of interaction energies and electron polarization densities in adsorption studies of aromatic molecules on carbon allotropes surfaces is analysed by comparing the results with those obtained using explicit dispersion through Grimme's empirical corrections. Several models of increasing size for the graphene sheet together with one-dimensional curved carbon structures, (5,5), (6,6) and (7,7) armchair single-walled nanotubes, and two-dimensional curved carbon structures, C60 fullerene, have been considered as substrates in this work, whereas pyridine has been chosen as an example for the adsorbed aromatic molecule. Comparison with recent experimental estimations of the adsorption energy and calculations using periodic boundary conditions on a supercell of 72 carbon atoms indicates that a finite model containing ninety six carbon atoms (C96) approaches quite well the adsorption on a graphene sheet. Analysis of the interaction energy components reveals that the M06-2X functional accounts for most of the dispersion energy implicitly, followed far by wB97X and B3LYP, whereas B97 and BLYP do not differ too much from HF. It has been found that M06-2X corrects only the energy component associated to dispersion and leaves the rest, electrostatic, Pauli and induction "unaltered" with respect to the other DFT functionals investigated. Moreover, only the M06-2X functional reflects the effect of dispersion on the electron polarization density, whereas for the remaining functionals the polarization density does not differ too much from the HF density. This makes the former functional more suitable a priori for the calculation of electron density related properties in these adsorption complexes.

  10. Understanding molecular crystals with dispersion-inclusive density functional theory: pairwise corrections and beyond.

    PubMed

    Kronik, Leeor; Tkatchenko, Alexandre

    2014-11-18

    CONSPECTUS: Molecular crystals are ubiquitous in many areas of science and engineering, including biology and medicine. Until recently, our ability to understand and predict their structure and properties using density functional theory was severely limited by the lack of approximate exchange-correlation functionals able to achieve sufficient accuracy. Here we show that there are many cases where the simple, minimally empirical pairwise correction scheme of Tkatchenko and Scheffler provides a useful prediction of the structure and properties of molecular crystals. After a brief introduction of the approach, we demonstrate its strength through some examples taken from our recent work. First, we show the accuracy of the approach using benchmark data sets of molecular complexes. Then we show its efficacy for structural determination using the hemozoin crystal, a challenging system possessing a wide range of strong and weak binding scenarios. Next, we show that it is equally useful for response properties by considering the elastic constants exhibited by the supramolecular diphenylalanine peptide solid and the infrared signature of water libration movements in brushite. Throughout, we emphasize lessons learned not only for the methodology but also for the chemistry and physics of the crystals in question. We further show that in many other scenarios where the simple pairwise correction scheme is not sufficiently accurate, one can go beyond it by employing a computationally inexpensive many-body dispersive approach that results in useful, quantitative accuracy, even in the presence of significant screening and/or multibody contributions to the dispersive energy. We explain the principles of the many-body approach and demonstrate its accuracy for benchmark data sets of small and large molecular complexes and molecular solids. PMID:24901508

  11. Study of polycyclic aromatic hydrocarbons adsorbed on graphene using density functional theory with empirical dispersion correction.

    PubMed

    Ershova, Olga V; Lillestolen, Timothy C; Bichoutskaia, Elena

    2010-06-28

    The interaction of polycyclic aromatic hydrocarbon molecules with hydrogen-terminated graphene is studied using density functional theory with empirical dispersion correction. The effective potential energy surfaces for the interaction of benzene, C(6)H(6), naphthalene, C(10)H(8), coronene, C(24)H(12), and ovalene, C(32)H(14), with hydrogen-terminated graphene are calculated as functions of the molecular displacement along the substrate. The potential energy surfaces are also described analytically using the lowest harmonics of the Fourier expansion. It is shown that inclusion of the dispersive interaction, which is the most important contribution to the binding of these weakly bound systems, does not change the shape of the interaction energy surfaces or the value of the barriers to the motion of polycyclic aromatic hydrocarbon molecules on graphene. The potential energy surfaces are used in the estimation of the friction forces acting on the molecules along the direction of motion. These results underpin the modelling, using density functional theory, of electromechanical devices based on the relative vibrations of graphene layers and telescoping carbon nanotubes.

  12. Self-interaction corrected density functional calculations of molecular Rydberg states

    SciTech Connect

    Gudmundsdóttir, Hildur; Zhang, Yao; Weber, Peter M.; Jónsson, Hannes

    2013-11-21

    A method is presented for calculating the wave function and energy of Rydberg excited states of molecules. A good estimate of the Rydberg state orbital is obtained using ground state density functional theory including Perdew-Zunger self-interaction correction and an optimized effective potential. The total energy of the excited molecule is obtained using the Delta Self-Consistent Field method where an electron is removed from the highest occupied orbital and placed in the Rydberg orbital. Results are presented for the first few Rydberg states of NH{sub 3}, H{sub 2}O, H{sub 2}CO, C{sub 2}H{sub 4}, and N(CH{sub 3}){sub 3}. The mean absolute error in the energy of the 33 molecular Rydberg states presented here is 0.18 eV. The orbitals are represented on a real space grid, avoiding the dependence on diffuse atomic basis sets. As in standard density functional theory calculations, the computational effort scales as NM{sup 2} where N is the number of orbitals and M is the number of grid points included in the calculation. Due to the slow scaling of the computational effort with system size and the high level of parallelism in the real space grid approach, the method presented here makes it possible to estimate Rydberg electron binding energy in large molecules.

  13. Enhanced Li capacity in functionalized graphene: A first principle study with van der Waals correction

    NASA Astrophysics Data System (ADS)

    Chouhan, Rajiv K.; Raghani, Pushpa

    2015-09-01

    We have investigated the adsorption of Li on graphene oxide using density functional theory. We show a novel and simple approach to achieve a positive lithiation potential on epoxy and hydroxyl functionalized graphene, compared to the negative lithiation potential that has been found on prestine graphene. We included the van der Waals correction into the calculation so as to get a better picture of weak interactions. A positive lithiation potential suggests a favorable adsorption of Li on graphene oxide sheets that can lead to an increase in the specific capacity, which in turn can be used as an anode material in Li-batteries. We find a high specific capacity of ˜860 mAhg-1 by functionalizing the graphene sheet. This capacity is higher than the previously reported capacities that were achieved on graphene with high concentration of Stone-Wales (75%) and divacancy (16%) defects. Creating such high density of defects can make the entire system energetically unstable, whereas graphene oxide is a naturally occurring substance.

  14. Exact low-temperature series expansion for the partition function of the zero-field Ising model on the infinite square lattice

    PubMed Central

    Siudem, Grzegorz; Fronczak, Agata; Fronczak, Piotr

    2016-01-01

    In this paper, we provide the exact expression for the coefficients in the low-temperature series expansion of the partition function of the two-dimensional Ising model on the infinite square lattice. This is equivalent to exact determination of the number of spin configurations at a given energy. With these coefficients, we show that the ferromagnetic–to–paramagnetic phase transition in the square lattice Ising model can be explained through equivalence between the model and the perfect gas of energy clusters model, in which the passage through the critical point is related to the complete change in the thermodynamic preferences on the size of clusters. The combinatorial approach reported in this article is very general and can be easily applied to other lattice models. PMID:27721435

  15. Exact low-temperature series expansion for the partition function of the zero-field Ising model on the infinite square lattice

    NASA Astrophysics Data System (ADS)

    Siudem, Grzegorz; Fronczak, Agata; Fronczak, Piotr

    2016-10-01

    In this paper, we provide the exact expression for the coefficients in the low-temperature series expansion of the partition function of the two-dimensional Ising model on the infinite square lattice. This is equivalent to exact determination of the number of spin configurations at a given energy. With these coefficients, we show that the ferromagnetic–to–paramagnetic phase transition in the square lattice Ising model can be explained through equivalence between the model and the perfect gas of energy clusters model, in which the passage through the critical point is related to the complete change in the thermodynamic preferences on the size of clusters. The combinatorial approach reported in this article is very general and can be easily applied to other lattice models.

  16. Ribosomal Stalk Protein Silencing Partially Corrects the ΔF508-CFTR Functional Expression Defect

    PubMed Central

    Veit, Guido; Oliver, Kathryn; Apaja, Pirjo M.; Perdomo, Doranda; Bidaud-Meynard, Aurélien; Guo, Jingyu; Icyuz, Mert; Sorscher, Eric J.; Hartman, John L.; Lukacs, Gergely L.

    2016-01-01

    The most common cystic fibrosis (CF) causing mutation, deletion of phenylalanine 508 (ΔF508 or Phe508del), results in functional expression defect of the CF transmembrane conductance regulator (CFTR) at the apical plasma membrane (PM) of secretory epithelia, which is attributed to the degradation of the misfolded channel at the endoplasmic reticulum (ER). Deletion of phenylalanine 670 (ΔF670) in the yeast oligomycin resistance 1 gene (YOR1, an ABC transporter) of Saccharomyces cerevisiae phenocopies the ΔF508-CFTR folding and trafficking defects. Genome-wide phenotypic (phenomic) analysis of the Yor1-ΔF670 biogenesis identified several modifier genes of mRNA processing and translation, which conferred oligomycin resistance to yeast. Silencing of orthologues of these candidate genes enhanced the ΔF508-CFTR functional expression at the apical PM in human CF bronchial epithelia. Although knockdown of RPL12, a component of the ribosomal stalk, attenuated the translational elongation rate, it increased the folding efficiency as well as the conformational stability of the ΔF508-CFTR, manifesting in 3-fold augmented PM density and function of the mutant. Combination of RPL12 knockdown with the corrector drug, VX-809 (lumacaftor) restored the mutant function to ~50% of the wild-type channel in primary CFTRΔF508/ΔF508 human bronchial epithelia. These results and the observation that silencing of other ribosomal stalk proteins partially rescue the loss-of-function phenotype of ΔF508-CFTR suggest that the ribosomal stalk modulates the folding efficiency of the mutant and is a potential therapeutic target for correction of the ΔF508-CFTR folding defect. PMID:27168400

  17. Ribosomal Stalk Protein Silencing Partially Corrects the ΔF508-CFTR Functional Expression Defect.

    PubMed

    Veit, Guido; Oliver, Kathryn; Apaja, Pirjo M; Perdomo, Doranda; Bidaud-Meynard, Aurélien; Lin, Sheng-Ting; Guo, Jingyu; Icyuz, Mert; Sorscher, Eric J; Hartman Iv, John L; Lukacs, Gergely L

    2016-05-01

    The most common cystic fibrosis (CF) causing mutation, deletion of phenylalanine 508 (ΔF508 or Phe508del), results in functional expression defect of the CF transmembrane conductance regulator (CFTR) at the apical plasma membrane (PM) of secretory epithelia, which is attributed to the degradation of the misfolded channel at the endoplasmic reticulum (ER). Deletion of phenylalanine 670 (ΔF670) in the yeast oligomycin resistance 1 gene (YOR1, an ABC transporter) of Saccharomyces cerevisiae phenocopies the ΔF508-CFTR folding and trafficking defects. Genome-wide phenotypic (phenomic) analysis of the Yor1-ΔF670 biogenesis identified several modifier genes of mRNA processing and translation, which conferred oligomycin resistance to yeast. Silencing of orthologues of these candidate genes enhanced the ΔF508-CFTR functional expression at the apical PM in human CF bronchial epithelia. Although knockdown of RPL12, a component of the ribosomal stalk, attenuated the translational elongation rate, it increased the folding efficiency as well as the conformational stability of the ΔF508-CFTR, manifesting in 3-fold augmented PM density and function of the mutant. Combination of RPL12 knockdown with the corrector drug, VX-809 (lumacaftor) restored the mutant function to ~50% of the wild-type channel in primary CFTRΔF508/ΔF508 human bronchial epithelia. These results and the observation that silencing of other ribosomal stalk proteins partially rescue the loss-of-function phenotype of ΔF508-CFTR suggest that the ribosomal stalk modulates the folding efficiency of the mutant and is a potential therapeutic target for correction of the ΔF508-CFTR folding defect.

  18. Ribosomal Stalk Protein Silencing Partially Corrects the ΔF508-CFTR Functional Expression Defect.

    PubMed

    Veit, Guido; Oliver, Kathryn; Apaja, Pirjo M; Perdomo, Doranda; Bidaud-Meynard, Aurélien; Lin, Sheng-Ting; Guo, Jingyu; Icyuz, Mert; Sorscher, Eric J; Hartman Iv, John L; Lukacs, Gergely L

    2016-05-01

    The most common cystic fibrosis (CF) causing mutation, deletion of phenylalanine 508 (ΔF508 or Phe508del), results in functional expression defect of the CF transmembrane conductance regulator (CFTR) at the apical plasma membrane (PM) of secretory epithelia, which is attributed to the degradation of the misfolded channel at the endoplasmic reticulum (ER). Deletion of phenylalanine 670 (ΔF670) in the yeast oligomycin resistance 1 gene (YOR1, an ABC transporter) of Saccharomyces cerevisiae phenocopies the ΔF508-CFTR folding and trafficking defects. Genome-wide phenotypic (phenomic) analysis of the Yor1-ΔF670 biogenesis identified several modifier genes of mRNA processing and translation, which conferred oligomycin resistance to yeast. Silencing of orthologues of these candidate genes enhanced the ΔF508-CFTR functional expression at the apical PM in human CF bronchial epithelia. Although knockdown of RPL12, a component of the ribosomal stalk, attenuated the translational elongation rate, it increased the folding efficiency as well as the conformational stability of the ΔF508-CFTR, manifesting in 3-fold augmented PM density and function of the mutant. Combination of RPL12 knockdown with the corrector drug, VX-809 (lumacaftor) restored the mutant function to ~50% of the wild-type channel in primary CFTRΔF508/ΔF508 human bronchial epithelia. These results and the observation that silencing of other ribosomal stalk proteins partially rescue the loss-of-function phenotype of ΔF508-CFTR suggest that the ribosomal stalk modulates the folding efficiency of the mutant and is a potential therapeutic target for correction of the ΔF508-CFTR folding defect. PMID:27168400

  19. An empirical method to correct for temperature-dependent variations in the overlap function of CHM15k ceilometers

    NASA Astrophysics Data System (ADS)

    Hervo, Maxime; Poltera, Yann; Haefele, Alexander

    2016-07-01

    Imperfections in a lidar's overlap function lead to artefacts in the background, range and overlap-corrected lidar signals. These artefacts can erroneously be interpreted as an aerosol gradient or, in extreme cases, as a cloud base leading to false cloud detection. A correct specification of the overlap function is hence crucial in the use of automatic elastic lidars (ceilometers) for the detection of the planetary boundary layer or of low cloud. In this study, an algorithm is presented to correct such artefacts. It is based on the assumption of a homogeneous boundary layer and a correct specification of the overlap function down to a minimum range, which must be situated within the boundary layer. The strength of the algorithm lies in a sophisticated quality-check scheme which allows the reliable identification of favourable atmospheric conditions. The algorithm was applied to 2 years of data from a CHM15k ceilometer from the company Lufft. Backscatter signals corrected for background, range and overlap were compared using the overlap function provided by the manufacturer and the one corrected with the presented algorithm. Differences between corrected and uncorrected signals reached up to 45 % in the first 300 m above ground. The amplitude of the correction turned out to be temperature dependent and was larger for higher temperatures. A linear model of the correction as a function of the instrument's internal temperature was derived from the experimental data. Case studies and a statistical analysis of the strongest gradient derived from corrected signals reveal that the temperature model is capable of a high-quality correction of overlap artefacts, in particular those due to diurnal variations. The presented correction method has the potential to significantly improve the detection of the boundary layer with gradient-based methods because it removes false candidates and hence simplifies the attribution of the detected gradients to the planetary boundary layer. A

  20. Finite ɛ2-corrections to the N = 2 SYM prepotential

    NASA Astrophysics Data System (ADS)

    Bourgine, Jean-Emile; Fioravanti, Davide

    2015-11-01

    We derive the first ɛ2-correction of the instanton partition functions in 4D N = 2 Super Yang-Mills (SYM) to the Nekrasov-Shatashvili limit ɛ2 → 0. In the latter we recall the emergence of the famous Thermodynamic Bethe Ansatz-like equation which has been found by Mayer expansion techniques. Here we combine efficiently these to field theory arguments. In a nutshell, we find natural and resolutive the introduction of a new operator ∇ that distinguishes the singularities within and outside the integration contour of the partition function.

  1. 30 CFR 1227.500 - What functions may a State perform to ensure that reporters correct erroneous report data?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... you request delegation of error correction functions for production reports or royalty reports, or... 30 Mineral Resources 3 2011-07-01 2011-07-01 false What functions may a State perform to ensure... SURFACE MINING RECLAMATION AND ENFORCEMENT, DEPARTMENT OF THE INTERIOR Natural Resources...

  2. On the logarithmic-singularity correction in the kernel function method of subsonic lifting-surface theory

    NASA Technical Reports Server (NTRS)

    Lan, C. E.; Lamar, J. E.

    1977-01-01

    A logarithmic-singularity correction factor is derived for use in kernel function methods associated with Multhopp's subsonic lifting-surface theory. Because of the form of the factor, a relation was formulated between the numbers of chordwise and spanwise control points needed for good accuracy. This formulation is developed and discussed. Numerical results are given to show the improvement of the computation with the new correction factor.

  3. Quantum principles and free particles. [evaluation of partitions

    NASA Technical Reports Server (NTRS)

    1976-01-01

    The quantum principles that establish the energy levels and degeneracies needed to evaluate the partition functions are explored. The uncertainty principle is associated with the dual wave-particle nature of the model used to describe quantized gas particles. The Schroedinger wave equation is presented as a generalization of Maxwell's wave equation; the former applies to all particles while the Maxwell equation applies to the special case of photon particles. The size of the quantum cell in phase space and the representation of momentum as a space derivative operator follow from the uncertainty principle. A consequence of this is that steady-state problems that are space-time dependent for the classical model become only space dependent for the quantum model and are often easier to solve. The partition function is derived for quantized free particles and, at normal conditions, the result is the same as that given by the classical phase integral. The quantum corrections that occur at very low temperatures or high densities are derived. These corrections for the Einstein-Bose gas qualitatively describe the condensation effects that occur in liquid helium, but are unimportant for most practical purposes otherwise. However, the corrections for the Fermi-Dirac gas are important because they quantitatively describe the behavior of high-density conduction electron gases in metals and explain the zero point energy and low specific heat exhibited in this case.

  4. Gait phase detection from sciatic nerve recordings in functional electrical stimulation systems for foot drop correction.

    PubMed

    Chu, Jun-Uk; Song, Kang-Il; Han, Sungmin; Lee, Soo Hyun; Kang, Ji Yoon; Hwang, Dosik; Suh, Jun-Kyo Francis; Choi, Kuiwon; Youn, Inchan

    2013-05-01

    Cutaneous afferent activities recorded by a nerve cuff electrode have been used to detect the stance phase in a functional electrical stimulation system for foot drop correction. However, the implantation procedure was difficult, as the cuff electrode had to be located on the distal branches of a multi-fascicular nerve to exclude muscle afferent and efferent activities. This paper proposes a new gait phase detection scheme that can be applied to a proximal nerve root that includes cutaneous afferent fibers as well as muscle afferent and efferent fibers. To test the feasibility of this scheme, electroneurogram (ENG) signals were measured from the rat sciatic nerve during treadmill walking at several speeds, and the signal properties of the sciatic nerve were analyzed for a comparison with kinematic data from the ankle joint. On the basis of these experiments, a wavelet packet transform was tested to define a feature vector from the sciatic ENG signals according to the gait phases. We also propose a Gaussian mixture model (GMM) classifier and investigate whether it could be used successfully to discriminate feature vectors into the stance and swing phases. In spite of no significant differences in the rectified bin-integrated values between the stance and swing phases, the sciatic ENG signals could be reliably classified using the proposed wavelet packet transform and GMM classification methods.

  5. Assembling a Correctly Folded and Functional Heptahelical Membrane Protein by Protein Trans-splicing.

    PubMed

    Mehler, Michaela; Eckert, Carl Elias; Busche, Alena; Kulhei, Jennifer; Michaelis, Jonas; Becker-Baldus, Johanna; Wachtveitl, Josef; Dötsch, Volker; Glaubitz, Clemens

    2015-11-13

    Protein trans-splicing using split inteins is well established as a useful tool for protein engineering. Here we show, for the first time, that this method can be applied to a membrane protein under native conditions. We provide compelling evidence that the heptahelical proteorhodopsin can be assembled from two separate fragments consisting of helical bundles A and B and C, D, E, F, and G via a splicing site located in the BC loop. The procedure presented here is on the basis of dual expression and ligation in vivo. Global fold, stability, and photodynamics were analyzed in detergent by CD, stationary, as well as time-resolved optical spectroscopy. The fold within lipid bilayers has been probed by high field and dynamic nuclear polarization-enhanced solid-state NMR utilizing a (13)C-labeled retinal cofactor and extensively (13)C-(15)N-labeled protein. Our data show unambiguously that the ligation product is identical to its non-ligated counterpart. Furthermore, our data highlight the effects of BC loop modifications onto the photocycle kinetics of proteorhodopsin. Our data demonstrate that a correctly folded and functionally intact protein can be produced in this artificial way. Our findings are of high relevance for a general understanding of the assembly of membrane proteins for elucidating intramolecular interactions, and they offer the possibility of developing novel labeling schemes for spectroscopic applications.

  6. Functional analysis and in vitro correction of splicing FAH mutations causing tyrosinemia type I.

    PubMed

    Pérez-Carro, R; Sánchez-Alcudia, R; Pérez, B; Navarrete, R; Pérez-Cerdá, C; Ugarte, M; Desviat, L R

    2014-08-01

    Hereditary tyrosinemia type I (HT1) is a rare disease caused by a deficiency of fumarylacetoacetate hydrolase (FAH) in the tyrosine catabolic pathway, resulting mainly in hepatic alterations due to accumulation of the toxic metabolites fumarylacetoacetate, maleylacetoacetate and succinylacetone. We have characterized using minigenes four splicing mutations affecting exonic or intronic nucleotides of the FAH gene identified in two HT1 patients. Two of the mutations are novel, c.82-1G>A and c.913G>C and the other two have been previously associated with a splicing defect (c.836A>G and c.1062+5G>A). All mutations were confirmed to affect splicing in minigenes, resulting in exon skipping or activation of a cryptic splice site. We have analyzed the effect of different compounds known to modulate splicing (valproic acid, phenyl butyrate, M344, EIPA, and resveratrol) and the overexpression of splice factors of the SR protein family on the transcriptional profile of the mutant minigenes. For the c.836A>G mutation, a partial recovery of the correctly spliced transcript was observed. These results confirm the relevance of performing functional studies for mutations potentially affecting the splicing process and open the possibility of supplementary therapeutic approaches to diseases caused by splicing defects.

  7. Correction for collimator-detector response in SPECT using point spread function template.

    PubMed

    Chun, Se Young; Fessler, Jeffrey A; Dewaraja, Yuni K

    2013-02-01

    Compensating for the collimator-detector response (CDR) in SPECT is important for accurate quantification. The CDR consists of both a geometric response and a septal penetration and collimator scatter response. The geometric response can be modeled analytically and is often used for modeling the whole CDR if the geometric response dominates. However, for radionuclides that emit medium or high-energy photons such as I-131, the septal penetration and collimator scatter response is significant and its modeling in the CDR correction is important for accurate quantification. There are two main methods for modeling the depth-dependent CDR so as to include both the geometric response and the septal penetration and collimator scatter response. One is to fit a Gaussian plus exponential function that is rotationally invariant to the measured point source response at several source-detector distances. However, a rotationally-invariant exponential function cannot represent the star-shaped septal penetration tails in detail. Another is to perform Monte-Carlo (MC) simulations to generate the depth-dependent point spread functions (PSFs) for all necessary distances. However, MC simulations, which require careful modeling of the SPECT detector components, can be challenging and accurate results may not be available for all of the different SPECT scanners in clinics. In this paper, we propose an alternative approach to CDR modeling. We use a Gaussian function plus a 2-D B-spline PSF template and fit the model to measurements of an I-131 point source at several distances. The proposed PSF-template-based approach is nearly non-parametric, captures the characteristics of the septal penetration tails, and minimizes the difference between the fitted and measured CDR at the distances of interest. The new model is applied to I-131 SPECT reconstructions of experimental phantom measurements, a patient study, and a MC patient simulation study employing the XCAT phantom. The proposed model

  8. Accurate description of van der Waals complexes by density functional theory including empirical corrections.

    PubMed

    Grimme, Stefan

    2004-09-01

    An empirical method to account for van der Waals interactions in practical calculations with the density functional theory (termed DFT-D) is tested for a wide variety of molecular complexes. As in previous schemes, the dispersive energy is described by damped interatomic potentials of the form C6R(-6). The use of pure, gradient-corrected density functionals (BLYP and PBE), together with the resolution-of-the-identity (RI) approximation for the Coulomb operator, allows very efficient computations for large systems. Opposed to previous work, extended AO basis sets of polarized TZV or QZV quality are employed, which reduces the basis set superposition error to a negligible extend. By using a global scaling factor for the atomic C6 coefficients, the functional dependence of the results could be strongly reduced. The "double counting" of correlation effects for strongly bound complexes is found to be insignificant if steep damping functions are employed. The method is applied to a total of 29 complexes of atoms and small molecules (Ne, CH4, NH3, H2O, CH3F, N2, F2, formic acid, ethene, and ethine) with each other and with benzene, to benzene, naphthalene, pyrene, and coronene dimers, the naphthalene trimer, coronene. H2O and four H-bonded and stacked DNA base pairs (AT and GC). In almost all cases, very good agreement with reliable theoretical or experimental results for binding energies and intermolecular distances is obtained. For stacked aromatic systems and the important base pairs, the DFT-D-BLYP model seems to be even superior to standard MP2 treatments that systematically overbind. The good results obtained suggest the approach as a practical tool to describe the properties of many important van der Waals systems in chemistry. Furthermore, the DFT-D data may either be used to calibrate much simpler (e.g., force-field) potentials or the optimized structures can be used as input for more accurate ab initio calculations of the interaction energies.

  9. 2d-4d connection between q-Virasoro/W block at root of unity limit and instanton partition function on ALE space

    NASA Astrophysics Data System (ADS)

    Itoyama, H.; Oota, T.; Yoshioka, R.

    2013-12-01

    We propose and demonstrate a limiting procedure in which, starting from the q-lifted version (or K-theoretic five-dimensional version) of the (W)AGT conjecture to be assumed in this paper, the Virasoro/W block is generated in the r-th root of unity limit in q in the 2d side, while the same limit automatically generates the projection of the five-dimensional instanton partition function onto that on the ALE space R4/Zr. This circumvents case-by-case conjectures to be made in a wealth of examples found so far. In the 2d side, we successfully generate the super-Virasoro algebra and the proper screening charge in the q→-1, t→-1 limit, from the defining relation of the q-Virasoro algebra and the q-deformed Heisenberg algebra. The central charge obtained coincides with that of the minimal series carrying odd integers of the N=1 superconformal algebra. In the r-th root of unity limit in q in the 2d side, we give some evidence of the appearance of the parafermion-like currents. Exploiting the q-analysis literatures, q-deformed su(n) block is readily generated both at generic q,t and the r-th root of unity limit. In the 4d side, we derive the proper normalization function for general (n,r) that accomplishes the automatic projection through the limit.

  10. Diel and Seasonal Behavior of Canopy Photosynthesis Revealed by Novel Isotopic Flux Partitioning in a Temperate Forest

    NASA Astrophysics Data System (ADS)

    Wehr, R. A.; Munger, J. W.; McManus, J. B.; Nelson, D. D.; Zahniser, M. S.; Saleska, S. R.

    2013-12-01

    Conventional methods for partitioning the net ecosystem-atmosphere exchange (NEE) of CO2 into gross primary production (GPP) and ecosystem respiration (R) work by extrapolating GPP or R using an empirical function fit to a week or a month of data. Accordingly, these methods do not allow investigation of short-term (e.g. diel) deviations of GPP or R from their monthly average behaviors. Moreover, these methods assume that daytime R is either constant or a smoothly varying function of temperature. Isotopic partitioning is an alternative that involves no assumptions about the behavior of R or GPP (though it requires knowledge or assumptions about the isotopic fractionations occurring in and around the leaves) and which allows for the investigation of diel variations because each flux measurement is partitioned separately. A novel isotopic flux partitioning approach using our unique long-term isotopic CO2 eddy flux record at the Harvard Forest reveals significant differences in both the diel and the seasonally averaged behavior of GPP as compared to conventional partitioning. At the diel timescale, large (~10 μmol m-2 s-1), rapid (~2 hours) variations in the respiratory component of measured NEE associated with subtle changes in wind direction (due to the breakdown of the basic EC assumption of horizontal landscape homogeneity) are misattributed to GPP by conventional partitioning, leading to inconsistency in the response of GPP to photosynthetically active radiation (PAR). Isotopically partitioned GPP responds much more consistently to PAR, and the seasonally averaged light response curve of isotopically partitioned GPP is much more linear than that of conventionally partitioned GPP (after controlling for the leaf-air water vapor gradient), suggesting that unsaturated (steeply inclined) leaves perform most of the canopy photosynthesis (Figure 1). The behavior of isotopically partitioned GPP follows largely from the observed behavior of the canopy-integrated stomatal

  11. Prediction of d^0 magnetism in self-interaction corrected density functional theory

    NASA Astrophysics Data System (ADS)

    Das Pemmaraju, Chaitanya

    2010-03-01

    Over the past couple of years, the phenomenon of ``d^0 magnetism'' has greatly intrigued the magnetism community [1]. Unlike conventional magnetic materials, ``d^0 magnets'' lack any magnetic ions with open d or f shells but surprisingly, exhibit signatures of ferromagnetism often with a Curie temperature exceeding 300 K. Current research in the field is geared towards trying to understand the mechanism underlying this observed ferromagnetism which is difficult to explain within the conventional m-J paradigm [1]. The most widely studied class of d^0 materials are un-doped and light element doped wide gap Oxides such as HfO2, MgO, ZnO, TiO2 all of which have been put forward as possible d0 ferromagnets. General experimental trends suggest that the magnetism is a feature of highly defective samples leading to the expectation that the phenomenon must be defect related. In particular, based on density functional theory (DFT) calculations acceptor defects formed from the O-2p states in these Oxides have been proposed as being responsible for the ferromagnetism [2,3]. However. predicting magnetism originating from 2p orbitals is a delicate problem, which depends on the subtle interplay between covalency and Hund's coupling. DFT calculations based on semi-local functionals such as the local spin-density approximation (LSDA) can lead to qualitative failures on several fronts. On one hand the excessive delocalization of spin-polarized holes leads to half-metallic ground states and the expectation of room-temperature ferromagnetism. On the other hand, in some cases a magnetic ground state may not be predicted at all as the Hund's coupling might be under estimated. Furthermore, polaronic distortions which are often a feature of acceptor defects in Oxides are not predicted [4,5]. In this presentation, we argue that the self interaction error (SIE) inherent to semi-local functionals is responsible for the failures of LSDA and demonstrate through various examples that beyond

  12. Fast Computation of Solvation Free Energies with Molecular Density Functional Theory: Thermodynamic-Ensemble Partial Molar Volume Corrections.

    PubMed

    Sergiievskyi, Volodymyr P; Jeanmairet, Guillaume; Levesque, Maximilien; Borgis, Daniel

    2014-06-01

    Molecular density functional theory (MDFT) offers an efficient implicit-solvent method to estimate molecule solvation free-energies, whereas conserving a fully molecular representation of the solvent. Even within a second-order approximation for the free-energy functional, the so-called homogeneous reference fluid approximation, we show that the hydration free-energies computed for a data set of 500 organic compounds are of similar quality as those obtained from molecular dynamics free-energy perturbation simulations, with a computer cost reduced by 2-3 orders of magnitude. This requires to introduce the proper partial volume correction to transform the results from the grand canonical to the isobaric-isotherm ensemble that is pertinent to experiments. We show that this correction can be extended to 3D-RISM calculations, giving a sound theoretical justification to empirical partial molar volume corrections that have been proposed recently.

  13. Motion artifacts in functional near-infrared spectroscopy: a comparison of motion correction techniques applied to real cognitive data.

    PubMed

    Brigadoi, Sabrina; Ceccherini, Lisa; Cutini, Simone; Scarpa, Fabio; Scatturin, Pietro; Selb, Juliette; Gagnon, Louis; Boas, David A; Cooper, Robert J

    2014-01-15

    Motion artifacts are a significant source of noise in many functional near-infrared spectroscopy (fNIRS) experiments. Despite this, there is no well-established method for their removal. Instead, functional trials of fNIRS data containing a motion artifact are often rejected completely. However, in most experimental circumstances the number of trials is limited, and multiple motion artifacts are common, particularly in challenging populations. Many methods have been proposed recently to correct for motion artifacts, including principle component analysis, spline interpolation, Kalman filtering, wavelet filtering and correlation-based signal improvement. The performance of different techniques has been often compared in simulations, but only rarely has it been assessed on real functional data. Here, we compare the performance of these motion correction techniques on real functional data acquired during a cognitive task, which required the participant to speak aloud, leading to a low-frequency, low-amplitude motion artifact that is correlated with the hemodynamic response. To compare the efficacy of these methods, objective metrics related to the physiology of the hemodynamic response have been derived. Our results show that it is always better to correct for motion artifacts than reject trials, and that wavelet filtering is the most effective approach to correcting this type of artifact, reducing the area under the curve where the artifact is present in 93% of the cases. Our results therefore support previous studies that have shown wavelet filtering to be the most promising and powerful technique for the correction of motion artifacts in fNIRS data. The analyses performed here can serve as a guide for others to objectively test the impact of different motion correction algorithms and therefore select the most appropriate for the analysis of their own fNIRS experiment.

  14. Niche partitioning of feeding microhabitats produces a unique function for herbivorous rabbitfishes (Perciformes, Siganidae) on coral reefs

    NASA Astrophysics Data System (ADS)

    Fox, R. J.; Bellwood, D. R.

    2013-03-01

    Niche theory predicts that coexisting species minimise competition by evolving morphological or behavioural specialisations that allow them to spread out along resource axes such as space, diet and temporal activity. These specialisations define how a species interacts with its environment and, by extension, determine its functional role. Here, we examine the feeding niche of three species of coral reef-dwelling rabbitfishes (Siganidae, Siganus). By comparing aspects of their feeding behaviour (bite location, bite rate, foraging distance) with that of representative species from two other abundant herbivorous fish families, the parrotfishes (Labridae, Scarus) and surgeonfishes (Acanthuridae, Acanthurus), we examine whether rabbitfishes have a feeding niche distinct from other members of the herbivore guild. Measurements of the penetration of the fishes' snouts and bodies into reef concavities when feeding revealed that rabbitfish fed to a greater degree from reef crevices and interstices than other herbivores. There was just a 40 % overlap in the penetration-depth niche between rabbitfish and surgeonfish and a 45 % overlap between rabbitfish and parrotfish, compared with the almost complete niche overlap (95 %) recorded for parrotfish and surgeonfish along this spatial niche axis. Aspects of the morphology of rabbitfish which may contribute to this niche segregation include a comparatively longer, narrower snout and narrower head. Our results suggest that sympatric coexistence of rabbitfish and other reef herbivores is facilitated by segregation along a spatial (and potentially dietary) axis. This segregation results in a unique functional role for rabbitfishes among roving herbivores that of "crevice-browser": a group that specifically feeds on crevice-dwelling algal or benthic organisms. This functional trait may have implications for reef ecosystem processes in terms of controlling the successional development of crevice-based algal communities, reducing their

  15. Correction of Correlation Errors in Greenland Ice Mass Variations from GRACE using Empirical Orthogonal Function

    NASA Astrophysics Data System (ADS)

    Eom, J.; Seo, K. W.

    2015-12-01

    Since its launch in March 2002, the Gravity Recovery And Climate Experiment (GRACE) has provided monthly geopotential fields represented by Stokes coefficients of spherical harmonics (SH). Nominally, GRACE gravity solutions exclude effects from tides, ocean dynamics and barometric pressure by incorporating geophysical models for them. However, those models are imperfect, and thus GRACE solutions include the residual gravity effects. Particularly, unmodeled gravity variations of sub-monthly or shorter time scale cause aliasing error, which produces peculiar longitudinal stripes. Those north-south patterns are removed by spatial filtering, but caution is necessary for the aliasing correction because signals with longitudinal patterns are possibly removed during the procedure. This would be particularly problematic for studies associated with Greenland ice mass balance since large ice mass variations are expected in the West and South-West coast of Greenland that are elongated along the longitudinal direction. In this study, we develop a novel method to remove the correlation error using extended Empirical Orthogonal Function (extended EOF). The extended EOF is useful to separate spatially and temporally coherent signal from high frequency variations. Since temporal variability of the correlation error is high, the error is possibly removed via the extended EOF. Ice mass variations reduced by the extended EOF show more detail patterns of ice mass loss/gain than those from the conventional spatial filtering. Large amount of ice loss has occurred along the West, South-West and East coastal area during summer. The extended EOF is potentially useful to enhance signal to noise ratio and increase spatial resolution of GRACE data.

  16. Disruption of cytokeratin-8 interaction with F508del-CFTR corrects its functional defect

    PubMed Central

    Colas, Julien; Faure, Grazyna; Saussereau, Emilie; Trudel, Stéphanie; Rabeh, Wael M.; Bitam, Sara; Guerrera, Ida Chiara; Fritsch, Janine; Sermet-Gaudelus, Isabelle; Davezac, Noëlie; Brouillard, Franck; Lukacs, Gergely L.; Herrmann, Harald; Ollero, Mario; Edelman, Aleksander

    2012-01-01

    We have previously reported an increased expression of cytokeratins 8/18 (K8/K18) in cells expressing the F508del mutation of cystic fibrosis transmembrane conductance regulator (CFTR). This is associated with increased colocalization of CFTR and K18 in the vicinity of the endoplasmic reticulum, although this is reversed by treating cells with curcumin, resulting in the rescue of F508del-CFTR. In the present work, we hypothesized that (i) the K8/K18 network may interact physically with CFTR, and that (ii) this interaction may modify CFTR function. CFTR was immunoprecipitated from HeLa cells transfected with either wild-type (WT) CFTR or F508del-CFTR. Precipitates were subjected to 2D-gel electrophoresis and differential spots identified by mass spectrometry. K8 and K18 were found significantly increased in F508del-CFTR precipitates. Using surface plasmon resonance, we demonstrate that K8, but not K18, binds directly and preferentially to the F508del over the WT human NBD1 (nucleotide-binding domain-1). In vivo K8 interaction with F508del-CFTR was confirmed by proximity ligation assay in HeLa cells and in primary cultures of human respiratory epithelial cells. Ablation of K8 expression by siRNA in F508del-expressing HeLa cells led to the recovery of CFTR-dependent iodide efflux. Moreover, F508del-expressing mice topically treated with K8-siRNA showed restored nasal potential difference, equivalent to that of WT mice. These results show that disruption of F508del-CFTR and K8 interaction leads to the correction of the F508del-CFTR processing defect, suggesting a novel potential therapeutic target in CF. PMID:22038833

  17. 30 CFR 227.500 - What functions may a State perform to ensure that reporters correct erroneous report data?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 2 2010-07-01 2010-07-01 false What functions may a State perform to ensure that reporters correct erroneous report data? 227.500 Section 227.500 Mineral Resources MINERALS MANAGEMENT SERVICE, DEPARTMENT OF THE INTERIOR MINERALS REVENUE MANAGEMENT DELEGATION TO STATES...

  18. Assessing the Performances of Dispersion-Corrected Density Functional Methods for Predicting the Crystallographic Properties of High Nitrogen Energetic Salts.

    PubMed

    Sorescu, Dan C; Byrd, Edward F C; Rice, Betsy M; Jordan, Kenneth D

    2014-11-11

    Several density functional methods with corrections for long-range dispersion interactions are evaluated for their capabilities to describe the crystallographic lattice properties of a set of 26 high nitrogen-content salts relevant for energetic materials applications. Computations were done using methods that ranged from adding atom-atom dispersion corrections with environment-independent and environment-dependent coefficients, to methods that incorporate dispersion effects via dispersion-corrected atom-centered potentials (DCACP), to methods that include nonlocal corrections. Among the functionals tested, the most successful is the nonlocal optPBE-vdW functional of Klimeš and Michaelides that predicts unit cell volumes for all crystals of the reference set within the target error range of ±3% and gives individual lattice parameters with a mean average percent error of less than 0.81%. The DCACP, Grimme's D3, and Becke and Johnson's exchange-hole (XDM) methods, when used with the BLYP, PBE, and B86b functionals, respectively, are also quite successful at predicting the lattice parameters of the test set. PMID:26584381

  19. The role of delocalization error in non-covalent interactions from dispersion-corrected density-functional theory

    NASA Astrophysics Data System (ADS)

    Otero de La Roza, Alberto

    2015-03-01

    Extensive benchmarking of dispersion-corrected density functional theory (dcDFT) methods has shown that it is nowadays feasible to calculate, with great accuracy, binding energies of small dimers and lattice energies of molecular crystals. However, there are many outstanding questions that can only be answered by a proper understanding of the interplay between base functional and dispersion correction. In this talk, I explore how delocalization error from the exchange-correlation functional impacts the calculation of non-covalent donor-acceptor interactions. Delocalization error arises from the failure of most functionals to model the long-range behavior of the exchange-correlation hole. Its primary consequence for non-covalent interactions is that the stability of donor-acceptor interactions is overestimated. Errors caused by delocalization error are particularly harmful in systems with strong and extensive hydrogen-bonded networks (water clusters and ice) or strong donor-acceptor interactions (halogen bonding), and can not be corrected using a pairwise dispersion correction. In addition, I present how delocalization error affects real-life applications of dcDFT, such as molecular adsorption on iron-oxide nanoparticles and surfaces.

  20. Accuracy of fuzzy burned area mapping as a function of the aerosol parameterization of atmospheric correction

    NASA Astrophysics Data System (ADS)

    Azar, Ramin; Stroppiana, Daniela; Bresciani, Mariano; Giardino, Claudia; Boschetti, Mirco; Brivio, Pietro A.

    2013-10-01

    Mediterranean forests are every year affected by wildfires which have a significant effect on the ecosystem. Mapping burned areas is an important field of application for optical remote sensing techniques and several methodologies have been developed in order to improve mapping accuracy. We developed an automated procedure based on spectral indices and fuzzy theory for mapping burned areas from atmospherically corrected Landsat TM images. The algorithm proved to provide consistent accuracy over Mediterranean areas. We further tested algorithm's performance to assess the influence of the atmospheric correction on the accuracy of burned areas. In particular, we ran the Second Simulation of a Satellite Signal in the Solar Spectrum (6S) code with different Atmospheric Optical Thickness (AOT) levels and two aerosol models (continental and maritime) on one TM image acquired over Portugal (12/08/2003). Burned area maps derived from atmospherically corrected images and from the non corrected image (Top Of Atmosphere, TOA) have been analyzed. In the output burned areas maps the omission error varies in the range 4.6-6.5% and the commission error fluctuates between 11.9 and 22.2%; the highest omission (commission) errors occur with the continental (maritime) model. The accuracy of burned area maps derived from non corrected image is very low, with omission error greater than 90%. These results show that, although atmospheric correction is needed for the application of the algorithm, the AOT value does not significantly affect the performance.

  1. Partitioning the impact of environment and spatial structure on alpha and beta components of taxonomic, functional, and phylogenetic diversity in European ants

    PubMed Central

    Cerdá, Xim; Retana, Javier

    2015-01-01

    We analyze the relative contribution of environmental and spatial variables to the alpha and beta components of taxonomic (TD), phylogenetic (PD), and functional (FD) diversity in ant communities found along different climate and anthropogenic disturbance gradients across western and central Europe, in order to assess the mechanisms structuring ant biodiversity. To this aim we calculated alpha and beta TD, PD, and FD for 349 ant communities, which included a total of 155 ant species; we examined 10 functional traits and phylogenetic relatedness. Variation partitioning was used to examine how much variation in ant diversity was explained by environmental and spatial variables. Autocorrelation in diversity measures and each trait’s phylogenetic signal were also analyzed. We found strong autocorrelation in diversity measures. Both environmental and spatial variables significantly contributed to variation in TD, PD, and FD at both alpha and beta scales; spatial structure had the larger influence. The different facets of diversity showed similar patterns along environmental gradients. Environment explained a much larger percentage of variation in FD than in TD or PD. All traits demonstrated strong phylogenetic signals. Our results indicate that environmental filtering and dispersal limitations structure all types of diversity in ant communities. Strong dispersal limitations appear to have led to clustering of TD, PD, and FD in western and central Europe, probably because different historical and evolutionary processes generated different pools of species. Remarkably, these three facets of diversity showed parallel patterns along environmental gradients. Trait-mediated species sorting and niche conservatism appear to structure ant diversity, as evidenced by the fact that more variation was explained for FD and that all traits had strong phylogenetic signals. Since environmental variables explained much more variation in FD than in PD, functional diversity should be a

  2. Evaluation of the grand-canonical partition function using expanded Wang-Landau simulations. III. Impact of combining rules on mixtures properties

    SciTech Connect

    Desgranges, Caroline; Delhommelle, Jerome

    2014-03-14

    Combining rules, such as the Lorentz-Berthelot rules, are routinely used to calculate the thermodynamic properties of mixtures using molecular simulations. Here we extend the expanded Wang-Landau simulation approach to determine the impact of the combining rules on the value of the partition function of binary systems, and, in turn, on the phase coexistence and thermodynamics of these mixtures. We study various types of mixtures, ranging from systems of rare gases to biologically and technologically relevant mixtures, such as water-urea and water-carbon dioxide. Comparing the simulation results to the experimental data on mixtures of rare gases allows us to rank the performance of combining rules. We find that the widely used Lorentz-Berthelot rules exhibit the largest deviations from the experimental data, both for the bulk and at coexistence, while the Kong and Waldman-Hagler provide much better alternatives. In particular, in the case of aqueous solutions of urea, we show that the use of the Lorentz-Berthelot rules has a strong impact on the Gibbs free energy of the solute, overshooting the value predicted by the Waldman-Hagler rules by 7%. This result emphasizes the importance of the combining rule for the determination of hydration free energies using molecular simulations.

  3. Evaluation of the grand-canonical partition function using expanded Wang-Landau simulations. III. Impact of combining rules on mixtures properties.

    PubMed

    Desgranges, Caroline; Delhommelle, Jerome

    2014-03-14

    Combining rules, such as the Lorentz-Berthelot rules, are routinely used to calculate the thermodynamic properties of mixtures using molecular simulations. Here we extend the expanded Wang-Landau simulation approach to determine the impact of the combining rules on the value of the partition function of binary systems, and, in turn, on the phase coexistence and thermodynamics of these mixtures. We study various types of mixtures, ranging from systems of rare gases to biologically and technologically relevant mixtures, such as water-urea and water-carbon dioxide. Comparing the simulation results to the experimental data on mixtures of rare gases allows us to rank the performance of combining rules. We find that the widely used Lorentz-Berthelot rules exhibit the largest deviations from the experimental data, both for the bulk and at coexistence, while the Kong and Waldman-Hagler provide much better alternatives. In particular, in the case of aqueous solutions of urea, we show that the use of the Lorentz-Berthelot rules has a strong impact on the Gibbs free energy of the solute, overshooting the value predicted by the Waldman-Hagler rules by 7%. This result emphasizes the importance of the combining rule for the determination of hydration free energies using molecular simulations.

  4. Synchrotron Micro-XANES Measurements of Vanadium Oxidation State in Glasses as a Function of Oxygen Fugacity: Experimental Calibration of Data Relevant to Partition Coefficient Determination

    NASA Technical Reports Server (NTRS)

    Delaney, J. S.; Sutton, S. R.; Newville, M.; Jones, J. H.; Hanson, B.; Dyar, M. D.; Schreiber, H.

    2000-01-01

    Oxidation state microanalyses for V in glass have been made by calibrating XANES spectral features with optical spectroscopic measurements. The oxidation state change with fugacity of O2 will strongly influence partitioning results.

  5. The Back Squat Part 2: Targeted Training Techniques to Correct Functional Deficits and Technical Factors that Limit Performance

    PubMed Central

    Kushner, Adam M.; Brent, Jensen L.; Schoenfeld, Brad J.; Hugentobler, Jason; Lloyd, Rhodri S.; Vermeil, Al; Chu, Donald A.; Harbin, Jason; McGill, Stuart M.; Myer, Gregory D.

    2015-01-01

    The back squat is a well-researched and widely used exercise to enhance fundamental movement competency that creates a foundation for optimal mechanical strategies during a broad range of activities. The primary commentary introduced the Back Squat Assessment (BSA): a criterion based assessment of the back squat that delineates 30 potentially observable functional deficits. This follow-up commentary provides a targeted system of training cues and exercises to supplement the BSA to guide corrective intervention. We propose a criterion driven approach to corrective exercise that can support practitioners in their goal to help individuals achieve movement competency in the back squat. PMID:26823657

  6. Duplication and partitioning in evolution and function of homoeologous Q loci governing domestication characters in polyploid wheat.

    PubMed

    Zhang, Zengcui; Belcram, Harry; Gornicki, Piotr; Charles, Mathieu; Just, Jérémy; Huneau, Cécile; Magdelenat, Ghislaine; Couloux, Arnaud; Samain, Sylvie; Gill, Bikram S; Rasmussen, Jack B; Barbe, Valérie; Faris, Justin D; Chalhoub, Boulos

    2011-11-15

    The Q gene encodes an AP2-like transcription factor that played an important role in domestication of polyploid wheat. The chromosome 5A Q alleles (5AQ and 5Aq) have been well studied, but much less is known about the q alleles on wheat homoeologous chromosomes 5B (5Bq) and 5D (5Dq). We investigated the organization, evolution, and function of the Q/q homoeoalleles in hexaploid wheat (Triticum aestivum L.). Q/q gene sequences are highly conserved within and among the A, B, and D genomes of hexaploid wheat, the A and B genomes of tetraploid wheat, and the A, S, and D genomes of the diploid progenitors, but the intergenic regions of the Q/q locus are highly divergent among homoeologous genomes. Duplication of the q gene 5.8 Mya was likely followed by selective loss of one of the copies from the A genome progenitor and the other copy from the B, D, and S genomes. A recent V(329)-to-I mutation in the A lineage is correlated with the Q phenotype. The 5Bq homoeoalleles became a pseudogene after allotetraploidization. Expression analysis indicated that the homoeoalleles are coregulated in a complex manner. Combined phenotypic and expression analysis indicated that, whereas 5AQ plays a major role in conferring domestication-related traits, 5Dq contributes directly and 5Bq indirectly to suppression of the speltoid phenotype. The evolution of the Q/q loci in polyploid wheat resulted in the hyperfunctionalization of 5AQ, pseudogenization of 5Bq, and subfunctionalization of 5Dq, all contributing to the domestication traits. PMID:22042872

  7. Duplication and partitioning in evolution and function of homoeologous Q loci governing domestication characters in polyploid wheat

    PubMed Central

    Zhang, Zengcui; Belcram, Harry; Gornicki, Piotr; Charles, Mathieu; Just, Jérémy; Huneau, Cécile; Magdelenat, Ghislaine; Couloux, Arnaud; Samain, Sylvie; Gill, Bikram S.; Rasmussen, Jack B.; Barbe, Valérie; Faris, Justin D.; Chalhoub, Boulos

    2011-01-01

    The Q gene encodes an AP2-like transcription factor that played an important role in domestication of polyploid wheat. The chromosome 5A Q alleles (5AQ and 5Aq) have been well studied, but much less is known about the q alleles on wheat homoeologous chromosomes 5B (5Bq) and 5D (5Dq). We investigated the organization, evolution, and function of the Q/q homoeoalleles in hexaploid wheat (Triticum aestivum L.). Q/q gene sequences are highly conserved within and among the A, B, and D genomes of hexaploid wheat, the A and B genomes of tetraploid wheat, and the A, S, and D genomes of the diploid progenitors, but the intergenic regions of the Q/q locus are highly divergent among homoeologous genomes. Duplication of the q gene 5.8 Mya was likely followed by selective loss of one of the copies from the A genome progenitor and the other copy from the B, D, and S genomes. A recent V329-to-I mutation in the A lineage is correlated with the Q phenotype. The 5Bq homoeoalleles became a pseudogene after allotetraploidization. Expression analysis indicated that the homoeoalleles are coregulated in a complex manner. Combined phenotypic and expression analysis indicated that, whereas 5AQ plays a major role in conferring domestication-related traits, 5Dq contributes directly and 5Bq indirectly to suppression of the speltoid phenotype. The evolution of the Q/q loci in polyploid wheat resulted in the hyperfunctionalization of 5AQ, pseudogenization of 5Bq, and subfunctionalization of 5Dq, all contributing to the domestication traits. PMID:22042872

  8. A table of integrals of the error function. II - Additions and corrections.

    NASA Technical Reports Server (NTRS)

    Geller, M.; Ng, E. W.

    1971-01-01

    Integrals of products of error functions with other functions are presented, taking into account a combination of the error function with powers, a combination of the error function with exponentials and powers, a combination of the error function with exponentials of more complicated arguments, definite integrals from Laplace transforms, and a combination of the error function with trigonometric functions. Other integrals considered include a combination of the error function with logarithms and powers, a combination of two error functions, and a combination of the error function with other special functions.

  9. Horizontal gene transfer and diverse functional constrains within a common replication-partitioning system in Alphaproteobacteria: the repABC operon

    PubMed Central

    2009-01-01

    Background The repABC plasmid family, which is extensively present within Alphaproteobacteria, and some secondary chromosomes of the Rhizobiales have the particular feature that all the elements involved in replication and partitioning reside within one transcriptional unit, the repABC operon. Given the functional interactions among the elements of the repABC operon, and the fact that they all reside in the same operon, a common evolutionary history would be expected if the entire operon had been horizontally transferred. Here, we tested whether there is a common evolutionary history within the repABC operon. We further examined different incompatibility groups in terms of their differentiation and degree of adaptation to their host. Results We did not find a single evolutionary history within the repABC operon. Each protein had a particular phylogeny, horizontal gene transfer events of the individual genes within the operon were detected, and different functional constraints were found within and between the Rep proteins. When different repABC operons coexisted in the same genome, they were well differentiated from one another. Finally, we found different levels of adaptation to the host genome within and between repABC operons coexisting in the same species. Conclusion Horizontal gene transfer with conservation of the repABC operon structure provides a highly dynamic operon in which each member of this operon has its own evolutionary dynamics. In addition, it seems that different incompatibility groups present in the same species have different degrees of adaptation to their host genomes, in proportion to the amount of time the incompatibility group has coexisted with the host genome. PMID:19919719

  10. Evaluation of the correctness of a 3D recording device for mandibular functional movement in laboratory

    NASA Astrophysics Data System (ADS)

    Zhao, Tian; Sui, Huaxin; Yang, Huifang; Wang, Yong; Sun, Yuchun

    2015-07-01

    Objectives: To quantitatively evaluate the correctness of a computer binocular vision mandibular 3D trajectory recording device. Methods: A specialized target shooting paper was neatly pasted on a high-precision three-axis electronic translation stage. A linear one-way movement was set at a speed of 1 mm/s along the X, Y, and Z directions for a distance of 10 mm each. The coordinates of 3 pre-set target points were recorded at the start and end by a computer binocular vision system with a frequency of 10 FPS and stored in TXT format. The TXT files were imported to Imageware 13.0, and the straight-line lengths between the start and end were measured. The mean difference between each length and 10 mm were calculated to evaluate the correctness of the distance measurement. The linear movement and recording procedure was repeated 3 times, but the speed was changed to 5 mm/s to simulate the human mandibular movement speed. The trajectories of the 3 target points were fitted and the vertical dimensions from each track point to the fitted lines were measured. The mean difference was calculated between the vertical dimensions and 0 mm to evaluate the correctness of recording trajectories using this device. Results: The correctness of distance measurements of the points 1, 2, and 3 were 0.06 mm, 0.16 mm, and 0.08 mm, respectively. The correctness of the trajectories of the points 1, 2, and 3 were 0.11 mm, 0.11 mm, and 0.10 mm, respectively. Conclusion: Using this computer binocular vision device, the correctness of the recorded linear trajectories in the range of 10 mm was better than 0.20 mm.

  11. Assessing the influence of van der Waals corrected exchange-correlation functionals on the anisotropic mechanical properties of coinage metals

    NASA Astrophysics Data System (ADS)

    Lee, Ji-Hwan; Park, Jong-Hun; Soon, Aloysius

    2016-07-01

    Current materials-related calculations employ density-functional theory (DFT), commonly using the (semi-)local-density approximations for the exchange-correlation (xc) functional. The difficulties in arriving at a reasonable description of van der Waals (vdW) interactions by DFT-based models is to date a big challenge. In this work, we use various flavors of vdW-corrected DFT xc functionals—ranging from the quasiempirical force-field add-on vdW corrections to self-consistent nonlocal correlation functionals—to study the bulk lattice and mechanical properties (including the elastic constants and anisotropic indices) of the coinage metals (copper, silver, and gold). We critically assess the reliability of the different vdW-corrected DFT methods in describing their anisotropic mechanical properties which have been less reported in the literature. In the context of this work, we regard that our results reiterate the fact that advocating a so-called perfect vdW-inclusive xc functional for describing the general physics and chemistry of these coinage metals could be a little premature. These challenges to modern-day functionals for anisotropically strained coinage metals (e.g., at the faceted surfaces of nanostructures) may well be relevant to other strained material systems.

  12. The Analytical Four-Loop Corrections to the QED β-FUNCTION in the MS Scheme and to the QED ψ-FUNCTION: Total Reevaluation

    NASA Astrophysics Data System (ADS)

    Gorishny, S. G.; Kataev, A. L.; Larin, S. A.; Surguladze, L. R.

    The results of the total reevaluation of the four-loop correction to the QED β-function in the minimal and momentum subtraction schemes (βMS and ψ-functions) and for the functions F1(α) and F (α) determined by the photon vacuum polarization diagrams without fermion-loop contributions to the internal photon lines are presented. It is found that the ζ(3), ζ(4) and ζ(S)-terms cancel in the ultimate result for the four-loop coefficient of the F1-function. The results obtained are briefly discussed.

  13. Exploring the limit of accuracy for density functionals based on the generalized gradient approximation: local, global hybrid, and range-separated hybrid functionals with and without dispersion corrections.

    PubMed

    Mardirossian, Narbe; Head-Gordon, Martin

    2014-05-14

    The limit of accuracy for semi-empirical generalized gradient approximation (GGA) density functionals is explored by parameterizing a variety of local, global hybrid, and range-separated hybrid functionals. The training methodology employed differs from conventional approaches in 2 main ways: (1) Instead of uniformly truncating the exchange, same-spin correlation, and opposite-spin correlation functional inhomogeneity correction factors, all possible fits up to fourth order are considered, and (2) Instead of selecting the optimal functionals based solely on their training set performance, the fits are validated on an independent test set and ranked based on their overall performance on the training and test sets. The 3 different methods of accounting for exchange are trained both with and without dispersion corrections (DFT-D2 and VV10), resulting in a total of 491 508 candidate functionals. For each of the 9 functional classes considered, the results illustrate the trade-off between improved training set performance and diminished transferability. Since all 491 508 functionals are uniformly trained and tested, this methodology allows the relative strengths of each type of functional to be consistently compared and contrasted. The range-separated hybrid GGA functional paired with the VV10 nonlocal correlation functional emerges as the most accurate form for the present training and test sets, which span thermochemical energy differences, reaction barriers, and intermolecular interactions involving lighter main group elements.

  14. Structure and properties of metal-exchanged zeolites studied using gradient-corrected and hybrid functionals. I. Structure and energetics

    NASA Astrophysics Data System (ADS)

    Göltl, Florian; Hafner, Jürgen

    2012-02-01

    The structural and energetic properties of purely siliceous, proton-, and Cu- and Co-exchanged chabazite have been studied using periodic density-functional (DFT) calculations with both conventional gradient-corrected exchange-correlation functionals and hybrid functionals mixing exact (i.e., Hartree-Fock) and DFT exchange. Spin-polarized and fixed-moment calculations have been performed to determine the equilibrium and excited spin-configurations of the metal-exchanged chabazites. For the purely siliceous chabazite, hybrid functionals predict a slightly more accurate cell volume and lattice geometry. For isolated Al/Si substitution sites, gradient-corrected functionals predict that the lattice distortion induced by the substitution preserves the local tetrahedral symmetry, whereas hybrid functionals lead to a distorted Al coordination with two short and two long Al-O bonds. Hybrid functionals yield a stronger cation-framework binding that conventional functionals in metal-exchanged zeolites, they favor shorter cation-oxygen bonds and eventually also a higher coordination of the cation. Both types of functionals predict the same spin in the ground-state. The structural optimization of the excited spin-states shows that the formation of a high-spin configuration leads to a strong lattice relaxation and a weaker cation-framework bonding. For both Cu- and Co-exchanged chabazite, the prediction of a preferred location of the cation in a six-membered ring of the zeolite agrees with experiment, but the energy differences between possible cation locations and the lattice distortion induced by the Al/Si substitution and the bonding of the cation depends quite significantly on the choice of the functional. All functionals predict similar energy differences for excited spin states. Spin-excitations are shown to be accompanied by significant changes in the cation coordination, which are more pronounced with hybrid functionals. The consequences of electronic spectra and

  15. Genus one correction to Seiberg-Witten prepotential from β-deformed matrix model

    NASA Astrophysics Data System (ADS)

    Baek, Jong-Hyun

    2013-04-01

    We study β-deformed matrix models with Penner type potentials, which correspond to {N}=2 SU(2) supersymmetric gauge theories with N F = 2 , 3, and 4 flavors. We compute explicitly the genus one corrections to the free energy of the matrix model and show that they match the corresponding results obtained from the Nekrasov partition function.

  16. How pervasive is the Hirshfeld partitioning?

    SciTech Connect

    Heidar-Zadeh, Farnaz; Ayers, Paul W.

    2015-01-28

    One can partition the molecular density into its atomic contributions by minimizing the divergence of the atom-in-molecule densities from their corresponding reference pro-atomic densities, subject to the constraint that the sum of the atom-in-molecule densities is the total molecular density. We expose conditions on the divergence measure that are necessary, and sufficient, to recover the popular Hirshfeld partitioning. Specifically, among all local measures of the divergence between two probability distribution functions, the Hirshfeld partitioning is obtained only for f-divergences.

  17. Geometrical correction for the inter- and intramolecular basis set superposition error in periodic density functional theory calculations.

    PubMed

    Brandenburg, Jan Gerit; Alessio, Maristella; Civalleri, Bartolomeo; Peintinger, Michael F; Bredow, Thomas; Grimme, Stefan

    2013-09-26

    We extend the previously developed geometrical correction for the inter- and intramolecular basis set superposition error (gCP) to periodic density functional theory (DFT) calculations. We report gCP results compared to those from the standard Boys-Bernardi counterpoise correction scheme and large basis set calculations. The applicability of the method to molecular crystals as the main target is tested for the benchmark set X23. It consists of 23 noncovalently bound crystals as introduced by Johnson et al. (J. Chem. Phys. 2012, 137, 054103) and refined by Tkatchenko et al. (J. Chem. Phys. 2013, 139, 024705). In order to accurately describe long-range electron correlation effects, we use the standard atom-pairwise dispersion correction scheme DFT-D3. We show that a combination of DFT energies with small atom-centered basis sets, the D3 dispersion correction, and the gCP correction can accurately describe van der Waals and hydrogen-bonded crystals. Mean absolute deviations of the X23 sublimation energies can be reduced by more than 70% and 80% for the standard functionals PBE and B3LYP, respectively, to small residual mean absolute deviations of about 2 kcal/mol (corresponding to 13% of the average sublimation energy). As a further test, we compute the interlayer interaction of graphite for varying distances and obtain a good equilibrium distance and interaction energy of 6.75 Å and -43.0 meV/atom at the PBE-D3-gCP/SVP level. We fit the gCP scheme for a recently developed pob-TZVP solid-state basis set and obtain reasonable results for the X23 benchmark set and the potential energy curve for water adsorption on a nickel (110) surface.

  18. Optimization of a Model Corrected Blood Input Function from Dynamic FDG-PET Images of Small Animal Heart In Vivo

    PubMed Central

    Zhong, Min; Kundu, Bijoy K.

    2013-01-01

    Quantitative evaluation of dynamic Positron Emission Tomography (PET) of mouse heart in vivo is challenging due to the small size of the heart and limited intrinsic spatial resolution of the PET scanner. Here, we optimized a compartment model which can simultaneously correct for spill over and partial volume effects for both blood pool and the myocardium, compute kinetic rate parameters and generate model corrected blood input function (MCBIF) from ordered subset expectation maximization – maximum a posteriori (OSEM-MAP) cardiac and respiratory gated 18F-FDG PET images of mouse heart with attenuation correction in vivo, without any invasive blood sampling. Arterial blood samples were collected from a single mouse to indicate the feasibility of the proposed method. In order to establish statistical significance, venous blood samples from n=6 mice were obtained at 2 late time points, when SP contamination from the tissue to the blood is maximum. We observed that correct bounds and initial guesses for the PV and SP coefficients accurately model the wash-in and wash-out dynamics of the tracer from mouse blood. The residual plot indicated an average difference of about 1.7% between the blood samples and MCBIF. The downstream rate of myocardial FDG influx constant, Ki (0.15±0.03 min−1), compared well with Ki obtained from arterial blood samples (P=0.716). In conclusion, the proposed methodology is not only quantitative but also reproducible. PMID:24741130

  19. A New, Self-Contained Asymptotic Correction Scheme To Exchange-Correlation Potentials For Time-Dependent Density Functional Theory

    SciTech Connect

    Hirata, So; Zhan, Chang-Guo; Apra, Edoardo; Windus, Theresa L.; Dixon, David A.

    2003-11-07

    By combining the asymptotic correction scheme of Casida and Salahub to exchange cor-relation potentials and the phenomenological linear correlation between experimental ionization potentials and highest occupied Kohn–Sham (KS) orbital energies found by Zhan, Nichols, and Dixon, we propose a new, expedient, and self-contained asymptotic correction to exchange-correlation potentials in KS density functional theory (DFT) for use in time-dependent density functional theory (TDDFT) that does not require an ionization potential as an external parameter from a separate calculation. The asymptotically-corrected (TD)DFT is implemented in the quan-tum chemistry program suite NWChem for both sequential and massively parallel execution. The method is shown to be well balanced for both valence- and Rydberg-type transitions with average errors in excitation energies of CO, N2, CH2O, and C2H4 being smaller than those of uncorrected BLYP and B3LYP TDDFT by a factor of 4 and 2, respectively. We demonstrate the general ap-plicability and accuracy of the method for the Rydberg excited states of mono- to tetra-fluorinated methanes, the valence and Rydberg excited states of benzene, and the Q, B, N, and L band posi-tions of free-base porphin.

  20. The use of high-resolution atmospheric simulations over mountainous terrain for deriving error correction functions of satellite precipitation products

    NASA Astrophysics Data System (ADS)

    Bartsotas, Nikolaos S.; Nikolopoulos, Efthymios I.; Anagnostou, Emmanouil N.; Kallos, George

    2015-04-01

    Mountainous regions account for a significant part of the Earth's surface. Such areas are persistently affected by heavy precipitation episodes, which induce flash floods and landslides. The limitation of inadequate in-situ observations has put remote sensing rainfall estimates on a pedestal concerning the analyses of these events, as in many mountainous regions worldwide they serve as the only available data source. However, well-known issues of remote sensing techniques over mountainous areas, such as the strong underestimation of precipitation associated with low-level orographic enhancement, limit the way these estimates can accommodate operational needs. Even locations that fall within the range of weather radars suffer from strong biases in precipitation estimates due to terrain blockage and vertical rainfall profile issues. A novel approach towards the reduction of error in quantitative precipitation estimates lies upon the utilization of high-resolution numerical simulations in order to derive error correction functions for corresponding satellite precipitation data. The correction functions examined consist of 1) mean field bias adjustment and 2) pdf matching, two procedures that are simple and have been widely used in gauge-based adjustment techniques. For the needs of this study, more than 15 selected storms over the mountainous Upper Adige region of Northern Italy were simulated at 1-km resolution from a state-of-the-art atmospheric model (RAMS/ICLAMS), benefiting from the explicit cloud microphysical scheme, prognostic treatment of natural pollutants such as dust and sea-salt and the detailed SRTM90 topography that are implemented in the model. The proposed error correction approach is applied on three quasi-global and widely used satellite precipitation datasets (CMORPH, TRMM 3B42 V7 and PERSIANN) and the evaluation of the error model is based on independent in situ precipitation measurements from a dense rain gauge network (1 gauge / 70 km2

  1. Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D).

    PubMed

    van de Streek, Jacco; Neumann, Marcus A

    2014-12-01

    In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.

  2. The three-dimensional point spread function of aberration-corrected scanning transmission electron microscopy.

    PubMed

    Lupini, Andrew R; de Jonge, Niels

    2011-10-01

    Aberration correction reduces the depth of field in scanning transmission electron microscopy (STEM) and thus allows three-dimensional (3D) imaging by depth sectioning. This imaging mode offers the potential for sub-Ångstrom lateral resolution and nanometer-scale depth sensitivity. For biological samples, which may be many microns across and where high lateral resolution may not always be needed, optimizing the depth resolution even at the expense of lateral resolution may be desired, aiming to image through thick specimens. Although there has been extensive work examining and optimizing the probe formation in two dimensions, there is less known about the probe shape along the optical axis. Here the probe shape is examined in three dimensions in an attempt to better understand the depth resolution in this mode. Examples are presented of how aberrations change the probe shape in three dimensions, and it is found that off-axial aberrations may need to be considered for focal series of large areas. It is shown that oversized or annular apertures theoretically improve the vertical resolution for 3D imaging of nanoparticles. When imaging nanoparticles of several nanometer size, regular STEM can thereby be optimized such that the vertical full-width at half-maximum approaches that of the aberration-corrected STEM with a standard aperture.

  3. Fuzzy Partition Models for Fitting a Set of Partitions.

    ERIC Educational Resources Information Center

    Gordon, A. D.; Vichi, M.

    2001-01-01

    Describes methods for fitting a fuzzy consensus partition to a set of partitions of the same set of objects. Describes and illustrates three models defining median partitions and compares these methods to an alternative approach to obtaining a consensus fuzzy partition. Discusses interesting differences in the results. (SLD)

  4. Carbon partitioning in photosynthesis.

    PubMed

    Melis, Anastasios

    2013-06-01

    The work seeks to raise awareness of a fundamental problem that impacts the renewable generation of fuels and chemicals via (photo)synthetic biology. At issue is regulation of the endogenous cellular carbon partitioning between different biosynthetic pathways, over which the living cell exerts stringent control. The regulation of carbon partitioning in photosynthesis is not understood. In plants, microalgae and cyanobacteria, methods need be devised to alter photosynthetic carbon partitioning between the sugar, terpenoid, and fatty acid biosynthetic pathways, to lower the prevalence of sugar biosynthesis and correspondingly upregulate terpenoid and fatty acid hydrocarbons production in the cell. Insight from unusual but naturally occurring carbon-partitioning processes can help in the design of blueprints for improved photosynthetic fuels and chemicals production.

  5. Energy ranking of molecular crystals using density functional theory calculations and an empirical van der waals correction.

    PubMed

    Neumann, Marcus A; Perrin, Marc-Antoine

    2005-08-18

    By combination of high level density functional theory (DFT) calculations with an empirical van der Waals correction, a hybrid method has been designed and parametrized that provides unprecedented accuracy for the structure optimization and the energy ranking of molecular crystals. All DFT calculations are carried out using the VASP program. The van der Waals correction is expressed as the sum over atom-atom pair potentials with each pair potential for two atoms A and B being the product of an asymptotic C(6,A,B)/r(6) term and a damping function d(A,B)(r). Empirical parameters are provided for the elements H, C, N, O, F, Cl, and S. Following Wu and Yang, the C(6) coefficients have been determined by least-squares fitting to molecular C(6) coefficients derived by Meath and co-workers from dipole oscillator strength distributions. The damping functions d(A,B)(r) guarantee the crossover from the asymptotic C(6,A,B)/r(6) behavior at large interatomic distances to a constant interaction energy at short distances. The careful parametrization of the damping functions is of crucial importance to obtain the correct balance between the DFT part of the lattice energy and the contribution from the empirical van der Waals correction. The damping functions have been adjusted to yield the best possible agreement between the unit cells of a set of experimental low temperature crystal structures and their counterparts obtained by lattice energy optimization using the hybrid method. On average, the experimental and the calculated unit cell lengths deviate by 1%. To assess the performance of the hybrid method with respect to the lattice energy ranking of molecular crystals, various crystal packings of ethane, ethylene, acetylene, methanol, acetic acid, and urea have been generated with Accelrys' Polymorph Predictor in a first step and optimized with the hybrid method in a second step. In five out of six cases, the experimentally observed low-temperature crystal structure corresponds

  6. The Benefits of Adaptive Partitioning for Parallel AMR Applications

    SciTech Connect

    Steensland, Johan

    2008-07-01

    Parallel adaptive mesh refinement methods potentially lead to realistic modeling of complex three-dimensional physical phenomena. However, the dynamics inherent in these methods present significant challenges in data partitioning and load balancing. Significant human resources, including time, effort, experience, and knowledge, are required for determining the optimal partitioning technique for each new simulation. In reality, scientists resort to using the on-board partitioner of the computational framework, or to using the partitioning industry standard, ParMetis. Adaptive partitioning refers to repeatedly selecting, configuring and invoking the optimal partitioning technique at run-time, based on the current state of the computer and application. In theory, adaptive partitioning automatically delivers superior performance and eliminates the need for repeatedly spending valuable human resources for determining the optimal static partitioning technique. In practice, however, enabling frameworks are non-existent due to the inherent significant inter-disciplinary research challenges. This paper presents a study of a simple implementation of adaptive partitioning and discusses implied potential benefits from the perspective of common groups of users within computational science. The study is based on a large set of data derived from experiments including six real-life, multi-time-step adaptive applications from various scientific domains, five complementing and fundamentally different partitioning techniques, a large set of parameters corresponding to a wide spectrum of computing environments, and a flexible cost function that considers the relative impact of multiple partitioning metrics and diverse partitioning objectives. The results show that even a simple implementation of adaptive partitioning can automatically generate results statistically equivalent to the best static partitioning. Thus, it is possible to effectively eliminate the problem of determining the

  7. Functional requirements for the man-vehicle systems research facility. [identifying and correcting human errors during flight simulation

    NASA Technical Reports Server (NTRS)

    Clement, W. F.; Allen, R. W.; Heffley, R. K.; Jewell, W. F.; Jex, H. R.; Mcruer, D. T.; Schulman, T. M.; Stapleford, R. L.

    1980-01-01

    The NASA Ames Research Center proposed a man-vehicle systems research facility to support flight simulation studies which are needed for identifying and correcting the sources of human error associated with current and future air carrier operations. The organization of research facility is reviewed and functional requirements and related priorities for the facility are recommended based on a review of potentially critical operational scenarios. Requirements are included for the experimenter's simulation control and data acquisition functions, as well as for the visual field, motion, sound, computation, crew station, and intercommunications subsystems. The related issues of functional fidelity and level of simulation are addressed, and specific criteria for quantitative assessment of various aspects of fidelity are offered. Recommendations for facility integration, checkout, and staffing are included.

  8. Polynomial scaling approximations and dynamic correlation corrections to doubly occupied configuration interaction wave functions.

    PubMed

    Van Raemdonck, Mario; Alcoba, Diego R; Poelmans, Ward; De Baerdemacker, Stijn; Torre, Alicia; Lain, Luis; Massaccesi, Gustavo E; Van Neck, Dimitri; Bultinck, Patrick

    2015-09-14

    A class of polynomial scaling methods that approximate Doubly Occupied Configuration Interaction (DOCI) wave functions and improve the description of dynamic correlation is introduced. The accuracy of the resulting wave functions is analysed by comparing energies and studying the overlap between the newly developed methods and full configuration interaction wave functions, showing that a low energy does not necessarily entail a good approximation of the exact wave function. Due to the dependence of DOCI wave functions on the single-particle basis chosen, several orbital optimisation algorithms are introduced. An energy-based algorithm using the simulated annealing method is used as a benchmark. As a computationally more affordable alternative, a seniority number minimising algorithm is developed and compared to the energy based one revealing that the seniority minimising orbital set performs well. Given a well-chosen orbital basis, it is shown that the newly developed DOCI based wave functions are especially suitable for the computationally efficient description of static correlation and to lesser extent dynamic correlation.

  9. Partitioning in Avionics Architectures: Requirements, Mechanisms, and Assurance

    NASA Technical Reports Server (NTRS)

    Rushby, John

    1999-01-01

    Automated aircraft control has traditionally been divided into distinct "functions" that are implemented separately (e.g., autopilot, autothrottle, flight management); each function has its own fault-tolerant computer system, and dependencies among different functions are generally limited to the exchange of sensor and control data. A by-product of this "federated" architecture is that faults are strongly contained within the computer system of the function where they occur and cannot readily propagate to affect the operation of other functions. More modern avionics architectures contemplate supporting multiple functions on a single, shared, fault-tolerant computer system where natural fault containment boundaries are less sharply defined. Partitioning uses appropriate hardware and software mechanisms to restore strong fault containment to such integrated architectures. This report examines the requirements for partitioning, mechanisms for their realization, and issues in providing assurance for partitioning. Because partitioning shares some concerns with computer security, security models are reviewed and compared with the concerns of partitioning.

  10. A comparison of ethanol partitioning in biological and model membranes: nonideal partitioning is enhanced in synaptosomal membranes.

    PubMed

    Sarasua, M M; Faught, K R; Steedman, S L; Gordin, M D; Washington, M K

    1989-10-01

    The partitioning of ethanol into mouse brain synaptosomes at 37 degrees C was characterized as a function of ethanol concentration. In addition, the partitioning of ethanol into multilamellar dipalmitoylphosphatidylcholine (DPPC) vesicles was characterized as a function of ethanol concentration and temperature. DPPC liposomes provided a model for ethanol partitioning into a phospholipid bilayer of defined composition allowing comparison to the more complex synaptosomal membrane. The values of the partition coefficients for ethanol depend on the convention used to express concentration in the partition coefficient ratio. We express these concentrations as mole fractions as ethanol in the membrane and aqueous phases. Ethanol partitioning is nonideal (ethanol membrane: buffer partition coefficients vary with total ethanol concentration). In synaptosomes, the partition coefficients vary markedly with concentration and asymptotically approach zero at higher concentrations. In the DPPC system, the variation of the partition coefficient is less pronounced, but significant. The ethanol: DPPC partition coefficients decrease by a factor of 2 at ethanol concentrations above 3.2 x 10(-3) M. This suggests a model involving at least two distinguishable types of interactions of ethanol with the membrane. Ethanol appears to undergo both bulk phase partitioning into the membrane bilayer core and nonspecific binding to the membrane surface. In pure DPPC, bulk phase hydrophobic partitioning predominates. In synaptosomes, nonspecific surface binding appears to be a major interaction. Temperature studies indicate ethanol partitioning into DPPC increases above the phospholipid gel to liquid crystalline phase transition temperature. This suggests a preferred partitioning of ethanol into fluid state lipid. However, significant membrane concentrations of ethanol are found in gel state DPPC.

  11. SU-E-T-299: Small Fields Profiles Correction Through Detectors Spatial Response Functions and Field Size Dependence Analysis

    SciTech Connect

    Filipuzzi, M; Garrigo, E; Venencia, C; Germanier, A

    2014-06-01

    Purpose: To calculate the spatial response function of various radiation detectors, to evaluate the dependence on the field size and to analyze the small fields profiles corrections by deconvolution techniques. Methods: Crossline profiles were measured on a Novalis Tx 6MV beam with a HDMLC. The configuration setup was SSD=100cm and depth=5cm. Five fields were studied (200×200mm2,100×100mm2, 20×20mm2, 10×10mm2and 5×5mm2) and measured were made with passive detectors (EBT3 radiochromic films and TLD700 thermoluminescent detectors), ionization chambers (PTW30013, PTW31003, CC04 and PTW31016) and diodes (PTW60012 and IBA SFD). The results of passive detectors were adopted as the actual beam profile. To calculate the detectors kernels, modeled by Gaussian functions, an iterative process based on a least squares criterion was used. The deconvolutions of the measured profiles were calculated with the Richardson-Lucy method. Results: The profiles of the passive detectors corresponded with a difference in the penumbra less than 0.1mm. Both diodes resolve the profiles with an overestimation of the penumbra smaller than 0.2mm. For the other detectors, response functions were calculated and resulted in Gaussian functions with a standard deviation approximate to the radius of the detector in study (with a variation less than 3%). The corrected profiles resolve the penumbra with less than 1% error. Major discrepancies were observed for cases in extreme conditions (PTW31003 and 5×5mm2 field size). Conclusion: This work concludes that the response function of a radiation detector is independent on the field size, even for small radiation beams. The profiles correction, using deconvolution techniques and response functions of standard deviation equal to the radius of the detector, gives penumbra values with less than 1% difference to the real profile. The implementation of this technique allows estimating the real profile, freeing from the effects of the detector used for the

  12. [Pharmacological correction of central nervous system function in exposure to Coriolis acceleration].

    PubMed

    Karkishchenko, N N; Dimitriadi, N A; Molchanovskiĭ, V V

    1986-01-01

    Healthy volunteers with a low vestibular tolerance were exposed to Coriolis acceleration. Potassium orotate, pyracetame and riboxine were used as prophylactic measures against disorders in the function of the vestibular apparatus and higher compartments of the higher nervous system. The central nervous function was assessed with respect to the spectral power of electroencephalograms, short-term memory and mental performance. Potassium orotate given at a dose of 40 mg/kg body weight/day during 12-14 days as well as pyracetame given at a dose of 30 mg/kg body weight/day during 3 or 7 days increased significantly statokinetic tolerance and produced a protective effect on the central nervous function against Coriolis acceleration.

  13. Understanding the Function of Visual Short-Term Memory: Transsaccadic Memory, Object Correspondence, and Gaze Correction

    ERIC Educational Resources Information Center

    Hollingworth, Andrew; Richard, Ashleigh M.; Luck, Steven J.

    2008-01-01

    Visual short-term memory (VSTM) has received intensive study over the past decade, with research focused on VSTM capacity and representational format. Yet, the function of VSTM in human cognition is not well understood. Here, the authors demonstrate that VSTM plays an important role in the control of saccadic eye movements. Intelligent human…

  14. Self-interaction corrected density functional calculations of Rydberg states of molecular clusters: N,N-dimethylisopropylamine

    SciTech Connect

    Gudmundsdóttir, Hildur; Zhang, Yao; Weber, Peter M.; Jónsson, Hannes

    2014-12-21

    Theoretical calculations of Rydberg excited states of molecular clusters consisting of N,N-dimethylisopropylamine molecules using a Perdew-Zunger self-interaction corrected energy functional are presented and compared with results of resonant multiphoton ionization measurements. The binding energy of the Rydberg electron in the monomer is calculated to be 2.79 eV and 2.27 eV in the 3s and 3p state, respectively, which compares well with measured values of 2.88 eV and 2.21 eV. Three different stable configurations of the dimer in the ground state were found using an energy functional that includes van der Waals interaction. The lowest ground state energy conformation has the two N-atoms widely separated, by 6.2 Å, while the Rydberg state energy is lowest for a configuration where the N-atoms of the two molecules come close together, separated by 3.7 Å. This conformational change is found to lower the Rydberg electron binding energy by 0.2 eV. The self-interaction corrected functional gives a highly localized hole on one of the two molecules, unlike results obtained using the PBE functional or the hybrid B3LYP functional which give a delocalized hole. For the trimer, the self-interaction corrected calculation gives a Rydberg electron binding energy lowered further by 0.13 eV as compared with the dimer. The calculated results compare well with trends observed in experimental measurements. The reduction of the Rydberg electron binding energy with cluster size can be ascribed to an effective delocalization of the positive charge of the hole by the induced and permanent dipole moments of the neighboring molecules. A further decrease observed to occur on a time scale of tens of ps can be ascribed to a structural rearrangement of the clusters in the Rydberg state where molecules rotate to orient their dipoles in response to the formation of the localized hole.

  15. Evaluation of dispersion-corrected density functional theory (B3LYP-DCP) for compounds of biochemical interest.

    PubMed

    Lill, Sten O Nilsson

    2010-09-01

    An evaluation of a dispersion-corrected density functional theory method (B3LYP-DCP) [I.D. Mackie, G.A. DiLabio, Interactions in large, polyaromatic hydrocarbon dimers: application of density functional theory with dispersion corrections, J. Phys. Chem. A 112 (2008) 10968-10976] for three systems of biochemical interest is presented. Firstly, structures and energies of isomers of the tripeptide Phe-Gly-Phe have been compared with CCSD(T)/CBS//RI-MP2/cc-pVTZ literature values. In the system aromatic interactions compete with XH-pi (X=C, N) interactions and hydrogen bonds which makes it a reliable model for proteins. The resulting mean absolute deviation between B3LYP-DCP and CCSD(T)/CBS relative energies is found to be 0.50 kcal mol(-1). Secondly, a phenylalanine derivative featuring a CH-pi interaction has been investigated. A comparison between the optimized geometry and X-ray crystal data shows that B3LYP-DCP accurately predicts the interaction between the two aromatic rings. Thirdly, the dipeptide Ac-Phe-Phe-NH(2) which contains an edge-to-face interaction between two aromatic rings has been studied. The study demonstrates the general applicability of the B3LYP-DCP method on systems which features interactions typically present in biochemical compounds.

  16. Propagation of soft tissue artifacts to the center of rotation: a model for the correction of functional calibration techniques.

    PubMed

    De Rosario, Helios; Page, Álvaro; Besa, Antonio; Valera, Ángel

    2013-10-18

    This paper presents a mathematical model for the propagation of errors in body segment kinematics to the location of the center of rotation. Three functional calibration techniques, usually employed for the gleno-humeral joint, are studied: the methods based on the pivot of the instantaneous helical axis (PIHA) or the finite helical axis (PFHA), and the "symmetrical center of rotation estimation" (SCoRE). A procedure for correcting the effect of soft tissue artifacts is also proposed, based on the equations of those techniques and a model of the artifact, like the one that can be obtained by double calibration. An experiment with a mechanical analog was performed to validate the procedure and compare the performance of each technique. The raw error (between 57 and 68mm) was reduced by a proportion of between 1:6 and less than 1:15, depending on the artifact model and the mathematical method. The best corrections were obtained by the SCoRE method. Some recommendations about the experimental setup for functional calibration techniques and the choice of a mathematical method are derived from theoretical considerations about the formulas and the results of the experiment. PMID:24011673

  17. A non-linear mixed effect modelling approach for metabolite correction of the arterial input function in PET studies.

    PubMed

    Veronese, Mattia; Gunn, Roger N; Zamuner, Stefano; Bertoldo, Alessandra

    2013-02-01

    Quantitative PET studies with arterial blood sampling usually require the correction of the measured total plasma activity for the presence of metabolites. In particular, if labelled metabolites are found in the plasma in significant amounts their presence has to be accounted for, because it is the concentration of the parent tracer which is required for data quantification. This is achieved by fitting a Parent Plasma fraction (PPf) model to discrete metabolite measurements. The commonly used method is based on an individual approach, i.e. for each subject the PPf model parameters are estimated from its own metabolite samples, which are, in general, sparse and noisy. This fact can compromise the quality of the reconstructed arterial input functions, and, consequently, affect the quantification of tissue kinetic parameters. In this study, we proposed a Non-Linear Mixed Effect Modelling (NLMEM) approach to describe metabolite kinetics. Since NLMEM has been developed to provide robust parameter estimates in the case of sparse and/or noisy data, it has the potential to be a reliable method for plasma metabolite correction. Three different PET datasets were considered: [11C]-(+)-PHNO (54 scans), [11C]-PIB (22 scans) and [11C]-DASB (30 scans). For each tracer both simulated and measured data were considered and NLMEM performance was compared with that provided by individual analysis. Results showed that NLMEM provided improved estimates of the plasma parent input function over the individual approach when the metabolite data were sparse or contained outliers.

  18. Re-Examining the Properties of the Aqueous Vapor-Liquid Interface Using Dispersion Corrected Density Functional Theory

    SciTech Connect

    Baer, Marcel D.; Mundy, Christopher J.; McGrath, Matthew J.; Kuo, I-F W.; Siepmann, Joern I.; Tobias, Douglas J.

    2011-09-28

    First-principles molecular dynamics simulations, in which the forces are computed from electronic structure calculations, have great potential to provide unique insight into structure, dynamics, electronic properties, and chemistry at aqueous interfaces that is not available from empirical force fields. The majority of current first-principles simulations are driven by forces derived from density functional theory with generalized gradient approximations to the exchange-correlation energy, which do not capture dispersion interactions. We have carried out first-principles molecular dynamics simulations of air-water interfaces employing a particular generalized gradient approximation to the exchange-correlation functional (BLYP), with and without empirical dispersion corrections. We assess the utility of the dispersion corrections by comparison of a variety of structural, dynamic, and thermodynamic properties of bulk and interfacial water with experimental data, as well as other first-principles and force field-based simulations. This work was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

  19. Propagation of soft tissue artifacts to the center of rotation: a model for the correction of functional calibration techniques.

    PubMed

    De Rosario, Helios; Page, Álvaro; Besa, Antonio; Valera, Ángel

    2013-10-18

    This paper presents a mathematical model for the propagation of errors in body segment kinematics to the location of the center of rotation. Three functional calibration techniques, usually employed for the gleno-humeral joint, are studied: the methods based on the pivot of the instantaneous helical axis (PIHA) or the finite helical axis (PFHA), and the "symmetrical center of rotation estimation" (SCoRE). A procedure for correcting the effect of soft tissue artifacts is also proposed, based on the equations of those techniques and a model of the artifact, like the one that can be obtained by double calibration. An experiment with a mechanical analog was performed to validate the procedure and compare the performance of each technique. The raw error (between 57 and 68mm) was reduced by a proportion of between 1:6 and less than 1:15, depending on the artifact model and the mathematical method. The best corrections were obtained by the SCoRE method. Some recommendations about the experimental setup for functional calibration techniques and the choice of a mathematical method are derived from theoretical considerations about the formulas and the results of the experiment.

  20. [Psychophysiological correlates of increasing the work ability of human operator owing to the programmable correction of the functional status].

    PubMed

    Tuzin, P S; Evdokimov, A V; Iznak, A F; Chaianov, N V

    1996-01-01

    There has been studied application of a complex approach to development of automated ways to gain contactless psychophysiological correction of functional status and improvement of performance of working up operators. The psychophysiological support of operator consisted in combined presentation of functional music, surf noise and pulsed dynamic green lighting under a special program built-up on the principle of biological feedback of heart and respiration rates. The individually adaptable audio and visual pulses on the programme showed a rather high efficiency as was confirmed by the change in the set of psychophysiological indices (heart rate, arterial pressure, cutaneogalvanic reaction, accommodation volume, critical rate of flicker fusion, electroencephalogram), and subjective SAM (self-feeling, activity, mood) estimates in the course of extended operator's activity.

  1. Robust motion correction and outlier rejection of in vivo functional MR images of the fetal brain and placenta during maternal hyperoxia

    NASA Astrophysics Data System (ADS)

    You, Wonsang; Serag, Ahmed; Evangelou, Iordanis E.; Andescavage, Nickie; Limperopoulos, Catherine

    2015-03-01

    Subject motion is a major challenge in functional magnetic resonance imaging studies (fMRI) of the fetal brain and placenta during maternal hyperoxia. We propose a motion correction and volume outlier rejection method for the correction of severe motion artifacts in both fetal brain and placenta. The method is optimized to the experimental design by processing different phases of acquisition separately. It also automatically excludes high-motion volumes and all the missing data are regressed from ROI-averaged signals. The results demonstrate that the proposed method is effective in enhancing motion correction in fetal fMRI without large data loss, compared to traditional motion correction methods.

  2. van der Waals forces in density functional theory: Perturbational long-range electron-interaction corrections

    SciTech Connect

    Angyan, Janos G.; Gerber, Iann C.; Savin, Andreas; Toulouse, Julien

    2005-07-15

    Long-range exchange and correlation effects, responsible for the failure of currently used approximate density functionals in describing van der Waals forces, are taken into account explicitly after a separation of the electron-electron interaction in the Hamiltonian into short- and long-range components. We propose a 'range-separated hybrid' functional based on a local density approximation for the short-range exchange-correlation energy, combined with a long-range exact exchange energy. Long-range correlation effects are added by a second-order perturbational treatment. The resulting scheme is general and is particularly well adapted to describe van der Waals complexes, such as rare gas dimers.

  3. Jitter Correction

    NASA Technical Reports Server (NTRS)

    Waegell, Mordecai J.; Palacios, David M.

    2011-01-01

    Jitter_Correct.m is a MATLAB function that automatically measures and corrects inter-frame jitter in an image sequence to a user-specified precision. In addition, the algorithm dynamically adjusts the image sample size to increase the accuracy of the measurement. The Jitter_Correct.m function takes an image sequence with unknown frame-to-frame jitter and computes the translations of each frame (column and row, in pixels) relative to a chosen reference frame with sub-pixel accuracy. The translations are measured using a Cross Correlation Fourier transformation method in which the relative phase of the two transformed images is fit to a plane. The measured translations are then used to correct the inter-frame jitter of the image sequence. The function also dynamically expands the image sample size over which the cross-correlation is measured to increase the accuracy of the measurement. This increases the robustness of the measurement to variable magnitudes of inter-frame jitter

  4. The externally corrected coupled cluster approach with four- and five-body clusters from the CASSCF wave function

    NASA Astrophysics Data System (ADS)

    Xu, Enhua; Li, Shuhua

    2015-03-01

    An externally corrected CCSDt (coupled cluster with singles, doubles, and active triples) approach employing four- and five-body clusters from the complete active space self-consistent field (CASSCF) wave function (denoted as ecCCSDt-CASSCF) is presented. The quadruple and quintuple excitation amplitudes within the active space are extracted from the CASSCF wave function and then fed into the CCSDt-like equations, which can be solved in an iterative way as the standard CCSDt equations. With a size-extensive CASSCF reference function, the ecCCSDt-CASSCF method is size-extensive. When the CASSCF wave function is readily available, the computational cost of the ecCCSDt-CASSCF method scales as the popular CCSD method (if the number of active orbitals is small compared to the total number of orbitals). The ecCCSDt-CASSCF approach has been applied to investigate the potential energy surface for the simultaneous dissociation of two O-H bonds in H2O, the equilibrium distances and spectroscopic constants of 4 diatomic molecules (F2+, O2+, Be2, and NiC), and the reaction barriers for the automerization reaction of cyclobutadiene and the Cl + O3 → ClO + O2 reaction. In most cases, the ecCCSDt-CASSCF approach can provide better results than the CASPT2 (second order perturbation theory with a CASSCF reference function) and CCSDT methods.

  5. Ghost-interaction correction in ensemble density-functional theory for excited states with and without range separation

    NASA Astrophysics Data System (ADS)

    Alam, Md. Mehboob; Knecht, Stefan; Fromager, Emmanuel

    2016-07-01

    Ensemble density-functional theory (eDFT) suffers from the so-called "ghost-interaction" error when approximate exchange-correlation functionals are used. In this work, we present a rigorous ghost-interaction correction (GIC) scheme in the context of range-separated eDFT. The method relies on an exact decomposition of the ensemble short-range exchange-correlation energy into a multideterminantal exact exchange term, which involves the long-range interacting ensemble density matrix, instead of the Kohn-Sham (KS) one, and a complementary density-functional correlation energy. A generalized adiabatic connection formula is derived for the latter. In order to perform practical calculations, the complementary correlation functional is simply modeled by its ground-state local density approximation (LDA), while long-range interacting ground- and excited-state wave functions are obtained self-consistently by combining a long-range configuration-interaction calculation with a short-range LDA potential. We show that the GIC reduces the curvature of approximate range-separated ensemble energies drastically while providing considerably more accurate excitation energies, even for charge-transfer and double excitations. Interestingly, the method performs well also in the context of standard KS-eDFT, which is recovered when the range-separation parameter is set to 0.

  6. Convergence behavior of multireference perturbation theory: Forced degeneracy and optimization partitioning applied to the beryllium atom

    NASA Astrophysics Data System (ADS)

    Finley, James P.; Chaudhuri, Rajat K.; Freed, Karl F.

    1996-07-01

    High-order multireference perturbation theory is applied to the 1S states of the beryllium atom using a reference (model) space composed of the \\|1s22s2> and the \\|1s22p2> configuration-state functions (CSF's), a system that is known to yield divergent expansions using Mo/ller-Plesset and Epstein-Nesbet partitioning methods. Computations of the eigenvalues are made through 40th order using forced degeneracy (FD) partitioning and the recently introduced optimization (OPT) partitioning. The former forces the 2s and 2p orbitals to be degenerate in zeroth order, while the latter chooses optimal zeroth-order energies of the (few) most important states. Our methodology employs simple models for understanding and suggesting remedies for unsuitable choices of reference spaces and partitioning methods. By examining a two-state model composed of only the \\|1s22p2> and \\|1s22s3s> states of the beryllium atom, it is demonstrated that the full computation with 1323 CSF's can converge only if the zeroth-order energy of the \\|1s22s3s> Rydberg state from the orthogonal space lies below the zeroth-order energy of the \\|1s22p2> CSF from the reference space. Thus convergence in this case requires a zeroth-order spectral overlap between the orthogonal and reference spaces. The FD partitioning is not capable of generating this type of spectral overlap and thus yields a divergent expansion. However, the expansion is actually asymptotically convergent, with divergent behavior not displayed until the 11th order because the \\|1s22s3s> Rydberg state is only weakly coupled with the \\|1s22p2> CSF and because these states are energetically well separated in zeroth order. The OPT partitioning chooses the correct zeroth-order energy ordering and thus yields a convergent expansion that is also very accurate in low orders compared to the exact solution within the basis.

  7. FNAS phase partitions

    NASA Technical Reports Server (NTRS)

    Vanalstine, James M.

    1993-01-01

    Project NAS8-36955 D.O. #100 initially involved the following tasks: (1) evaluation of various coatings' ability to control wall wetting and surface zeta potential expression; (2) testing various methods to mix and control the demixing of phase systems; and (3) videomicroscopic investigation of cell partition. Three complementary areas were identified for modification and extension of the original contract. They were: (1) identification of new supports for column cell partition; (2) electrokinetic detection of protein adsorption; and (3) emulsion studies related to bioseparations.

  8. Charge localization in a diamine cation provides a test of energy functionals and self-interaction correction

    PubMed Central

    Cheng, Xinxin; Zhang, Yao; Jónsson, Elvar; Jónsson, Hannes; Weber, Peter M.

    2016-01-01

    Density functional theory (DFT) is widely applied in calculations of molecules and materials. Yet, it suffers from a well-known over-emphasis on charge delocalization arising from self-interaction error that destabilizes localized states. Here, using the symmetric diamine N,N′-dimethylpiperazine as a model, we have experimentally determined the relative energy of a state with positive charge localized on one of the two nitrogen atoms, and a state with positive charge delocalized over both nitrogen atoms. The charge-localized state was found to be 0.33 (0.04) eV higher in energy than the charge-delocalized state. This provides an important test of theoretical approaches to electronic structure calculations. Calculations with all DFT functionals commonly used today, including hybrid functionals with exact exchange, fail to predict a stable charge-localized state. However, the application of an explicit self-interaction correction to a semi-local functional identifies both states and gives relative energy in excellent agreement with both experiment and CCSD(T) calculations. PMID:26980327

  9. Correction of motion artifacts and serial correlations for real-time functional near-infrared spectroscopy.

    PubMed

    Barker, Jeffrey W; Rosso, Andrea L; Sparto, Patrick J; Huppert, Theodore J

    2016-07-01

    Functional near-infrared spectroscopy (fNIRS) is a relatively low-cost, portable, noninvasive neuroimaging technique for measuring task-evoked hemodynamic changes in the brain. Because fNIRS can be applied to a wide range of populations, such as children or infants, and under a variety of study conditions, including those involving physical movement, gait, or balance, fNIRS data are often confounded by motion artifacts. Furthermore, the high sampling rate of fNIRS leads to high temporal autocorrelation due to systemic physiology. These two factors can reduce the sensitivity and specificity of detecting hemodynamic changes. In a previous work, we showed that these factors could be mitigated by autoregressive-based prewhitening followed by the application of an iterative reweighted least squares algorithm offline. This current work extends these same ideas to real-time analysis of brain signals by modifying the linear Kalman filter, resulting in an algorithm for online estimation that is robust to systemic physiology and motion artifacts. We evaluated the performance of the proposed method via simulations of evoked hemodynamics that were added to experimental resting-state data, which provided realistic fNIRS noise. Last, we applied the method post hoc to data from a standing balance task. Overall, the new method showed good agreement with the analogous offline algorithm, in which both methods outperformed ordinary least squares methods.

  10. Correction of motion artifacts and serial correlations for real-time functional near-infrared spectroscopy.

    PubMed

    Barker, Jeffrey W; Rosso, Andrea L; Sparto, Patrick J; Huppert, Theodore J

    2016-07-01

    Functional near-infrared spectroscopy (fNIRS) is a relatively low-cost, portable, noninvasive neuroimaging technique for measuring task-evoked hemodynamic changes in the brain. Because fNIRS can be applied to a wide range of populations, such as children or infants, and under a variety of study conditions, including those involving physical movement, gait, or balance, fNIRS data are often confounded by motion artifacts. Furthermore, the high sampling rate of fNIRS leads to high temporal autocorrelation due to systemic physiology. These two factors can reduce the sensitivity and specificity of detecting hemodynamic changes. In a previous work, we showed that these factors could be mitigated by autoregressive-based prewhitening followed by the application of an iterative reweighted least squares algorithm offline. This current work extends these same ideas to real-time analysis of brain signals by modifying the linear Kalman filter, resulting in an algorithm for online estimation that is robust to systemic physiology and motion artifacts. We evaluated the performance of the proposed method via simulations of evoked hemodynamics that were added to experimental resting-state data, which provided realistic fNIRS noise. Last, we applied the method post hoc to data from a standing balance task. Overall, the new method showed good agreement with the analogous offline algorithm, in which both methods outperformed ordinary least squares methods. PMID:27226974

  11. Nonredundant function of zeins and their correct stoichiometric ratio drive protein body formation in maize endosperm.

    PubMed

    Guo, Xiaomei; Yuan, Lingling; Chen, Han; Sato, Shirley J; Clemente, Thomas E; Holding, David R

    2013-07-01

    Zeins, the maize (Zea mays) prolamin storage proteins, accumulate at very high levels in developing endosperm in endoplasmic reticulum membrane-bound protein bodies. Products of the multigene α-zein families and the single-gene γ-zein family are arranged in the central hydrophobic core and the cross-linked protein body periphery, respectively, but little is known of the specific roles of family members in protein body formation. Here, we used RNA interference suppression of different zein subclasses to abolish vitreous endosperm formation through a variety of effects on protein body density, size, and morphology. We showed that the 27-kilodalton (kD) γ-zein controls protein body initiation but is not involved in protein body filling. Conversely, other γ-zein family members function more in protein body expansion and not in protein body initiation. Reduction in both 19- and 22-kD α-zein subfamilies severely restricted protein body expansion but did not induce morphological abnormalities, which result from reduction of only the 22-kD α-zein class. Concomitant reduction of all zein classes resulted in severe reduction in protein body number but normal protein body size and morphology. PMID:23677936

  12. [The nasal valve area: structure, function, clinical aspects and treatment. Sulsenti's technic for correction of valve deformities].

    PubMed

    Sulsenti, G; Palma, P

    1989-01-01

    nostrils as well as to properly correct the columella and naso-labial angle. The technique, therefore, permits maximum correction of valvular deformities with the concomitant functional modification of any abnormalities of the nasal pyramid.

  13. Use of kinase inhibitors to correct ΔF508-CFTR function.

    PubMed

    Trzcinska-Daneluti, Agata M; Nguyen, Leo; Jiang, Chong; Fladd, Christopher; Uehling, David; Prakesch, Michael; Al-awar, Rima; Rotin, Daniela

    2012-09-01

    The most common mutation in cystic fibrosis (CF) is a deletion of Phe at position 508 (ΔF508-CFTR). ΔF508-CFTR is a trafficking mutant that is retained in the ER, unable to reach the plasma membrane. To identify compounds and drugs that rescue this trafficking defect, we screened a kinase inhibitor library enriched for small molecules already in the clinic or in clinical trials for the treatment of cancer and inflammation, using our recently developed high-content screen technology (Trzcinska-Daneluti et al. Mol. Cell. Proteomics 8:780, 2009). The top hits of the screen were further validated by (1) biochemical analysis to demonstrate the presence of mature (Band C) ΔF508-CFTR, (2) flow cytometry to reveal the presence of ΔF508-CFTR at the cell surface, (3) short-circuit current (Isc) analysis in Ussing chambers to show restoration of function of the rescued ΔF508-CFTR in epithelial MDCK cells stably expressing this mutant (including EC(50) determinations), and importantly (4) Isc analysis of Human Bronchial Epithelial (HBE) cells harvested from homozygote ΔF508-CFTR transplant patients. Interestingly, several inhibitors of receptor Tyr kinases (RTKs), such as SU5402 and SU6668 (which target FGFRs, VEGFR, and PDGFR) exhibited strong rescue of ΔF508-CFTR, as did several inhibitors of the Ras/Raf/MEK/ERK or p38 pathways (e.g. (5Z)-7-oxozeaenol). Prominent rescue was also observed by inhibitors of GSK-3β (e.g. GSK-3β Inhibitor II and Kenpaullone). These results identify several kinase inhibitors that can rescue ΔF508-CFTR to various degrees, and suggest that use of compounds or drugs already in the clinic or in clinical trials for other diseases can expedite delivery of treatment for CF patients.

  14. Correction of biochemical and functional disorders in brain ischaemia with laser therapy

    NASA Astrophysics Data System (ADS)

    Musienko, Julia I.; Nechipurenko, Natalia I.; Vasilevskaya, Ludmila A.

    2005-08-01

    Application of intravenous laser irradiation of blood (ILIB) is considered to be the most effective method of laser therapy and its application is expedient pathogenetically in the ischemic disturbances. The aim of this study is to investigate ILIB influence with red helium-neon laser (HNL) with 630 nm wavelength and different powers on blood oxygen transport (BOT), cerebral and dermal microhaemodynamics (MGD), hydro-ion balance in normal rabbits and after modeling of local ischemia of brain (LIB). Experimental cerebral ischemia is characterized by development of BOT disturbance, ionic disbalance and edema in the ischemic brain region. Microcirculation disturbances with worsening of the cerebral and dermal MHD were revealed. ILIB with HNL radiation of 2.5 and 4.5 mW powers provokes dehydratation of brain structure alone with the K+, Na+ concentration decreasing and hemoglobin-oxygen affinity increasing in intact group of animals. There was not revealed marked changes of cerebral MHD condition here. Using of ILIB in rabbits after LIB contributes for improving function of BOT, normalizing of water content in all cerebral structures compared to operated animals. Preventive ILIB provoked improvement of speckl-optical parameters and marked protective effect on microhaemodynamics processes in superficial brain structures. HNL radiation with 1.0 mW power results in worsening of oxygen transport, cerebral and skin MHD, hydro-ion homeostasis in animals with LIB modeling. Thus, laser haemotherapy contributes for improving of hydro-ion status, blood oxygen transport and cerebral microcirculation in brain ischemia, what allows considering that helium-neon radiation with the pointed regimen is substantiated pathogenetically in brain ischaemia.

  15. Electronic structure of novel charge transfer compounds: application of Fermi orbital self-interaction corrected density functional theory

    NASA Astrophysics Data System (ADS)

    Hahn, Torsten; Rückerl, Florian; Liebing, Simon; Pederson, Mark

    We present our experimental and theoretical results on novel Picene/F4TCNQ and Manganese-Phthalocyanine/F4TCNQ donor / acceptor systems. We apply the recently developed Fermi-orbital based approach for self-interaction corrected density functional theory (FO-SIC DFT) to these materials and compare the results to standard DFT calculations and to experimental data obtained by photoemission spectroscopy. We focus our analysis on the description of the magnitude of the ground state charge transfer and on the details of the formed hybrid orbitals. Further, we show that for weakly bound donor / acceptor systems the FO-SIC approach delivers a more realistic description of the electronic structure compared to standard DFT calculations Support by DFG FOR1154 is greatly acknowledged.

  16. Political Correctness--Correct?

    ERIC Educational Resources Information Center

    Boase, Paul H.

    1993-01-01

    Examines the phenomenon of political correctness, its roots and objectives, and its successes and failures in coping with the conflicts and clashes of multicultural campuses. Argues that speech codes indicate failure in academia's primary mission to civilize and educate through talk, discussion, thought,166 and persuasion. (SR)

  17. [The recovery of cognitive functions in the patients with organic brain disorders as a component of combined rehabilitation with the use of the method of bioacoustic correction].

    PubMed

    Konstantinov, K V; Gritsyshina, M A; Nefedova, G É

    2012-01-01

    This study was designed to follow up dynamics of the recovery of cognitive functions after comprehensive medical rehabilitation of the patients with organic brain disorders using a bioacoutsic correction technique. A peculiar feature of this method is it allows for involuntary self-regulation of the functional state of the central nervous system and therefore can be used to treat patients experiencing cognitive problems. It was shown that the application of the method of bioacoustic correction promotes restoration of cognitive functions, reduces anxiety, and normalizes parameters of electroencephalograms. PMID:22993949

  18. A localized orbital analysis of the thermochemical errors in hybrid density functional theory: achieving chemical accuracy via a simple empirical correction scheme.

    PubMed

    Friesner, Richard A; Knoll, Eric H; Cao, Yixiang

    2006-09-28

    This paper describes an empirical localized orbital correction model which improves the accuracy of density functional theory (DFT) methods for the prediction of thermochemical properties for molecules of first and second row elements. The B3LYP localized orbital correction version of the model improves B3LYP DFT atomization energy calculations on the G3 data set of 222 molecules from a mean absolute deviation (MAD) from experiment of 4.8 to 0.8 kcal/mol. The almost complete elimination of large outliers and the substantial reduction in MAD yield overall results comparable to the G3 wave-function-based method; furthermore, the new model has zero additional computational cost beyond standard DFT calculations. The following four classes of correction parameters are applied to a molecule based on standard valence bond assignments: corrections to atoms, corrections to individual bonds, corrections for neighboring bonds of a given bond, and radical environmental corrections. Although the model is heuristic and is based on a 22 parameter multiple linear regression to experimental errors, each of the parameters is justified on physical grounds, and each provides insight into the fundamental limitations of DFT, most importantly the failure of current DFT methods to accurately account for nondynamical electron correlation.

  19. Multimedia partitioning of dioxin

    SciTech Connect

    Travis, C.C.; Hattemer-Frey, H.A.

    1988-01-01

    The general population is continuously being exposed to trace amounts of dioxin as exemplified by the fact that virtually all human adipose tissue samples contain dioxin levels of three parts per trillion (ppT) or greater. The purpose of this study is to investigate how 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is partitioned in the environment and to identify the major pathways of human exposure. 61 refs., 6 tabs.

  20. Non-linear corrections to the time-covariance function derived from a multi-state chemical master equation.

    PubMed

    Scott, M

    2012-08-01

    The time-covariance function captures the dynamics of biochemical fluctuations and contains important information about the underlying kinetic rate parameters. Intrinsic fluctuations in biochemical reaction networks are typically modelled using a master equation formalism. In general, the equation cannot be solved exactly and approximation methods are required. For small fluctuations close to equilibrium, a linearisation of the dynamics provides a very good description of the relaxation of the time-covariance function. As the number of molecules in the system decrease, deviations from the linear theory appear. Carrying out a systematic perturbation expansion of the master equation to capture these effects results in formidable algebra; however, symbolic mathematics packages considerably expedite the computation. The authors demonstrate that non-linear effects can reveal features of the underlying dynamics, such as reaction stoichiometry, not available in linearised theory. Furthermore, in models that exhibit noise-induced oscillations, non-linear corrections result in a shift in the base frequency along with the appearance of a secondary harmonic.

  1. Design of an organic zeolite toward the selective adsorption of small molecules at the dispersion corrected density functional theory level.

    PubMed

    Li, Wenliang; Gahungu, Godefroid; Zhang, Jingping; Hao, Lizhu

    2009-12-31

    Tris(o-phenylenedioxy)cyclotriphosphazene (TPP) became the compound of choice to investigate the structural features of organic zeolites and their potential applications as soft materials. A van der Waals crystal of the TPP analogue (host) with the thiophene side fragment tris(3,4-thiophenedioxy)cyclotriphosphazene (TTP) was designed to investigate the selective adsorption among some common gases (guest): methane (CH(4)), carbon dioxide (CO(2)), nitrogen (N(2)), or hydrogen (H(2)). The crystal structure of TTP was modeled by applying minimization methods using the COMPASS (condensed-phase optimized molecular potentials for atomic simulation studies) force field. Interaction energies and structural properties of van der Waals complexes of the crystal of TTP and gas molecules were studied using the dispersion corrected density functional theory (DFT-D). The proper functional and basis set were selected after comparing with benchmark data of the coupled-cluster calculations with singles, doubles, and perturbative triple excitations [CCSD(T)] estimated at the complete basis set (CBS) limit. On the basis of our results, the interaction energy between the host and the guest molecules was predicted in the increasing order of host-H(2) < host-N(2) < host-CH(4) < host-CO(2), suggesting the designed TTP is a good candidate as an organic zeolite for potential fuel storage, hydrogen purification, carbon dioxide removal from the air, as well as safety care in a coal mine. PMID:19968318

  2. [Transpiration water consumption of young Platycladus orientalis and Robinia pseudoacacia trees and their correction functions under different water supply].

    PubMed

    Wang, Jinxin; Huang, Baolong; Wang, Mingchun; Wang, Dihai

    2005-03-01

    Through artificial water control in the shed of rain-free, this paper studied the physiological water requirement patterns of 2-3 years old Platycladus orientalis and Robinia pseudoacacia trees during their growth period, and the relationships between their transpiration water consumption and soil water supply. The results showed that the transpiration water consumption of Robinia pseudoacacia was increased with increasing soil water supply within the range of 40%-100% of field water-holding capacity. Its maximum transpiration water consumption was at the early and accelerating growth stages, accounted for 80.5% of total annual water consumption. The transpiration water consumption of Robinia pseudoacacia was 5.13 times as much as that of Platycladus orientalis. Platycladus orientalis had a peak value of transpiration water consumption when the soil moisture content was 40%-100% of field water-holding capacity. Its transpiration water consumption was the maximum at accelerating growth stage, accounted for 46.27% of total annual water consumption, next at later growth stage, and relatively small at early growth stage. The correction functions of transpiration water consumption to soil water supply and the time-soil moisture functions of practical transpiration water consumption under insufficient water supply for two test species were put forward for the first time.

  3. Kaluza-Klein masses in nonprime orbifolds: Z{sub 12-I} compactification and threshold correction

    SciTech Connect

    Kim, Jihn E.; Kyae, Bumseok

    2008-05-15

    Analyzing the one-loop partition function, we discuss possible Kaluza-Klein (KK) states in the orbifold compactification of the heterotic string theory, toward the application to the threshold correction. The KK massive states associated with (relatively) large extra dimensions can arise only in nonprime orbifolds. The Gliozzi-Scherk-Olive (GSO) projection condition by a shift vector V{sup I} is somewhat relaxed above the compactification scale 1/R. We also present the other condition on Wilson line W, P{center_dot}W=integer. With the knowledge of the partition function, we obtain the threshold corrections to gauge couplings, which include the Wilson line effects. We point out the differences in string and field theoretic orbifolds.

  4. CO2 adsorption on TiO2(101) anatase: a dispersion-corrected density functional theory study.

    PubMed

    Sorescu, Dan C; Al-Saidi, Wissam A; Jordan, Kenneth D

    2011-09-28

    Adsorption, diffusion, and dissociation of CO(2) on the anatase (101) surface were investigated using dispersion-corrected density functional theory. On the oxidized surface several different local minima were identified of which the most stable corresponds to a CO(2) molecule adsorbed at a five-fold coordinated Ti site in a tilted configuration. Surface diffusion is characterized by relatively small activation barriers. Preferential diffusion takes place along Ti rows and involves a cartwheel type of motion. The presence of a bridging oxygen defect or a surface interstitial Ti atom allows creation of several new strong binding configurations the most stable of which have bent CO(2) structures with simultaneous bonding to two surface Ti atoms. Subsurface oxygen vacancy or interstitial Ti defects are found to enhance the bonding of CO(2) molecules to the surface. CO(2) dissociation from these defect sites is calculated to be exothermic with barriers less than 21 kcal/mol. The use of such defects for catalytic activation of CO(2) on anatase (101) surface would require a mechanism for their regeneration.

  5. Functional renormalization group study of orbital fluctuation mediated superconductivity: Impact of the electron-boson coupling vertex corrections

    NASA Astrophysics Data System (ADS)

    Tazai, Rina; Yamakawa, Youichi; Tsuchiizu, Masahisa; Kontani, Hiroshi

    2016-09-01

    In various multiorbital systems, the emergence of the orbital fluctuations and their role on the pairing mechanism attract increasing attention. To achieve deep understanding on these issues, we perform a functional renormalization group (fRG) study for the two-orbital Hubbard model. The vertex corrections for the electron-boson coupling (U -VC), which are dropped in the Migdal-Eliashberg gap equation, are obtained by solving the RG equation. We reveal that the dressed electron-boson coupling for the charge channel Ûeffc becomes much larger than the bare Coulomb interaction Û 0 due to the U -VC in the presence of moderate spin fluctuations. For this reason, the attractive pairing interaction due to the charge or orbital fluctuations is enlarged by the factor (Ûeffc/Û0) 2≫1 . In contrast, the spin fluctuation pairing interaction is suppressed by the spin-channel U -VC, because of the relation Ûeffs≪Û 0 . The present study demonstrates that the orbital or charge fluctuation pairing mechanism can be realized in various multiorbital systems thanks to the U -VC, such as in Fe-based superconductors.

  6. Pressure dependent stability and structure of carbon dioxide--a density functional study including long-range corrections.

    PubMed

    Gohr, Sebastian; Grimme, Stefan; Söhnel, Tilo; Paulus, Beate; Schwerdtfeger, Peter

    2013-11-01

    First-principles density functional theory (DFT) is used to study the solid-state modifications of carbon dioxide up to pressures of 60 GPa. All known molecular CO2 structures are investigated in this pressure range, as well as three non-molecular modifications. To account for long-range van der Waals interactions, the dispersion corrected DFT method developed by Grimme and co-workers (DFT-D3) is applied. We find that the DFT-D3 method substantially improves the results compared to the uncorrected DFT methods for the molecular carbon dioxide crystals. Enthalpies at 0 K and cohesive energies support only one possibility of the available experimental solutions for the structure of phase IV: the R3c modification, proposed by Datchi and co-workers [Phys. Rev. Lett. 103, 185701 (2009)]. Furthermore, comparing bulk moduli with experimental values, we cannot reproduce the quite large--rather typical for covalent crystal structures--experimental values for the molecular phases II and III. PMID:24206310

  7. Reaching a Uniform Accuracy for Complex Molecular Systems: Long-Range-Corrected XYG3 Doubly Hybrid Density Functional.

    PubMed

    Zhang, Igor Ying; Xu, Xin

    2013-05-16

    An unbiased understanding of complex molecular systems from first-principles critically demands theoretical methods with uniform accuracy for diverse interactions with different natures covering short-, medium-, and long-range correlations. Among the state-of-the-art density functional approximations (DFAs), doubly hybrid (DH) DFAs (e.g., XYG3 in this Letter) provide a remarkable improvement over the conventional DFAs (e.g., B3LYP in this Letter). Even though XYG3 works quite well in many cases of noncovalent bonding interactions (NCIs), it is incomplete in describing the pure long-range dispersive interactions. Here, we address such concerns by adding a scaled long-range contribution from the second-order perturbation theory (PT2). The long-range-corrected XYG3 (lrc-XYG3) is proposed without reparameterizing the three parameters in the original XYG3. Due to its overall excellent performance for all testing sets constructed for various purposes, lrc-XYG3 is the recommended method, which is expected to provide a balanced description of diverse interactions in complex molecular systems. PMID:26282977

  8. Successes and failures of Hubbard-corrected density functional theory. The case of Mg doped LiCoO2

    DOE PAGES

    Santana Palacio, Juan A.; Kim, Jeongnim; Kent, Paul R.; Reboredo, Fernando A.

    2014-10-28

    We have evaluated the successes and failures of the Hubbard-corrected density functional theory approach to study Mg doping of LiCoO2. We computed the effect of the U parameter on the energetic, geometric, and electronic properties of two possible doping mechanisms: (1) substitution of Mg onto a Co (or Li) site with an associated impurity state and (2) formation of impurity-state-free complexes of substitutional Mg and point defects in LiCoO2. We find that formation of impurity states results in changes on the valency of Co in LiCoO2. Variation of the Co U shifts the energy of the impurity state, resulting inmore » energetic, geometric, and electronic properties that depend significantly on the specific value of U. In contrast, the properties of the impurity-state-free complexes are insensitive to U. These results identify reasons for the strong dependence on the doping properties on the chosen value of U and for the overall difficulty of achieving agreement with the experimentally known energetic and electronic properties of doped transition metal oxides such as LiCoO2.« less

  9. ASXL1 mutation correction by CRISPR/Cas9 restores gene function in leukemia cells and increases survival in mouse xenografts

    PubMed Central

    Valletta, Simona; Dolatshad, Hamid; Bartenstein, Matthias; Yip, Bon Ham; Bello, Erica; Gordon, Shanisha; Yu, Yiting; Shaw, Jacqueline; Roy, Swagata; Scifo, Laura; Schuh, Anna; Pellagatti, Andrea; Fulga, Tudor A.; Verma, Amit; Boultwood, Jacqueline

    2015-01-01

    Recurrent somatic mutations of the epigenetic modifier and tumor suppressor ASXL1 are common in myeloid malignancies, including chronic myeloid leukemia (CML), and are associated with poor clinical outcome. CRISPR/Cas9 has recently emerged as a powerful and versatile genome editing tool for genome engineering in various species. We have used the CRISPR/Cas9 system to correct the ASXL1 homozygous nonsense mutation present in the CML cell line KBM5, which lacks ASXL1 protein expression. CRISPR/Cas9-mediated ASXL1 homozygous correction resulted in protein re-expression with restored normal function, including down-regulation of Polycomb repressive complex 2 target genes. Significantly reduced cell growth and increased myeloid differentiation were observed in ASXL1 mutation-corrected cells, providing new insights into the role of ASXL1 in human myeloid cell differentiation. Mice xenografted with mutation-corrected KBM5 cells showed significantly longer survival than uncorrected xenografts. These results show that the sole correction of a driver mutation in leukemia cells increases survival in vivo in mice. This study provides proof-of-concept for driver gene mutation correction via CRISPR/Cas9 technology in human leukemia cells and presents a strategy to illuminate the impact of oncogenic mutations on cellular function and survival. PMID:26623729

  10. MULTIVARIATE KERNEL PARTITION PROCESS MIXTURES

    PubMed Central

    Dunson, David B.

    2013-01-01

    Mixtures provide a useful approach for relaxing parametric assumptions. Discrete mixture models induce clusters, typically with the same cluster allocation for each parameter in multivariate cases. As a more flexible approach that facilitates sparse nonparametric modeling of multivariate random effects distributions, this article proposes a kernel partition process (KPP) in which the cluster allocation varies for different parameters. The KPP is shown to be the driving measure for a multivariate ordered Chinese restaurant process that induces a highly-flexible dependence structure in local clustering. This structure allows the relative locations of the random effects to inform the clustering process, with spatially-proximal random effects likely to be assigned the same cluster index. An exact block Gibbs sampler is developed for posterior computation, avoiding truncation of the infinite measure. The methods are applied to hormone curve data, and a dependent KPP is proposed for classification from functional predictors. PMID:24478563

  11. Influence of size-corrected bound-electron contribution on nanometric silver dielectric function. Sizing through optical extinction spectroscopy

    NASA Astrophysics Data System (ADS)

    Santillán, J. M. J.; Videla, F. A.; Fernández van Raap, M. B.; Muraca, D.; Scaffardi, L. B.; Schinca, D. C.

    2013-10-01

    The study of metal nanoparticles (NPs) is of great interest due to their ability to enhance optical fields on the nanometric scale, which makes them interesting for various applications in several fields of science and technology. In particular, their optical properties depend on the dielectric function of the metal, its size, shape and surrounding environment. This work analyses the contributions of free and bound electrons to the complex dielectric function of spherical silver NPs and their influence on the optical extinction spectra. The contribution of free electrons is usually corrected for particle size under 10 nm, introducing a modification of the damping constant to account for the extra collisions with the particle's boundary. For the contribution of bound electrons, we considered the interband transitions from the d-band to the conduction band including the size dependence of the electronic density states for radii below 2 nm. Bearing in mind these specific modifications, it was possible to determine optical and band energy parameters by fitting the bulk complex dielectric function. The results obtained from the optimum fit are: Kbulk = 2 × 1024 (coefficient for bound-electron contribution), Eg = 1.91 eV (gap energy), EF = 4.12 eV (Fermi energy), and γb = 1.5 × 1014 Hz (damping constant for bound electrons). Based on this size-dependent dielectric function, extinction spectra of silver particles in the nanometric-subnanometric radius range can be calculated using Mie's theory, and its size behaviour analysed. These studies are applied to fit experimental extinction spectrum of very small spherical particles fabricated by fs laser ablation of a solid target in water. From the fitting, the structure and size distribution of core radius and shell thickness of the colloidal suspension could be determined. The spectroscopic results suggest that the colloidal suspension is composed by two types of structures: bare core and core-shell. The former is composed

  12. Energy partitioning schemes: a dilemma.

    PubMed

    Mayer, I

    2007-01-01

    Two closely related energy partitioning schemes, in which the total energy is presented as a sum of atomic and diatomic contributions by using the "atomic decomposition of identity", are compared on the example of N,N-dimethylformamide, a simple but chemically rich molecule. Both schemes account for different intramolecular interactions, for instance they identify the weak C-H...O intramolecular interactions, but give completely different numbers. (The energy decomposition scheme based on the virial theorem is also considered.) The comparison of the two schemes resulted in a dilemma which is especially striking when these schemes are applied for molecules distorted from their equilibrium structures: one either gets numbers which are "on the chemical scale" and have quite appealing values at the equilibrium molecular geometries, but exhibiting a counter-intuitive distance dependence (the two-center energy components increase in absolute value with the increase of the interatomic distances)--or numbers with too large absolute values but "correct" distance behaviour. The problem is connected with the quick decay of the diatomic kinetic energy components.

  13. Energy partitioning schemes: a dilemma.

    PubMed

    Mayer, I

    2007-01-01

    Two closely related energy partitioning schemes, in which the total energy is presented as a sum of atomic and diatomic contributions by using the "atomic decomposition of identity", are compared on the example of N,N-dimethylformamide, a simple but chemically rich molecule. Both schemes account for different intramolecular interactions, for instance they identify the weak C-H...O intramolecular interactions, but give completely different numbers. (The energy decomposition scheme based on the virial theorem is also considered.) The comparison of the two schemes resulted in a dilemma which is especially striking when these schemes are applied for molecules distorted from their equilibrium structures: one either gets numbers which are "on the chemical scale" and have quite appealing values at the equilibrium molecular geometries, but exhibiting a counter-intuitive distance dependence (the two-center energy components increase in absolute value with the increase of the interatomic distances)--or numbers with too large absolute values but "correct" distance behaviour. The problem is connected with the quick decay of the diatomic kinetic energy components. PMID:17328441

  14. Force correcting atom centred potentials for generalised gradient approximated density functional theory: Approaching hybrid functional accuracy for geometries and harmonic frequencies in small chlorofluorocarbons

    NASA Astrophysics Data System (ADS)

    Anatole von Lilienfeld, O.

    2013-08-01

    Generalised gradient approximated (GGA) density functional theory (DFT) typically overestimates polarisability and bond-lengths, and underestimates force constants of covalent bonds. To overcome this problem we show that one can use empirical force correcting atom centred potentials (FCACPs), parametrised for every nuclear species. Parameters are obtained through minimisation of a penalty functional that explicitly encodes hybrid DFT forces and static polarisabilities of reference molecules. For hydrogen, fluorine, chlorine and carbon the respective reference molecules consist of H2, F2, Cl2 and CH4. The transferability of this approach is assessed for harmonic frequencies in a small set of chlorofluorocarbon molecules. Numerical evidence, gathered for CF4, CCl4, CCl3F, CCl2F2, CClF3, ClF, HF, HCl, CFH3, CF2H2, CF3H, CHCl3, CH2Cl2 and CH3Cl indicates that the GGA+FCACP level of theory yields harmonic frequencies that are significantly more consistent with hybrid DFT values, as well as slightly reduced molecular polarisability.

  15. Prospective motion correction of 3D echo-planar imaging data for functional MRI using optical tracking.

    PubMed

    Todd, Nick; Josephs, Oliver; Callaghan, Martina F; Lutti, Antoine; Weiskopf, Nikolaus

    2015-06-01

    We evaluated the performance of an optical camera based prospective motion correction (PMC) system in improving the quality of 3D echo-planar imaging functional MRI data. An optical camera and external marker were used to dynamically track the head movement of subjects during fMRI scanning. PMC was performed by using the motion information to dynamically update the sequence's RF excitation and gradient waveforms such that the field-of-view was realigned to match the subject's head movement. Task-free fMRI experiments on five healthy volunteers followed a 2 × 2 × 3 factorial design with the following factors: PMC on or off; 3.0mm or 1.5mm isotropic resolution; and no, slow, or fast head movements. Visual and motor fMRI experiments were additionally performed on one of the volunteers at 1.5mm resolution comparing PMC on vs PMC off for no and slow head movements. Metrics were developed to quantify the amount of motion as it occurred relative to k-space data acquisition. The motion quantification metric collapsed the very rich camera tracking data into one scalar value for each image volume that was strongly predictive of motion-induced artifacts. The PMC system did not introduce extraneous artifacts for the no motion conditions and improved the time series temporal signal-to-noise by 30% to 40% for all combinations of low/high resolution and slow/fast head movement relative to the standard acquisition with no prospective correction. The numbers of activated voxels (p<0.001, uncorrected) in both task-based experiments were comparable for the no motion cases and increased by 78% and 330%, respectively, for PMC on versus PMC off in the slow motion cases. The PMC system is a robust solution to decrease the motion sensitivity of multi-shot 3D EPI sequences and thereby overcome one of the main roadblocks to their widespread use in fMRI studies.

  16. Prospective motion correction of 3D echo-planar imaging data for functional MRI using optical tracking

    PubMed Central

    Todd, Nick; Josephs, Oliver; Callaghan, Martina F.; Lutti, Antoine; Weiskopf, Nikolaus

    2015-01-01

    We evaluated the performance of an optical camera based prospective motion correction (PMC) system in improving the quality of 3D echo-planar imaging functional MRI data. An optical camera and external marker were used to dynamically track the head movement of subjects during fMRI scanning. PMC was performed by using the motion information to dynamically update the sequence's RF excitation and gradient waveforms such that the field-of-view was realigned to match the subject's head movement. Task-free fMRI experiments on five healthy volunteers followed a 2 × 2 × 3 factorial design with the following factors: PMC on or off; 3.0 mm or 1.5 mm isotropic resolution; and no, slow, or fast head movements. Visual and motor fMRI experiments were additionally performed on one of the volunteers at 1.5 mm resolution comparing PMC on vs PMC off for no and slow head movements. Metrics were developed to quantify the amount of motion as it occurred relative to k-space data acquisition. The motion quantification metric collapsed the very rich camera tracking data into one scalar value for each image volume that was strongly predictive of motion-induced artifacts. The PMC system did not introduce extraneous artifacts for the no motion conditions and improved the time series temporal signal-to-noise by 30% to 40% for all combinations of low/high resolution and slow/fast head movement relative to the standard acquisition with no prospective correction. The numbers of activated voxels (p < 0.001, uncorrected) in both task-based experiments were comparable for the no motion cases and increased by 78% and 330%, respectively, for PMC on versus PMC off in the slow motion cases. The PMC system is a robust solution to decrease the motion sensitivity of multi-shot 3D EPI sequences and thereby overcome one of the main roadblocks to their widespread use in fMRI studies. PMID:25783205

  17. Interaction of n-octyl β,D-glucopyranoside with giant magnetic-fluid-loaded phosphatidylcholine vesicles: direct visualization of membrane curvature fluctuations as a function of surfactant partitioning between water and lipid bilayer.

    PubMed

    Ménager, Christine; Guemghar, Dihya; Cabuil, Valérie; Lesieur, Sylviane

    2010-10-01

    The present study deals with the morphological modifications of giant dioleoyl phosphatidylcholine vesicles (DOPC GUVs) induced by the nonionic surfactant n-octyl β,D-glucopyranoside at sublytic levels, i.e., in the first steps of the vesicle-to-micelle transition process, when surfactant inserts into the vesicle bilayer without disruption. Experimental conditions were perfected to exactly control the surfactant bilayer composition of the vesicles, in line with former work focused on the mechanical properties of the membrane of magnetic-fluid-loaded DOPC GUVs submitted to a magnetic field. The purpose here was to systematically examine, in the absence of any external mechanical constraint, the dynamics of giant vesicle shape and membrane deformations as a function of surfactant partitioning between the aqueous phase and the lipid membrane, beforehand established by turbidity measurements from small unilamellar vesicles. PMID:20825201

  18. STRUCTURAL DYNAMICS OF METAL PARTITIONING TO MINERAL SURFACES

    EPA Science Inventory

    The conceptual understanding of surface complexation reactions that control trace element partitioning to mineral surfaces is limited by the assumption that the solid reactant possesses a finite, time-invariant population of surface functional groups. This assumption has limited...

  19. First-order exchange and self-energy corrections to static density correlation function of a spin-polarized two-dimensional quantum electron fluid

    SciTech Connect

    Arora, Priya; Moudgil, R. K.; Bhukal, Nisha

    2015-05-15

    Static density-density correlation function has been calculated for a spin-polarized two-dimensional quantum electron fluid by including the first-order exchange and self-energy corrections to the random-phase approximation (RPA). This is achieved by determining these corrections to the RPA linear density-density response function, obtained by solving the equation of motion for the single-particle Green’s function. Resulting infinite hierarchy of equations (involving higher-order Green’s functions) is truncated by factorizing the two-particle Green’s function as a product of the single-particle Green’s function and one-particle distribution function. Numerical results of correlation function are compared directly against the quantum Monte Carlo simulation data due to Tanatar and Ceperley for different coupling parameter (r{sub s}) values. We find almost exact agreement for r{sub s}=1, with a noticeable improvement over the RPA. Its quality, however, deteriorates with increasing r{sub s}, but correction to RPA is quite significant.

  20. Chemical amplification based on fluid partitioning

    SciTech Connect

    Anderson, Brian L.; Colston, Jr., Billy W.; Elkin, Chris

    2006-05-09

    A system for nucleic acid amplification of a sample comprises partitioning the sample into partitioned sections and performing PCR on the partitioned sections of the sample. Another embodiment of the invention provides a system for nucleic acid amplification and detection of a sample comprising partitioning the sample into partitioned sections, performing PCR on the partitioned sections of the sample, and detecting and analyzing the partitioned sections of the sample.

  1. Partitioning the Quaternary

    NASA Astrophysics Data System (ADS)

    Gibbard, Philip L.; Lewin, John

    2016-11-01

    We review the historical purposes and procedures for stratigraphical division and naming within the Quaternary, and summarize the current requirements for formal partitioning through the International Commission on Stratigraphy (ICS). A raft of new data and evidence has impacted traditional approaches: quasi-continuous records from ocean sediments and ice cores, new numerical dating techniques, and alternative macro-models, such as those provided through Sequence Stratigraphy and Earth-System Science. The practical usefulness of division remains, but there is now greater appreciation of complex Quaternary detail and the modelling of time continua, the latter also extending into the future. There are problems both of commission (what is done, but could be done better) and of omission (what gets left out) in partitioning the Quaternary. These include the challenge set by the use of unconformities as stage boundaries, how to deal with multiphase records in ocean and terrestrial sediments, what happened at the 'Early-Mid- (Middle) Pleistocene Transition', dealing with trends that cross phase boundaries, and the current controversial focus on how to subdivide the Holocene and formally define an 'Anthropocene'.

  2. Long-range corrected density functional theory with accelerated Hartree-Fock exchange integration using a two-Gaussian operator [LC-ωPBE(2Gau)

    SciTech Connect

    Song, Jong-Won; Hirao, Kimihiko

    2015-10-14

    Since the advent of hybrid functional in 1993, it has become a main quantum chemical tool for the calculation of energies and properties of molecular systems. Following the introduction of long-range corrected hybrid scheme for density functional theory a decade later, the applicability of the hybrid functional has been further amplified due to the resulting increased performance on orbital energy, excitation energy, non-linear optical property, barrier height, and so on. Nevertheless, the high cost associated with the evaluation of Hartree-Fock (HF) exchange integrals remains a bottleneck for the broader and more active applications of hybrid functionals to large molecular and periodic systems. Here, we propose a very simple yet efficient method for the computation of long-range corrected hybrid scheme. It uses a modified two-Gaussian attenuating operator instead of the error function for the long-range HF exchange integral. As a result, the two-Gaussian HF operator, which mimics the shape of the error function operator, reduces computational time dramatically (e.g., about 14 times acceleration in C diamond calculation using periodic boundary condition) and enables lower scaling with system size, while maintaining the improved features of the long-range corrected density functional theory.

  3. Long-range corrected density functional theory with accelerated Hartree-Fock exchange integration using a two-Gaussian operator [LC-ωPBE(2Gau)].

    PubMed

    Song, Jong-Won; Hirao, Kimihiko

    2015-10-14

    Since the advent of hybrid functional in 1993, it has become a main quantum chemical tool for the calculation of energies and properties of molecular systems. Following the introduction of long-range corrected hybrid scheme for density functional theory a decade later, the applicability of the hybrid functional has been further amplified due to the resulting increased performance on orbital energy, excitation energy, non-linear optical property, barrier height, and so on. Nevertheless, the high cost associated with the evaluation of Hartree-Fock (HF) exchange integrals remains a bottleneck for the broader and more active applications of hybrid functionals to large molecular and periodic systems. Here, we propose a very simple yet efficient method for the computation of long-range corrected hybrid scheme. It uses a modified two-Gaussian attenuating operator instead of the error function for the long-range HF exchange integral. As a result, the two-Gaussian HF operator, which mimics the shape of the error function operator, reduces computational time dramatically (e.g., about 14 times acceleration in C diamond calculation using periodic boundary condition) and enables lower scaling with system size, while maintaining the improved features of the long-range corrected density functional theory. PMID:26472368

  4. HPAM: Hirshfeld partitioned atomic multipoles

    NASA Astrophysics Data System (ADS)

    Elking, Dennis M.; Perera, Lalith; Pedersen, Lee G.

    2012-02-01

    molecular charge density ρ(r) is partitioned into Hirshfeld (HD) and Hirshfeld-Iterated (HD-I) atomic charge densities ρ(r) on a grid. Atomic charges q and multipoles Qlma are calculated from the partitioned atomic charge densities ρ(r) by numerical integration. Solution method: Molecular and isolated atomic grids are generated for the molecule of interest. The ab initio density matrix P and basis functions χ(r) are read in from 'formatted checkpoint' files obtained from the Gaussian 03 or 09 quantum chemistry programs. The ab initio density is evaluated for the molecule and the isolated atoms/atomic ions on grids and used to construct Hirshfeld (HD) and Hirshfeld-I (HD-I) partitioned atomic charges densities ρ(r), which are used to calculate atomic charges q and atomic multipoles Qlma by integration. Restrictions: The ab initio density matrix can be calculated at the HF, DFT, MP2, or CCSD levels with ab initio Gaussian basis sets that include up to s, p, d, f, g functions for either closed shell or open shell molecules. Running time: The running time varies with the size of the molecule, the size of the ab initio basis set, and the coarseness of the desired grid. The run time can range from a minute or less for water to ˜15 minutes for neopentane.

  5. Instanton corrections of 1/6 BPS Wilson loops in ABJM theory

    NASA Astrophysics Data System (ADS)

    Okuyama, Kazumi

    2016-09-01

    We study instanton corrections to the vacuum expectation value (VEV) of 1/6 BPS Wilson loops in ABJM theory from the Fermi gas approach. We mainly consider Wilson loops in the fundamental representation and winding Wilson loops, but we also initiate the study of Wilson loops with two boundaries. We find that the membrane instanton corrections to the Wilson loop VEV are determined by the refined topological string in the Nekrasov-Shatashvili limit, and the pole cancellation mechanism between membrane instantons and worldsheet instantons works also in the Wilson loop VEVs as in the case of the partition functions.

  6. 30 CFR 1227.500 - What functions may a State perform to ensure that reporters correct erroneous report data?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... indicators; (b) Verifying whether production reports are missing; (c) Contacting production reporters or royalty reporters about missing reports and resolving exceptions; (d) Documenting all corrections made... to report, and bills as needed, including, but not limited to, imposing assessments on a person...

  7. 30 CFR 1227.500 - What functions may a State perform to ensure that reporters correct erroneous report data?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... indicators; (b) Verifying whether production reports are missing; (c) Contacting production reporters or royalty reporters about missing reports and resolving exceptions; (d) Documenting all corrections made... to report, and bills as needed, including, but not limited to, imposing assessments on a person...

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

    SciTech Connect

    Lao, Ka Un; Herbert, John M.

    2014-01-28

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

  9. Targeted Integration of a Super-Exon into the CFTR Locus Leads to Functional Correction of a Cystic Fibrosis Cell Line Model.

    PubMed

    Bednarski, Christien; Tomczak, Katja; Vom Hövel, Beate; Weber, Wolf-Michael; Cathomen, Toni

    2016-01-01

    In vitro disease models have enabled insights into the pathophysiology of human disease as well as the functional evaluation of new therapies, such as novel genome engineering strategies. In the context of cystic fibrosis (CF), various cellular disease models have been established in recent years, including organoids based on induced pluripotent stem cell technology that allowed for functional readouts of CFTR activity. Yet, many of these in vitro CF models require complex and expensive culturing protocols that are difficult to implement and may not be amenable for high throughput screens. Here, we show that a simple cellular CF disease model based on the bronchial epithelial ΔF508 cell line CFBE41o- can be used to validate functional CFTR correction. We used an engineered nuclease to target the integration of a super-exon, encompassing the sequences of CFTR exons 11 to 27, into exon 11 and re-activated endogenous CFTR expression by treating CFBE41o- cells with a demethylating agent. We demonstrate that the integration of this super-exon resulted in expression of a corrected mRNA from the endogenous CFTR promoter and used short-circuit current measurements in Ussing chambers to corroborate restored ion transport of the repaired CFTR channels. In conclusion, this study proves that the targeted integration of a large super-exon in CFTR exon 11 leads to functional correction of CFTR, suggesting that this strategy can be used to functionally correct all CFTR mutations located downstream of the 5' end of exon 11. PMID:27526025

  10. Targeted Integration of a Super-Exon into the CFTR Locus Leads to Functional Correction of a Cystic Fibrosis Cell Line Model

    PubMed Central

    Bednarski, Christien; Tomczak, Katja; vom Hövel, Beate; Weber, Wolf-Michael

    2016-01-01

    In vitro disease models have enabled insights into the pathophysiology of human disease as well as the functional evaluation of new therapies, such as novel genome engineering strategies. In the context of cystic fibrosis (CF), various cellular disease models have been established in recent years, including organoids based on induced pluripotent stem cell technology that allowed for functional readouts of CFTR activity. Yet, many of these in vitro CF models require complex and expensive culturing protocols that are difficult to implement and may not be amenable for high throughput screens. Here, we show that a simple cellular CF disease model based on the bronchial epithelial ΔF508 cell line CFBE41o- can be used to validate functional CFTR correction. We used an engineered nuclease to target the integration of a super-exon, encompassing the sequences of CFTR exons 11 to 27, into exon 11 and re-activated endogenous CFTR expression by treating CFBE41o- cells with a demethylating agent. We demonstrate that the integration of this super-exon resulted in expression of a corrected mRNA from the endogenous CFTR promoter and used short-circuit current measurements in Ussing chambers to corroborate restored ion transport of the repaired CFTR channels. In conclusion, this study proves that the targeted integration of a large super-exon in CFTR exon 11 leads to functional correction of CFTR, suggesting that this strategy can be used to functionally correct all CFTR mutations located downstream of the 5’ end of exon 11. PMID:27526025

  11. Suppressing Respiration Effects when Geometric Distortion Is Corrected Dynamically by Phase Labeling for Additional Coordinate Encoding (PLACE) during Functional MRI.

    PubMed

    Faraji-Dana, Zahra; Tam, Fred; Chen, J Jean; Graham, Simon J

    2016-01-01

    Echo planar imaging (EPI) suffers from geometric distortions caused by magnetic field inhomogeneities, which can be time-varying as a result of small amounts of head motion that occur over seconds and minutes during fMRI experiments, also known as "dynamic geometric distortion". Phase Labeling for Additional Coordinate Encoding (PLACE) is a promising technique for geometric distortion correction without reduced temporal resolution and in principle can be used to correct for motion-induced dynamic geometric distortion. PLACE requires at least two EPI images of the same anatomy that are ideally acquired with no variation in the magnetic field inhomogeneities. However, head motion and lung ventilation during the respiratory cycle can cause changes in magnetic field inhomogeneities within the EPI pair used for PLACE. In this work, we exploited dynamic off-resonance in k-space (DORK) and averaging to correct the within EPI pair magnetic field inhomogeneities; and hence proposed a combined technique (DORK+PLACE+averaging) to mitigate dynamic geometric distortion in EPI-based fMRI while preserving the temporal resolution. The performance of the combined DORK, PLACE and averaging technique was characterized through several imaging experiments involving test phantoms and six healthy adult volunteers. Phantom data illustrate reduced temporal standard deviation of fMRI signal intensities after use of combined dynamic PLACE, DORK and averaging compared to the standard processing and static geometric distortion correction. The combined technique also substantially improved the temporal standard deviation and activation maps obtained from human fMRI data in comparison to the results obtained by standard processing and static geometric distortion correction, highlighting the utility of the approach. PMID:27258194

  12. Suppressing Respiration Effects when Geometric Distortion Is Corrected Dynamically by Phase Labeling for Additional Coordinate Encoding (PLACE) during Functional MRI

    PubMed Central

    Faraji-Dana, Zahra; Tam, Fred; Chen, J. Jean; Graham, Simon J.

    2016-01-01

    Echo planar imaging (EPI) suffers from geometric distortions caused by magnetic field inhomogeneities, which can be time-varying as a result of small amounts of head motion that occur over seconds and minutes during fMRI experiments, also known as “dynamic geometric distortion”. Phase Labeling for Additional Coordinate Encoding (PLACE) is a promising technique for geometric distortion correction without reduced temporal resolution and in principle can be used to correct for motion-induced dynamic geometric distortion. PLACE requires at least two EPI images of the same anatomy that are ideally acquired with no variation in the magnetic field inhomogeneities. However, head motion and lung ventilation during the respiratory cycle can cause changes in magnetic field inhomogeneities within the EPI pair used for PLACE. In this work, we exploited dynamic off-resonance in k-space (DORK) and averaging to correct the within EPI pair magnetic field inhomogeneities; and hence proposed a combined technique (DORK+PLACE+averaging) to mitigate dynamic geometric distortion in EPI-based fMRI while preserving the temporal resolution. The performance of the combined DORK, PLACE and averaging technique was characterized through several imaging experiments involving test phantoms and six healthy adult volunteers. Phantom data illustrate reduced temporal standard deviation of fMRI signal intensities after use of combined dynamic PLACE, DORK and averaging compared to the standard processing and static geometric distortion correction. The combined technique also substantially improved the temporal standard deviation and activation maps obtained from human fMRI data in comparison to the results obtained by standard processing and static geometric distortion correction, highlighting the utility of the approach. PMID:27258194

  13. Temporal stability of network partitions.

    PubMed

    Petri, Giovanni; Expert, Paul

    2014-08-01

    We present a method to find the best temporal partition at any time scale and rank the relevance of partitions found at different time scales. This method is based on random walkers coevolving with the network and as such constitutes a generalization of partition stability to the case of temporal networks. We show that, when applied to a toy model and real data sets, temporal stability uncovers structures that are persistent over meaningful time scales as well as important isolated events, making it an effective tool to study both abrupt changes and gradual evolution of a network mesoscopic structures.

  14. Quantum field theory of partitions

    SciTech Connect

    Bender, C.M.; Brody, D.C.; Meister, B.K.

    1999-07-01

    Given a sequence of numbers {l_brace}a{sub n}{r_brace}, it is always possible to find a set of Feynman rules that reproduce that sequence. For the special case of the partitions of the integers, the appropriate Feynman rules give rise to graphs that represent the partitions in a clear pictorial fashion. These Feynman rules can be used to generate the Bell numbers B(n) and the Stirling numbers S(n,k) that are associated with the partitions of the integers. {copyright} {ital 1999 American Institute of Physics.}

  15. Temporal stability of network partitions.

    PubMed

    Petri, Giovanni; Expert, Paul

    2014-08-01

    We present a method to find the best temporal partition at any time scale and rank the relevance of partitions found at different time scales. This method is based on random walkers coevolving with the network and as such constitutes a generalization of partition stability to the case of temporal networks. We show that, when applied to a toy model and real data sets, temporal stability uncovers structures that are persistent over meaningful time scales as well as important isolated events, making it an effective tool to study both abrupt changes and gradual evolution of a network mesoscopic structures. PMID:25215787

  16. Partitioning ecosystems for sustainability.

    PubMed

    Murray, Martyn G

    2016-03-01

    Decline in the abundance of renewable natural resources (RNRs) coupled with increasing demands of an expanding human population will greatly intensify competition for Earth's natural resources during this century, yet curiously, analytical approaches to the management of productive ecosystems (ecological theory of wildlife harvesting, tragedy of the commons, green economics, and bioeconomics) give only peripheral attention to the driving influence of competition on resource exploitation. Here, I apply resource competition theory (RCT) to the exploitation of RNRs and derive four general policies in support of their sustainable and equitable use: (1) regulate resource extraction technology to avoid damage to the resource base; (2) increase efficiency of resource use and reduce waste at every step in the resource supply chain and distribution network; (3) partition ecosystems with the harvesting niche as the basic organizing principle for sustainable management of natural resources by multiple users; and (4) increase negative feedback between consumer and resource to bring about long-term sustainable use. A simple policy framework demonstrates how RCT integrates with other elements of sustainability science to better manage productive ecosystems. Several problem areas of RNR management are discussed in the light of RCT, including tragedy of the commons, overharvesting, resource collapse, bycatch, single species quotas, and simplification of ecosystems.

  17. Partitioning ecosystems for sustainability.

    PubMed

    Murray, Martyn G

    2016-03-01

    Decline in the abundance of renewable natural resources (RNRs) coupled with increasing demands of an expanding human population will greatly intensify competition for Earth's natural resources during this century, yet curiously, analytical approaches to the management of productive ecosystems (ecological theory of wildlife harvesting, tragedy of the commons, green economics, and bioeconomics) give only peripheral attention to the driving influence of competition on resource exploitation. Here, I apply resource competition theory (RCT) to the exploitation of RNRs and derive four general policies in support of their sustainable and equitable use: (1) regulate resource extraction technology to avoid damage to the resource base; (2) increase efficiency of resource use and reduce waste at every step in the resource supply chain and distribution network; (3) partition ecosystems with the harvesting niche as the basic organizing principle for sustainable management of natural resources by multiple users; and (4) increase negative feedback between consumer and resource to bring about long-term sustainable use. A simple policy framework demonstrates how RCT integrates with other elements of sustainability science to better manage productive ecosystems. Several problem areas of RNR management are discussed in the light of RCT, including tragedy of the commons, overharvesting, resource collapse, bycatch, single species quotas, and simplification of ecosystems. PMID:27209800

  18. Biogeography of time partitioning in mammals

    PubMed Central

    Bennie, Jonathan J.; Duffy, James P.; Inger, Richard; Gaston, Kevin J.

    2014-01-01

    Many animals regulate their activity over a 24-h sleep–wake cycle, concentrating their peak periods of activity to coincide with the hours of daylight, darkness, or twilight, or using different periods of light and darkness in more complex ways. These behavioral differences, which are in themselves functional traits, are associated with suites of physiological and morphological adaptations with implications for the ecological roles of species. The biogeography of diel time partitioning is, however, poorly understood. Here, we document basic biogeographic patterns of time partitioning by mammals and ecologically relevant large-scale patterns of natural variation in “illuminated activity time” constrained by temperature, and we determine how well the first of these are predicted by the second. Although the majority of mammals are nocturnal, the distributions of diurnal and crepuscular species richness are strongly associated with the availability of biologically useful daylight and twilight, respectively. Cathemerality is associated with relatively long hours of daylight and twilight in the northern Holarctic region, whereas the proportion of nocturnal species is highest in arid regions and lowest at extreme high altitudes. Although thermal constraints on activity have been identified as key to the distributions of organisms, constraints due to functional adaptation to the light environment are less well studied. Global patterns in diversity are constrained by the availability of the temporal niche; disruption of these constraints by the spread of artificial lighting and anthropogenic climate change, and the potential effects on time partitioning, are likely to be critical influences on species’ future distributions. PMID:25225371

  19. Spectral partitioning in diffraction tomography

    SciTech Connect

    Lehman, S K; Chambers, D H; Candy, J V

    1999-06-14

    The scattering mechanism of diffraction tomography is described by the integral form of the Helmholtz equation. The goal of diffraction tomography is to invert this equation in order to reconstruct the object function from the measured scattered fields. During the forward propagation process, the spatial spectrum of the object under investigation is ''smeared,'' by a convolution in the spectral domain, across the propagating and evanescent regions of the received field. Hence, care must be taken in performing the reconstruction, as the object's spectral information has been moved into regions where it may be considered to be noise rather than useful information. This will reduce the quality and resolution of the reconstruction. We show haw the object's spectrum can be partitioned into resolvable and non-resolvable parts based upon the cutoff between the propagating and evanescent fields. Operating under the Born approximation, we develop a beam-forming on transmit approach to direct the energy into either the propagating or evanescent parts of the spectrum. In this manner, we may individually interrogate the propagating and evanescent regions of the object spectrum.

  20. Graph Partitioning and Sequencing Software

    1995-09-19

    Graph partitioning is a fundemental problem in many scientific contexts. CHACO2.0 is a software package designed to partition and sequence graphs. CHACO2.0 allows for recursive application of several methods for finding small edge separators in weighted graphs. These methods include inertial, spectral, Kernighan Lin and multilevel methods in addition to several simpler strategies. Each of these approaches can be used to partition the graph into two, four, or eight pieces at each level of recursion.more » In addition, the Kernighan Lin method can be used to improve partitions generated by any of the other algorithms. CHACO2.0 can also be used to address various graph sequencing problems, with applications to scientific computing, database design, gene sequencing and other problems.« less

  1. Investigation of impact loading rate effects on the ligamentous cervical spinal load-partitioning using finite element model of functional spinal unit C2-C3.

    PubMed

    Mustafy, Tanvir; El-Rich, Marwan; Mesfar, Wissal; Moglo, Kodjo

    2014-09-22

    The cervical spine functions as a complex mechanism that responds to sudden loading in a unique manner, due to intricate structural features and kinematics. The spinal load-sharing under pure compression and sagittal flexion/extension at two different impact rates were compared using a bio-fidelic finite element (FE) model of the ligamentous cervical functional spinal unit (FSU) C2-C3. This model was developed using a comprehensive and realistic geometry of spinal components and material laws that include strain rate dependency, bone fracture, and ligament failure. The range of motion, contact pressure in facet joints, failure forces in ligaments were compared to experimental findings. The model demonstrated that resistance of spinal components to impact load is dependent on loading rate and direction. For the loads applied, stress increased with loading rate in all spinal components, and was concentrated in the outer intervertebral disc (IVD), regions of ligaments to bone attachment, and in the cancellous bone of the facet joints. The highest stress in ligaments was found in capsular ligament (CL) in all cases. Intradiscal pressure (IDP) in the nucleus was affected by loading rate change. It increased under compression/flexion but decreased under extension. Contact pressure in the facet joints showed less variation under compression, but increased significantly under flexion/extension particularly under extension. Cancellous bone of the facet joints region was the only component fractured and fracture occurred under extension at both rates. The cervical ligaments were the primary load-bearing component followed by the IVD, endplates and cancellous bone; however, the latter was the most vulnerable to extension as it fractured at low energy impact.

  2. Effects of van der Waals density functional corrections on trends in furfural adsorption and hydrogenation on close-packed transition metal surfaces

    NASA Astrophysics Data System (ADS)

    Liu, Bin; Cheng, Lei; Curtiss, Larry; Greeley, Jeffrey

    2014-04-01

    The hydrogenation of furfural to furfuryl alcohol on Pd(111), Cu(111) and Pt(111) is studied with both standard Density Functional Theory (DFT)-GGA functionals and with van der Waals-corrected density functionals. VdW-DF functionals, including optPBE, optB88, optB86b, and Grimme's method, are used to optimize the adsorption configurations of furfural, furfuryl alcohol, and related intermediates resulting from hydrogenation of furfural, and the results are compared to corresponding values determined with GGA functionals, including PW91 and PBE. On Pd(111) and Pt(111), the adsorption geometries of the intermediates are not noticeably different between the two classes of functionals, while on Cu(111), modest changes are seen in both the perpendicular distance and the orientation of the aromatic ring with respect to the planar surface. In general, the binding energies increase substantially in magnitude as a result of van der Waals contributions on all metals. In contrast, however, dispersion effects on the kinetics of hydrogenation are relatively small. It is found that activation barriers are not significantly affected by the inclusion of dispersion effects, and a Brønsted-Evans-Polanyi relationship developed solely from PW91 calculations on Pd(111) is capable of describing corresponding results on Cu(111) and Pt(111), even when the dispersion effects are included. Finally, the reaction energies and barriers derived from the dispersion-corrected and pure GGA calculations are used to plot simple potential energy profiles for furfural hydrogenation to furfuryl alcohol on the three considered metals, and an approximately constant downshift of the energetics due to the dispersion corrections is observed.

  3. Effects of van der Waals Density Functional Corrections on Trends in Furfural Adsorption and Hydrogenation on Close-Packed Transition Metal Surfaces

    SciTech Connect

    Liu, Bin; Cheng, Lei; Curtiss, Larry A.; Greeley, Jeffrey P.

    2014-04-01

    The hydrogenation of furfural to furfuryl alcohol on Pd(111), Cu(111) and Pt(111) is studied with both standard Density Functional Theory (DFT)-GGA functionals and with van der Waals-corrected density functionals. VdWDF functionals, including optPBE, optB88, optB86b, and Grimme's method, are used to optimize the adsorption configurations of furfural, furfuryl alcohol, and related intermediates resulting from hydrogenation of furfural, and the results are compared to corresponding values determined with GGA functionals, including PW91 and PBE. On Pd(111) and Pt(111), the adsorption geometries of the intermediates are not noticeably different between the two classes of functionals, while on Cu(111), modest changes are seen in both the erpendicular distance and the orientation of the aromatic ringwith respect to the planar surface. In general, the binding energies increase substantially in magnitude as a result of van derWaals contributions on all metals. In contrast, however, dispersion effects on the kinetics of hydrogenation are relatively small. It is found that activation barriers are not significantly affected by the inclusion of dispersion effects, and a Brønsted–Evans–Polanyi relationship developed solely fromPW91 calculations on Pd(111) is capable of describing corresponding results on Cu(111) and Pt(111), even when the dispersion effects are included. Finally, the reaction energies and barriers derived from the dispersion-corrected and pure GGA calculations are used to plot simple potential energy profiles for furfural hydrogenation to furfuryl alcohol on the three considered metals, and an approximately constant downshift of the energetics due to the dispersion corrections is observed.

  4. Partitioning of hydrophobic CdSe quantum dots into aqueous dispersions of humic substances: influence of capping-group functionality on the phase-transfer mechanism.

    PubMed

    Navarro, Divina A; Banerjee, Sarbajit; Aga, Diana S; Watson, David F

    2010-08-01

    Studies of the fate and transport of engineered nanomaterials are invaluable in predicting environmental impact, bioavailability, and toxicity. We report on the influence of humic and fulvic acids (models of natural organic matter) on the phase transfer of organic-capped CdSe quantum dots (QDs) from hexane to water. QDs capped with tri-n-octylphosphine oxide, tetradecylphosphonic acid, and oleic acid, which were otherwise insoluble in water, were transferred into aqueous solutions of humic substances (HS) (Suwannee River humic acid and fulvic acid standards) within 1-10 days after mixing. Phase transfer was characterized by infrared and UV/Vis absorption spectroscopy, emission spectroscopy, dynamic light scattering, electron microscopy, and inductively coupled plasma mass spectrometry. Phase-transferred QDs were intact and temporarily stabilized by HS. On longer timescales, Cd(2+) leached into aqueous solution. Our data suggest that two mechanisms promote the phase transfer of QD-HS agglomerates: (1) an overcoating mechanism involving dispersion interactions between non-polar moieties of HS and hydrocarbon chains of organic capping groups and (2) a coordinative mechanism involving displacement of capping groups by Lewis basic functionalities of HS. The structure of the capping group of QDs influenced the relative contributions of the two mechanisms and the extent to which Cd(2+) leached into water.

  5. 25 CFR 152.33 - Partition.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 25 Indians 1 2011-04-01 2011-04-01 false Partition. 152.33 Section 152.33 Indians BUREAU OF INDIAN..., REMOVAL OF RESTRICTIONS, AND SALE OF CERTAIN INDIAN LANDS Partitions in Kind of Inherited Allotments § 152.33 Partition. (a) Partition without application. If the Secretary of the Interior shall find that...

  6. 25 CFR 152.33 - Partition.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Partition. 152.33 Section 152.33 Indians BUREAU OF INDIAN..., REMOVAL OF RESTRICTIONS, AND SALE OF CERTAIN INDIAN LANDS Partitions in Kind of Inherited Allotments § 152.33 Partition. (a) Partition without application. If the Secretary of the Interior shall find that...

  7. Functional characterization and expression analysis of cucumber (Cucumis sativus L.) hexose transporters, involving carbohydrate partitioning and phloem unloading in sink tissues.

    PubMed

    Cheng, Jin-Tao; Li, Xiang; Yao, Feng-Zhen; Shan, Nan; Li, Ya-Hui; Zhang, Zhen-Xian; Sui, Xiao-Lei

    2015-08-01

    Many hexose transporters (HTs) have been reported to play roles in sucrose-transporting plants. However, little information about roles of HTs in RFOs (raffinose family oligosaccharides)-transporting plants has been reported. Here, three hexose transporters (CsHT2, CsHT3, and CsHT4) were cloned from Cucumis sativus L. Heterologous expression in yeast demonstrated that CsHT3 transported glucose, galactose and mannose, with a K(m) of 131.9 μM for glucose, and CsHT4 only transported galactose, while CsHT2 was non-functional. Both CsHT3 and CsHT4 were targeted to the plasma membrane of cucumber protoplasts. Spatio-temporal expression indicated that transcript level of CsHT3 was much higher than that of CsHT2 and CsHT4 in most tissues, especially in peduncles and fruit tissues containing vascular bundles. GUS staining of CsHT3-promoter-β-glucuronidase (GUS) transgenic Arabidopsis plants revealed CsHT3 expression in tissues with high metabolic turnover, suggesting that CsHT3 is involved in sugar competition among different sink organs during plant development. The transcript levels of CsHT3 and cell wall invertase genes increased in peduncles and fruit tissues along with cucumber fruit enlargement, and CsHT3 localized to phloem tissues by immunohistochemical localization; These results suggest that CsHT3 probably plays an important role in apoplastic phloem unloading of cucumber fruit.

  8. Functional characterization and expression analysis of cucumber (Cucumis sativus L.) hexose transporters, involving carbohydrate partitioning and phloem unloading in sink tissues.

    PubMed

    Cheng, Jin-Tao; Li, Xiang; Yao, Feng-Zhen; Shan, Nan; Li, Ya-Hui; Zhang, Zhen-Xian; Sui, Xiao-Lei

    2015-08-01

    Many hexose transporters (HTs) have been reported to play roles in sucrose-transporting plants. However, little information about roles of HTs in RFOs (raffinose family oligosaccharides)-transporting plants has been reported. Here, three hexose transporters (CsHT2, CsHT3, and CsHT4) were cloned from Cucumis sativus L. Heterologous expression in yeast demonstrated that CsHT3 transported glucose, galactose and mannose, with a K(m) of 131.9 μM for glucose, and CsHT4 only transported galactose, while CsHT2 was non-functional. Both CsHT3 and CsHT4 were targeted to the plasma membrane of cucumber protoplasts. Spatio-temporal expression indicated that transcript level of CsHT3 was much higher than that of CsHT2 and CsHT4 in most tissues, especially in peduncles and fruit tissues containing vascular bundles. GUS staining of CsHT3-promoter-β-glucuronidase (GUS) transgenic Arabidopsis plants revealed CsHT3 expression in tissues with high metabolic turnover, suggesting that CsHT3 is involved in sugar competition among different sink organs during plant development. The transcript levels of CsHT3 and cell wall invertase genes increased in peduncles and fruit tissues along with cucumber fruit enlargement, and CsHT3 localized to phloem tissues by immunohistochemical localization; These results suggest that CsHT3 probably plays an important role in apoplastic phloem unloading of cucumber fruit. PMID:26089151

  9. Evaluation of a combination of local hybrid functionals with DFT-D3 corrections for the calculation of thermochemical and kinetic data.

    PubMed

    Theilacker, Kolja; Arbuznikov, Alexei V; Bahmann, Hilke; Kaupp, Martin

    2011-08-18

    Due to their position-dependent exact exchange admixture, local hybrid functionals offer a higher flexibility and thus the potential for more universal and accurate exchange correlation functionals compared to global hybrids with a constant admixture, as has been demonstrated in previous work. Yet, the local hybrid constructions used so far do not account for the inclusion of dispersion-type interactions. As a first exploratory step toward a more general approach that includes van der Waals-type interactions with local hybrids, the present work has added DFT-D3-type corrections to a number of simple local hybrid functionals. Optimization of only the s(8) and s(r,6) parameters for the S22 set provides good results for weak interaction energies but deteriorates the excellent performance of the local hybrids for G3 atomization energies and for classical reaction barriers. A combined optimization of the two DFT-D3 parameters with one of the two parameters of the spin-polarized local mixing function (LMF) of a local hybrid for a more general optimization set provides simultaneously accurate dispersion energies, improved atomization energies, and accurate reaction barriers, as well as excellent alkane protobranching ratios. For other LMFs, the improvements of such a combined optimization for the S22 energies have been less satisfactory. The most notable advantage of the dispersion-corrected local hybrids over, for example, a B3LYP-D3 approach, is in the much more accurate reaction barriers.

  10. LETTER TO THE EDITOR: Accurate Hylleraas-like functions for the He atom with correct cusp conditions

    NASA Astrophysics Data System (ADS)

    Rodriguez, K. V.; Gasaneo, G.

    2005-08-01

    In this letter, a set of ground state wavefunctions for the He atom is given. The functions are constructed in terms of exponential and power series as similar as possible to the Hylleraas functions of Chandrasekhar and Herzberg (1955 Phys. Rev. 98 1050). The accuracy of the calculated energies is found to be about 10-4 au and all the cusp conditions at the Coulomb singularities are satisfied. The nine-parameter functions proposed here are found to have better local energy than those given by the 6 and 14 terms Hylleraas functions of Chandrasekhar. The mean value of various functions evaluated with the different proposals shows their good quality. These properties highly qualify the function to be used as an alternative to the Chandrasekhar functions in collisional problems. The whole set of functions given here can be considered as an alternative to the proposals of Chandrasekhar (1955 Phys. Rev. 98 1050), Bonham and Kohl (1966 J. Chem. Phys. 45 2471) and Le Sech (1997 J. Phys. B: At. Mol. Opt. Phys. 30 L47).

  11. Using the Deutsch-Jozsa algorithm to partition arrays

    NASA Astrophysics Data System (ADS)

    Lipovaca, Samir

    2010-03-01

    Using the Deutsch-Jozsa algorithm, we will develop a method for solving a class of problems in which we need to determine parts of an array and then apply a specified function to each independent part. Since present quantum computers are not robust enough for code writing and execution, we will build a model of a vector quantum computer that implements the Deutsch-Jozsa algorithm from a machine language view using the APL2 programming language. The core of the method is an operator (DJBOX) which allows evaluation of an arbitrary function f by the Deutsch-Jozsa algorithm. Two key functions of the method are GET/PARTITION and CALC/WITH/PARTITIONS. The GET/PARTITION function determines parts of an array based on the function f. The CALC/WITH/PARTITIONS function determines parts of an array based on the function f and then applies another function to each independent part. We will imagine the method is implemented on the above vector quantum computer. We will show that the method can be successfully executed.

  12. Stability and performance of ant queue inspired task partitioning methods.

    PubMed

    Scheidler, Alexander; Merkle, Daniel; Middendorf, Martin

    2008-06-01

    In this paper, we consider computing systems that have autonomous helper components which fulfill support functions and that possess reconfigurable hardware so that they can specialize to different types of service tasks. Several self-organized task partitioning methods are proposed that can be used by the helper components to decide how to reconfigure and which service tasks to execute. The proposed task partitioning methods are inspired by the so-called ant queue system that can be found in real ants for partitioning tasks between the individuals. The aim of this study is to investigate basic properties of the task partitioning methods, like stability and efficiency, in order to obtain basic insights into the design of task partitioning methods in self-organized service systems. More precisely, the investigations are threefold: (1) discrete event simulations are used to investigate systems, (2) for a simple version of the task partitioning system analytical stability results are obtained by means of delay differential equation systems and (3) by numerically solving initial value problems.

  13. Spectral zeta function and non-perturbative effects in ABJM Fermi-gas

    NASA Astrophysics Data System (ADS)

    Hatsuda, Yasuyuki

    2015-11-01

    The exact partition function in ABJM theory on three-sphere can be regarded as a canonical partition function of a non-interacting Fermi-gas with an unconventional Hamiltonian. All the information on the partition function is encoded in the discrete spectrum of this Hamiltonian. We explain how (quantum mechanical) non-perturbative corrections in the Fermi-gas system appear from a spectral consideration. Basic tools in our analysis are a Mellin-Barnes type integral representation and a spectral zeta function. From a consistency with known results, we conjecture that the spectral zeta function in the ABJM Fermi-gas has an infinite number of "non-perturbative" poles, which are invisible in the semi-classical expansion of the Planck constant. We observe that these poles indeed appear after summing up perturbative corrections. As a consequence, the perturbative resummation of the spectral zeta function causes non-perturbative corrections to the grand canonical partition function. We also present another example associated with a spectral problem in topological string theory. A conjectured non-perturbative free energy on the resolved conifold is successfully reproduced in this framework.

  14. Partitioning as a cooling rate indicator. [in chemical analysis of moon rocks

    NASA Technical Reports Server (NTRS)

    Onorato, P. I.; Yinnon, H.; Uhlmann, D. R.; Taylor, L. A.

    1979-01-01

    The paper presents a mathematical model for describing solute partitioning under continuous cooling conditions. It is shown that solute concentration profiles can be calculated for any cooling rate as a function of temperature provided that the appropriate data on diffusion and partitioning are known. As an example, the model is applied to zirconium partitioning between ilmenite and ulvospinel in a number of Apollo 15 Elbow Crater rocks in order to estimate the rates at which they cooled.

  15. Including screening in van der Waals corrected density functional theory calculations: the case of atoms and small molecules physisorbed on graphene.

    PubMed

    Silvestrelli, Pier Luigi; Ambrosetti, Alberto

    2014-03-28

    The Density Functional Theory (DFT)/van der Waals-Quantum Harmonic Oscillator-Wannier function (vdW-QHO-WF) method, recently developed to include the vdW interactions in approximated DFT by combining the quantum harmonic oscillator model with the maximally localized Wannier function technique, is applied to the cases of atoms and small molecules (X=Ar, CO, H2, H2O) weakly interacting with benzene and with the ideal planar graphene surface. Comparison is also presented with the results obtained by other DFT vdW-corrected schemes, including PBE+D, vdW-DF, vdW-DF2, rVV10, and by the simpler Local Density Approximation (LDA) and semilocal generalized gradient approximation approaches. While for the X-benzene systems all the considered vdW-corrected schemes perform reasonably well, it turns out that an accurate description of the X-graphene interaction requires a proper treatment of many-body contributions and of short-range screening effects, as demonstrated by adopting an improved version of the DFT/vdW-QHO-WF method. We also comment on the widespread attitude of relying on LDA to get a rough description of weakly interacting systems. PMID:24697424

  16. Including screening in van der Waals corrected density functional theory calculations: the case of atoms and small molecules physisorbed on graphene.

    PubMed

    Silvestrelli, Pier Luigi; Ambrosetti, Alberto

    2014-03-28

    The Density Functional Theory (DFT)/van der Waals-Quantum Harmonic Oscillator-Wannier function (vdW-QHO-WF) method, recently developed to include the vdW interactions in approximated DFT by combining the quantum harmonic oscillator model with the maximally localized Wannier function technique, is applied to the cases of atoms and small molecules (X=Ar, CO, H2, H2O) weakly interacting with benzene and with the ideal planar graphene surface. Comparison is also presented with the results obtained by other DFT vdW-corrected schemes, including PBE+D, vdW-DF, vdW-DF2, rVV10, and by the simpler Local Density Approximation (LDA) and semilocal generalized gradient approximation approaches. While for the X-benzene systems all the considered vdW-corrected schemes perform reasonably well, it turns out that an accurate description of the X-graphene interaction requires a proper treatment of many-body contributions and of short-range screening effects, as demonstrated by adopting an improved version of the DFT/vdW-QHO-WF method. We also comment on the widespread attitude of relying on LDA to get a rough description of weakly interacting systems.

  17. Including screening in van der Waals corrected density functional theory calculations: The case of atoms and small molecules physisorbed on graphene

    SciTech Connect

    Silvestrelli, Pier Luigi; Ambrosetti, Alberto

    2014-03-28

    The Density Functional Theory (DFT)/van der Waals-Quantum Harmonic Oscillator-Wannier function (vdW-QHO-WF) method, recently developed to include the vdW interactions in approximated DFT by combining the quantum harmonic oscillator model with the maximally localized Wannier function technique, is applied to the cases of atoms and small molecules (X=Ar, CO, H{sub 2}, H{sub 2}O) weakly interacting with benzene and with the ideal planar graphene surface. Comparison is also presented with the results obtained by other DFT vdW-corrected schemes, including PBE+D, vdW-DF, vdW-DF2, rVV10, and by the simpler Local Density Approximation (LDA) and semilocal generalized gradient approximation approaches. While for the X-benzene systems all the considered vdW-corrected schemes perform reasonably well, it turns out that an accurate description of the X-graphene interaction requires a proper treatment of many-body contributions and of short-range screening effects, as demonstrated by adopting an improved version of the DFT/vdW-QHO-WF method. We also comment on the widespread attitude of relying on LDA to get a rough description of weakly interacting systems.

  18. Evaluation of the grand-canonical partition function using expanded Wang-Landau simulations. IV. Performance of many-body force fields and tight-binding schemes for the fluid phases of silicon.

    PubMed

    Desgranges, Caroline; Delhommelle, Jerome

    2016-03-28

    We extend Expanded Wang-Landau (EWL) simulations beyond classical systems and develop the EWL method for systems modeled with a tight-binding Hamiltonian. We then apply the method to determine the partition function and thus all thermodynamic properties, including the Gibbs free energy and entropy, of the fluid phases of Si. We compare the results from quantum many-body (QMB) tight binding models, which explicitly calculate the overlap between the atomic orbitals of neighboring atoms, to those obtained with classical many-body (CMB) force fields, which allow to recover the tetrahedral organization in condensed phases of Si through, e.g., a repulsive 3-body term that favors the ideal tetrahedral angle. Along the vapor-liquid coexistence, between 3000 K and 6000 K, the densities for the two coexisting phases are found to vary significantly (by 5 orders of magnitude for the vapor and by up to 25% for the liquid) and to provide a stringent test of the models. Transitions from vapor to liquid are predicted to occur for chemical potentials that are 10%-15% higher for CMB models than for QMB models, and a ranking of the force fields is provided by comparing the predictions for the vapor pressure to the experimental data. QMB models also reveal the formation of a gap in the electronic density of states of the coexisting liquid at high temperatures. Subjecting Si to a nanoscopic confinement has a dramatic effect on the phase diagram with, e.g. at 6000 K, a decrease in liquid densities by about 50% for both CMB and QMB models and an increase in vapor densities between 90% (CMB) and 170% (QMB). The results presented here provide a full picture of the impact of the strategy (CMB or QMB) chosen to model many-body effects on the thermodynamic properties of the fluid phases of Si. PMID:27036464

  19. Evaluation of the grand-canonical partition function using expanded Wang-Landau simulations. IV. Performance of many-body force fields and tight-binding schemes for the fluid phases of silicon

    NASA Astrophysics Data System (ADS)

    Desgranges, Caroline; Delhommelle, Jerome

    2016-03-01

    We extend Expanded Wang-Landau (EWL) simulations beyond classical systems and develop the EWL method for systems modeled with a tight-binding Hamiltonian. We then apply the method to determine the partition function and thus all thermodynamic properties, including the Gibbs free energy and entropy, of the fluid phases of Si. We compare the results from quantum many-body (QMB) tight binding models, which explicitly calculate the overlap between the atomic orbitals of neighboring atoms, to those obtained with classical many-body (CMB) force fields, which allow to recover the tetrahedral organization in condensed phases of Si through, e.g., a repulsive 3-body term that favors the ideal tetrahedral angle. Along the vapor-liquid coexistence, between 3000 K and 6000 K, the densities for the two coexisting phases are found to vary significantly (by 5 orders of magnitude for the vapor and by up to 25% for the liquid) and to provide a stringent test of the models. Transitions from vapor to liquid are predicted to occur for chemical potentials that are 10%-15% higher for CMB models than for QMB models, and a ranking of the force fields is provided by comparing the predictions for the vapor pressure to the experimental data. QMB models also reveal the formation of a gap in the electronic density of states of the coexisting liquid at high temperatures. Subjecting Si to a nanoscopic confinement has a dramatic effect on the phase diagram with, e.g. at 6000 K, a decrease in liquid densities by about 50% for both CMB and QMB models and an increase in vapor densities between 90% (CMB) and 170% (QMB). The results presented here provide a full picture of the impact of the strategy (CMB or QMB) chosen to model many-body effects on the thermodynamic properties of the fluid phases of Si.

  20. The adsorption of h-BN monolayer on the Ni(111) surface studied by density functional theory calculations with a semiempirical long-range dispersion correction

    SciTech Connect

    Sun, X.; Pratt, A.; Li, Z. Y.; Ohtomo, M.; Sakai, S.; Yamauchi, Y.

    2014-05-07

    The geometric and spin-resolved electronic structure of a h-BN adsorbed Ni(111) surface has been investigated by density functional theory calculations. Two energy minima (physisorption and chemisorption) are obtained when the dispersive van der Waals correction is included. The geometry of N atom on top site and B atom on fcc site is the most energetically favorable. Strong hybridization with the ferromagnetic Ni substrate induces considerable gap states in the h-BN monolayer. The induced π* states are spin-polarized.

  1. Methanol clusters (CH3OH)n: putative global minimum-energy structures from model potentials and dispersion-corrected density functional theory.

    PubMed

    Kazachenko, Sergey; Bulusu, Satya; Thakkar, Ajit J

    2013-06-14

    Putative global minima are reported for methanol clusters (CH3OH)n with n ≤ 15. The predictions are based on global optimization of three intermolecular potential energy models followed by local optimization and single-point energy calculations using two variants of dispersion-corrected density functional theory. Recurring structural motifs include folded and/or twisted rings, folded rings with a short branch, and stacked rings. Many of the larger structures are stabilized by weak C-H···O bonds.

  2. A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems.

    PubMed

    Kruse, Holger; Grimme, Stefan

    2012-04-21

    A semi-empirical counterpoise-type correction for basis set superposition error (BSSE) in molecular systems is presented. An atom pair-wise potential corrects for the inter- and intra-molecular BSSE in supermolecular Hartree-Fock (HF) or density functional theory (DFT) calculations. This geometrical counterpoise (gCP) denoted scheme depends only on the molecular geometry, i.e., no input from the electronic wave-function is required and hence is applicable to molecules with ten thousands of atoms. The four necessary parameters have been determined by a fit to standard Boys and Bernadi counterpoise corrections for Hobza's S66×8 set of non-covalently bound complexes (528 data points). The method's target are small basis sets (e.g., minimal, split-valence, 6-31G*), but reliable results are also obtained for larger triple-ζ sets. The intermolecular BSSE is calculated by gCP within a typical error of 10%-30% that proves sufficient in many practical applications. The approach is suggested as a quantitative correction in production work and can also be routinely applied to estimate the magnitude of the BSSE beforehand. The applicability for biomolecules as the primary target is tested for the crambin protein, where gCP removes intramolecular BSSE effectively and yields conformational energies comparable to def2-TZVP basis results. Good mutual agreement is also found with Jensen's ACP(4) scheme, estimating the intramolecular BSSE in the phenylalanine-glycine-phenylalanine tripeptide, for which also a relaxed rotational energy profile is presented. A variety of minimal and double-ζ basis sets combined with gCP and the dispersion corrections DFT-D3 and DFT-NL are successfully benchmarked on the S22 and S66 sets of non-covalent interactions. Outstanding performance with a mean absolute deviation (MAD) of 0.51 kcal/mol (0.38 kcal/mol after D3-refit) is obtained at the gCP-corrected HF-D3/(minimal basis) level for the S66 benchmark. The gCP-corrected B3LYP-D3/6-31G* model

  3. [Combined correction of impairments of the functional state of the haemostasis system in patients with ischaemic stroke].

    PubMed

    Bekbosynov, A Zh

    2013-01-01

    The present study was aimed at assessing the results of combined administration of fractionated heparin and clopidogrel in treatment of patients with ischaemic stroke. We examined a total of seventy-three patients with acute impairments of cerebral circulation (41 men and 32 women). The patients average age amounted to 54.1± 2.0 years (range from 45 to 65). Depending upon the treatment conducted, the patients were subdivided into 2 groups. The comparison group comprised 35 patients. Of these, 20 were diagnosed as having ischaemic stroke and 15 had transitory ischaemic attack and treated by conventional complex conservative therapy. The study group comprised 38 patients (20 with ischaemic stroke and 18 with transitory ischaemic attack) receiving combined conservative treatment using the method of correction of the haemostasis state, including combined use of fractionated heparin and clopidogrel. With a considerable clinical effect, combined use of fractionated heparin and clopidogrel was not accompanied by a pronounced decrease in the indices of the haemostasis system, posing the risk for the development of haemorrhagic complications.

  4. Rectilinear partitioning of irregular data parallel computations

    NASA Technical Reports Server (NTRS)

    Nicol, David M.

    1991-01-01

    New mapping algorithms for domain oriented data-parallel computations, where the workload is distributed irregularly throughout the domain, but exhibits localized communication patterns are described. Researchers consider the problem of partitioning the domain for parallel processing in such a way that the workload on the most heavily loaded processor is minimized, subject to the constraint that the partition be perfectly rectilinear. Rectilinear partitions are useful on architectures that have a fast local mesh network. Discussed here is an improved algorithm for finding the optimal partitioning in one dimension, new algorithms for partitioning in two dimensions, and optimal partitioning in three dimensions. The application of these algorithms to real problems are discussed.

  5. Inter-comparison of the phase partitioning of cloud water among global climate models

    NASA Astrophysics Data System (ADS)

    Komurcu, Muge; Storelvmo, Trude; Tan, Ivy; Lohmann, Ulrike; Yun, Yuxing; Penner, Joyce E.; Wang, Yong; Liu, Xiaohong; Takemura, Toshihiko

    2013-05-01

    Cloud water phase partitioning of global climate models is investigated using four different models. Two simulations are done: One with the models' default heterogeneous ice nucleation and another one using a fixed ice nucleation for all models. Results show that heterogeneous ice nucleation can influence the water phase partitioning, however, its influence is not the dominant factor leading to the phase partitioning differences among models. The name of the second author, "Trude Storelvmo" was mistakenly written as "Trude Storevlmo". All online versions of the article have been corrected.

  6. Electroweak Corrections

    NASA Astrophysics Data System (ADS)

    Barbieri, Riccardo

    2016-10-01

    The test of the electroweak corrections has played a major role in providing evidence for the gauge and the Higgs sectors of the Standard Model. At the same time the consideration of the electroweak corrections has given significant indirect information on the masses of the top and the Higgs boson before their discoveries and important orientation/constraints on the searches for new physics, still highly valuable in the present situation. The progression of these contributions is reviewed.

  7. [Use of terahertz electromagnetic radiation at nitric oxide frequencies for the correction of thyroid functional state during stress].

    PubMed

    Kirichuk, V F; Tsymbal, A A

    2010-01-01

    The influence of terahertz electromagnetic radiation at nitric oxide frequencies (150.176-150.664 Ghz) on the functional activity of rat thyroid gland subjected to acute immobilization stress has been studied. It is shown that terahertz radiation totally normalizes thyroid activity in stressed animals within 30 min after application. PMID:20540354

  8. [Use of terahertz electromagnetic radiation at nitric oxide frequencies for the correction of thyroid functional state during stress].

    PubMed

    Kirichuk, V F; Tsymbal, A A

    2010-01-01

    The influence of terahertz electromagnetic radiation at nitric oxide frequencies (150.176-150.664 Ghz) on the functional activity of rat thyroid gland subjected to acute immobilization stress has been studied. It is shown that terahertz radiation totally normalizes thyroid activity in stressed animals within 30 min after application.

  9. Partitioning of Nanoparticles into Organic Phases and Model Cells

    SciTech Connect

    Posner, J.D.; Westerhoff, P.; Hou, W-C.

    2011-08-25

    dissolved substances" or "more like colloids" as the division between behaviors of macromolecules versus colloids remains ill-defined. Below we detail our work on two broadly defined objectives: (i) Partitioning of ENP into octanol, lipid bilayer, and water, and (ii) disruption of lipid bilayers by ENPs. We have found that the partitioning of NP reaches pseudo-equilibrium distributions between water and organic phases. The equilibrium partitioning most strongly depends on the particle surface charge, which leads us to the conclusion that electrostatic interactions are critical to understanding the fate of NP in the environment. We also show that the kinetic rate at which particle partition is a function of their size (small particles partition faster by number) as can be predicted from simple DLVO models. We have found that particle number density is the most effective dosimetry to present our results and provide quantitative comparison across experiments and experimental platforms. Cumulatively, our work shows that lipid bilayers are a more effective organic phase than octanol because of the definable surface area and ease of interpretation of the results. Our early comparison of NP partitioning between water and lipids suggest that this measurement can be predictive of bioaccumulation in aquatic organisms. We have shown that nanoparticle disrupt lipid bilayer membranes and detail how NP-bilayer interaction leads to the malfunction of lipid bilayers in regulating the fluxes of ionic charges and molecules. Our results show that the disruption of the lipid membranes is similar to that of toxin melittin, except single particles can disrupt a bilayer. We show that only a single particle is required to disrupt a 150 nm DOPC liposome. The equilibrium leakage of membranes is a function of the particle number density and particle surface charge, consistent with results from our partitioning experiments. Our disruption experiments with varying surface functionality show that

  10. A Nucleotide-Analogue-Induced Gain of Function Corrects the Error-Prone Nature of Human DNA Polymerase iota

    SciTech Connect

    Ketkar, Amit; Zafar, Maroof K.; Banerjee, Surajit; Marquez, Victor E.; Egli, Martin; Eoff, Robert L.

    2012-10-25

    Y-family DNA polymerases participate in replication stress and DNA damage tolerance mechanisms. The properties that allow these enzymes to copy past bulky adducts or distorted template DNA can result in a greater propensity for them to make mistakes. Of the four human Y-family members, human DNA polymerase iota (hpol{iota}) is the most error-prone. In the current study, we elucidate the molecular basis for improving the fidelity of hpol{iota} through use of the fixed-conformation nucleotide North-methanocarba-2{prime}-deoxyadenosine triphosphate (N-MC-dATP). Three crystal structures were solved of hpol{iota} in complex with DNA containing a template 2{prime}-deoxythymidine (dT) paired with an incoming dNTP or modified nucleotide triphosphate. The ternary complex of hpol{iota} inserting N-MC-dATP opposite dT reveals that the adenine ring is stabilized in the anti orientation about the pseudo-glycosyl torsion angle, which mimics precisely the mutagenic arrangement of dGTP:dT normally preferred by hpol{iota}. The stabilized anti conformation occurs without notable contacts from the protein but likely results from constraints imposed by the bicyclo[3.1.0]hexane scaffold of the modified nucleotide. Unmodified dATP and South-MC-dATP each adopt syn glycosyl orientations to form Hoogsteen base pairs with dT. The Hoogsteen orientation exhibits weaker base-stacking interactions and is less catalytically favorable than anti N-MC-dATP. Thus, N-MC-dATP corrects the error-prone nature of hpol{iota} by preventing the Hoogsteen base-pairing mode normally observed for hpol{iota}-catalyzed insertion of dATP opposite dT. These results provide a previously unrecognized means of altering the efficiency and the fidelity of a human translesion DNA polymerase.

  11. METAL PARTITIONING IN COMBUSTION PROCESSES

    EPA Science Inventory

    This article summarizes ongoing research efforts at the National Risk Management Research Laboratory of the U.S. Environmental Protection Agency examining [high temperature] metal behavior within combustion environments. The partitioning of non-volatile (Cr and Ni), semi-volatil...

  12. The accurate calculation of the band gap of liquid water by means of GW corrections applied to plane-wave density functional theory molecular dynamics simulations.

    PubMed

    Fang, Changming; Li, Wun-Fan; Koster, Rik S; Klimeš, Jiří; van Blaaderen, Alfons; van Huis, Marijn A

    2015-01-01

    Knowledge about the intrinsic electronic properties of water is imperative for understanding the behaviour of aqueous solutions that are used throughout biology, chemistry, physics, and industry. The calculation of the electronic band gap of liquids is challenging, because the most accurate ab initio approaches can be applied only to small numbers of atoms, while large numbers of atoms are required for having configurations that are representative of a liquid. Here we show that a high-accuracy value for the electronic band gap of water can be obtained by combining beyond-DFT methods and statistical time-averaging. Liquid water is simulated at 300 K using a plane-wave density functional theory molecular dynamics (PW-DFT-MD) simulation and a van der Waals density functional (optB88-vdW). After applying a self-consistent GW correction the band gap of liquid water at 300 K is calculated as 7.3 eV, in good agreement with recent experimental observations in the literature (6.9 eV). For simulations of phase transformations and chemical reactions in water or aqueous solutions whereby an accurate description of the electronic structure is required, we suggest to use these advanced GW corrections in combination with the statistical analysis of quantum mechanical MD simulations.

  13. A new method for point-spread function correction using the ellipticity of re-smeared artificial images in weak gravitational lensing shear analysis

    SciTech Connect

    Okura, Yuki; Futamase, Toshifumi E-mail: tof@astr.tohoku.ac.jp

    2014-09-10

    Highly accurate weak lensing analysis is urgently required for planned cosmic shear observations. For this purpose we have eliminated various systematic noises in the measurement. The point-spread function (PSF) effect is one of them. A perturbative approach for correcting the PSF effect on the observed image ellipticities has been previously employed. Here we propose a new non-perturbative approach for PSF correction that avoids the systematic error associated with the perturbative approach. The new method uses an artificial image for measuring shear which has the same ellipticity as the lensed image. This is done by re-smearing the observed galaxy images and observed star images (PSF) with an additional smearing function to obtain the original lensed galaxy images. We tested the new method with simple simulated objects that have Gaussian or Sérsic profiles smeared by a Gaussian PSF with sufficiently large size to neglect pixelization. Under the condition of no pixel noise, it is confirmed that the new method has no systematic error even if the PSF is large and has a high ellipticity.

  14. Increasing the applicability of density functional theory. V. X-ray absorption spectra with ionization potential corrected exchange and correlation potentials

    NASA Astrophysics Data System (ADS)

    Verma, Prakash; Bartlett, Rodney J.

    2016-07-01

    Core excitation energies are computed with time-dependent density functional theory (TD-DFT) using the ionization energy corrected exchange and correlation potential QTP(0,0). QTP(0,0) provides C, N, and O K-edge spectra to about an electron volt. A mean absolute error (MAE) of 0.77 and a maximum error of 2.6 eV is observed for QTP(0,0) for many small molecules. TD-DFT based on QTP (0,0) is then used to describe the core-excitation spectra of the 22 amino acids. TD-DFT with conventional functionals greatly underestimates core excitation energies, largely due to the significant error in the Kohn-Sham occupied eigenvalues. To the contrary, the ionization energy corrected potential, QTP(0,0), provides excellent approximations (MAE of 0.53 eV) for core ionization energies as eigenvalues of the Kohn-Sham equations. As a consequence, core excitation energies are accurately described with QTP(0,0), as are the core ionization energies important in X-ray photoionization spectra or electron spectroscopy for chemical analysis.

  15. ɛ-CORRECTED Seiberg-Witten Prepotential Obtained from Half-Genus Expansion in β-DEFORMED Matrix Model

    NASA Astrophysics Data System (ADS)

    Itoyama, H.; Yonezawa, N.

    We consider the half-genus expansion of the resolvent function in the β-deformed matrix model with three-Penner potential under the AGT conjecture and the 0d-4d dictionary. The partition function of the model, after the specification of the paths, becomes the DF conformal block for fixed c and provides the Nekrasov partition function expanded both in gs = √ {-ɛ 1&epsilon_2; } and in ɛ = ɛ1+ɛ2. Exploiting the explicit expressions for the lower terms of the free energy extracted from the above expansion, we derive the first few ɛ corrections to the Seiberg-Witten prepotential in terms of the parameters of SU(2), Nf = 4, { N} = 2 supersymmetric gauge theory.

  16. Self-energy-corrected electronic energy level alignment in molecular junctions and at interfaces with hybrid functionals

    NASA Astrophysics Data System (ADS)

    Kotiuga, Michele; Egger, David; Kronik, Leeor; Neaton, Jeffrey B.

    2015-03-01

    Accurate calculations of energy level alignment at complex interfaces are imperative for understanding a variety of transport and spectroscopy measurements, as well as for elucidating new interfacial electronic structure phenomena. However, standard approaches to such calculations, based on density functional theory (DFT), are well known to be deficient. In prior work on molecular junctions and physisorbed molecules on surfaces, an approximate GW approach, DFT+ Σ, has been successful in describing the conductance and level alignment of amine and pyridine terminated molecules on gold surfaces and in junctions. Here, via the use of hybrid functionals, we preform quantitative studies of the level alignment of thiol- and carbon-terminated phenyls on gold, where the formation of a strong chemical bond and presence of gateway states limit the validity of the DFT+ Σ approximation as currently formulated. We contrast these systems to prior work on weakly-coupled molecules, including bipyridine or phenyl-diamines. Additionally, we compute transmission functions using both DFT-PBE and DFT-HSE starting points and predict conductance and thermopower with these methods, comparing to experiments where possible. We acknowledge DOE, DOD, NERSC, ERC, ISF, and FWF.

  17. The Parameterization of Solid Metal-Liquid Metal Partitioning of Siderophile Elements

    NASA Technical Reports Server (NTRS)

    Chabot, N. L.; Jones, J. H.

    2003-01-01

    The composition of a metallic liquid can significantly affect the partitioning behavior of elements. For example, some experimental solid metal-liquid metal partition coefficients have been shown to increase by three orders of magnitude with increasing S-content of the metallic liquid. Along with S, the presence of other light elements, such as P and C, has also been demonstrated to affect trace element partitioning behavior. Understanding the effects of metallic composition on partitioning behavior is important for modeling the crystallization of magmatic iron meteorites and the chemical effects of planetary differentiation. It is thus useful to have a mathematical expression that parameterizes the partition coefficient as a function of the composition of the metal. Here we present a revised parameterization method, which builds on the theory of the current parameterization of Jones and Malvin and which better handles partitioning in multi-light-element systems.

  18. Crystal/Silicate Melt Partitioning of HFSE, Mo, W, U and Th as a Function of TiO2, with Implications for the Petrogenesis of Lunar Mare Basalts

    NASA Astrophysics Data System (ADS)

    Leitzke, F. P.; Fonseca, R. O. C.; Michely, L. T.; Sprung, P.; Heuser, A.; Münker, C.

    2016-08-01

    We present results from an experimental work that aimed to obtain partition coefficients for the HFSE, Mo, W, U and Th between major silicate and oxide phases present in the lunar mantle and silicate melts with a broad range of TiO2 contents.

  19. Inversion of hematocrit partition at microfluidic bifurcations.

    PubMed

    Shen, Zaiyi; Coupier, Gwennou; Kaoui, Badr; Polack, Benoît; Harting, Jens; Misbah, Chaouqi; Podgorski, Thomas

    2016-05-01

    Partitioning of red blood cells (RBCs) at the level of bifurcations in the microcirculatory system affects many physiological functions yet it remains poorly understood. We address this problem by using T-shaped microfluidic bifurcations as a model. Our computer simulations and in vitro experiments reveal that the hematocrit (ϕ0) partition depends strongly on RBC deformability, as long as ϕ0<20% (within the normal range in microcirculation), and can even lead to complete deprivation of RBCs in a child branch. Furthermore, we discover a deviation from the Zweifach-Fung effect which states that the child branch with lower flow rate recruits less RBCs than the higher flow rate child branch. At small enough ϕ0, we get the inverse scenario, and the hematocrit in the lower flow rate child branch is even higher than in the parent vessel. We explain this result by an intricate up-stream RBC organization and we highlight the extreme dependence of RBC transport on geometrical and cell mechanical properties. These parameters can lead to unexpected behaviors with consequences on the microcirculatory function and oxygen delivery in healthy and pathological conditions.

  20. Some trees with partition dimension three

    NASA Astrophysics Data System (ADS)

    Fredlina, Ketut Queena; Baskoro, Edy Tri

    2016-02-01

    The concept of partition dimension of a graph was introduced by Chartrand, E. Salehi and P. Zhang (1998) [2]. Let G(V, E) be a connected graph. For S ⊆ V (G) and v ∈ V (G), define the distance d(v, S) from v to S is min{d(v, x)|x ∈ S}. Let Π be an ordered partition of V (G) and Π = {S1, S2, ..., Sk }. The representation r(v|Π) of vertex v with respect to Π is (d(v, S1), d(v, S2), ..., d(v, Sk)). If the representations of all vertices are distinct, then the partition Π is called a resolving partition of G. The partition dimension of G is the minimum k such that G has a resolving partition with k partition classes. In this paper, we characterize some classes of trees with partition dimension three, namely olive trees, weeds, and centipedes.

  1. Terminology for trace-element partitioning

    SciTech Connect

    Beattie, P. ); Drake, M. ); Jones, J.; McKay, G. ); Leeman, W. ); Longhi, J. ); Nielsen, R. ); Palme, H. ); Shaw, D. ); Takahashi, E. ); Watson, B. )

    1993-04-01

    A self-consistent terminology for partitioning data is presented. Ratios of the concentration of a component in two phases are termed partition coefficients and given the symbol D. Ratios of partition coefficients are termed exchange coefficients and given the symbol K[sub D]. The prefix bulk implies that these coefficients are weighted according to the proportions of coexisting phases. Bulk partition and bulk exchange coefficients are denoted by [bar D] and [ovr K[sub D

  2. New Insights on Canopy Photosynthesis from novel Isotopic Flux Partitioning in a temperate forest

    NASA Astrophysics Data System (ADS)

    Saleska, Scott; Wehr, Richard; Munger, William; Zahniser, Mark; McManus, Barry; Nelson, David

    2014-05-01

    Standard approaches for partitioning net eddy fluxes of CO2 into gross primary production (GPP) and ecosystem respiration (R) typically work by extrapolating R from night to day using an empirical function fit to a week or a month of data. Such methods assume that daytime R behaves like nighttime R, and is either constant or a smoothly varying function of temperature. Isotopic partitioning is an alternative that involves no assumptions about the behavior of R or GPP (though it requires knowledge or assumptions about the isotopic fractionations occurring in and around the leaves) and which allows for the investigation of diel variations because each flux measurement is partitioned separately. A novel isotopic flux partitioning approach using the first long-term isotopic CO2 eddy flux record (measured at Harvard Forest) reveals differences in both the diel and the seasonally averaged behavior of GPP as compared to conventional partitioning. At the diel timescale, large (~10 umol m-2 s-1), rapid (~2 hours) variations in the respiratory component of measured NEE associated with subtle changes in wind direction are misattributed to GPP by conventional partitioning, leading to inconsistency in the response of GPP to photosynthetically active radiation (PAR). Isotopically partitioned GPP responds more consistently to PAR, and the seasonally averaged light response curve of isotopically partitioned GPP is more linear than that of conventionally partitioned GPP, suggesting that unsaturated (steeply inclined) leaves perform most of the canopy photosynthesis. Isotopic partitioning further suggests that conventional partitioning based on the temperature-dependent extrapolation of nighttime R overestimates GPP by 10-20%, on average, consistent with its neglect of the suppression of foliar dark respiration by sunlight. Isotopic partitioning is thus changing our interpretation of ecosystem CO2 exchange at the Harvard Forest.

  3. When structure affects function--the need for partial volume effect correction in functional and resting state magnetic resonance imaging studies.

    PubMed

    Dukart, Juergen; Bertolino, Alessandro

    2014-01-01

    Both functional and also more recently resting state magnetic resonance imaging have become established tools to investigate functional brain networks. Most studies use these tools to compare different populations without controlling for potential differences in underlying brain structure which might affect the functional measurements of interest. Here, we adapt a simulation approach combined with evaluation of real resting state magnetic resonance imaging data to investigate the potential impact of partial volume effects on established functional and resting state magnetic resonance imaging analyses. We demonstrate that differences in the underlying structure lead to a significant increase in detected functional differences in both types of analyses. Largest increases in functional differences are observed for highest signal-to-noise ratios and when signal with the lowest amount of partial volume effects is compared to any other partial volume effect constellation. In real data, structural information explains about 25% of within-subject variance observed in degree centrality--an established resting state connectivity measurement. Controlling this measurement for structural information can substantially alter correlational maps obtained in group analyses. Our results question current approaches of evaluating these measurements in diseased population with known structural changes without controlling for potential differences in these measurements.

  4. Concurrent targeting of nitrosative stress-PARP pathway corrects functional, behavioral and biochemical deficits in experimental diabetic neuropathy

    SciTech Connect

    Negi, Geeta; Kumar, Ashutosh; Sharma, Shyam S.

    2010-01-01

    Peroxynitrite mediated nitrosative stress, an indisputable initiator of DNA damage and overactivation of poly(ADP-ribose) polymerase (PARP), a nuclear enzyme activated after sensing DNA damage, are two crucial pathogenetic mechanisms in diabetic neuropathy. The intent of the present study was to investigate the effect of combination of a peroxynitrite decomposition catalyst (PDC), FeTMPyP and a PARP inhibitor, 4-ANI against diabetic peripheral neuropathy. The end points of evaluation of the study included motor nerve conduction velocity (MNCV) and nerve blood flow (NBF) for evaluating nerve functions; thermal hyperalgesia and mechanical allodynia for assessing nociceptive alterations, malondialdehyde and peroxynitrite levels to detect oxidative stress-nitrosative stress; NAD concentration in sciatic nerve to assess overactivation of PARP. Additionally immunohistochemical studies for nitrotyrosine and Poly(ADP-ribose) (PAR) was also performed. Treatment with the combination of FeTMPyP and 4-ANI led to significant improvement in nerve functions and pain parameters and also attenuated the oxidative-nitrosative stress markers. Further, the combination also reduced the overactivation of PARP as evident from increased NAD levels and decreased PAR immunopositivity in sciatic nerve microsections. Thus, it can be concluded that treatment with the combination of a PDC and PARP inhibitor attenuates alteration in peripheral nerves in diabetic neuropathy (DN).

  5. [The application of the emulsified turpentine baths for the correction of the functional state of the cross-country skiers].

    PubMed

    Garnov, I O; Kuchin, A V; Loginova, T P; Varlamova, N G; Boiko, E R

    2016-01-01

    The baths with emulsified turpentine find the wide application in balneotherapy. They produce especially pronounced beneficial prophylactic effects in the patients presenting with microtrombosis and microvascular stasis. Moreover, these baths may be prescribed to improve microcirculation, increase the functional reserves and physical capacity in the athletes. At the same time, the current literature appears to contain no scientific publications on the application of emulsified turpentine baths for the restoration of the physical capacity of the professional ski runners. The lack of relevant information motivated the study reported in the present article. The main objective of the study involving 10 subjects was to evaluate the effectiveness of the modified emulsified turpentine baths as a method by which to restore and enhance the physical capacity of the professional cross-country skiers. The physical capacity of the athletes was evaluated from the results of the bicycle ergometer exercise test with the use of the «Oxycon Pro» system. The data obtained suggest that a course of the emulsified turpentine baths increases the activity of the cardiorespiratory system, improves the physical capacity, and enhances the functional reserves of the body in the anaerobic zone.

  6. [The application of the emulsified turpentine baths for the correction of the functional state of the cross-country skiers].

    PubMed

    Garnov, I O; Kuchin, A V; Loginova, T P; Varlamova, N G; Boiko, E R

    2016-01-01

    The baths with emulsified turpentine find the wide application in balneotherapy. They produce especially pronounced beneficial prophylactic effects in the patients presenting with microtrombosis and microvascular stasis. Moreover, these baths may be prescribed to improve microcirculation, increase the functional reserves and physical capacity in the athletes. At the same time, the current literature appears to contain no scientific publications on the application of emulsified turpentine baths for the restoration of the physical capacity of the professional ski runners. The lack of relevant information motivated the study reported in the present article. The main objective of the study involving 10 subjects was to evaluate the effectiveness of the modified emulsified turpentine baths as a method by which to restore and enhance the physical capacity of the professional cross-country skiers. The physical capacity of the athletes was evaluated from the results of the bicycle ergometer exercise test with the use of the «Oxycon Pro» system. The data obtained suggest that a course of the emulsified turpentine baths increases the activity of the cardiorespiratory system, improves the physical capacity, and enhances the functional reserves of the body in the anaerobic zone. PMID:27213946

  7. 25 CFR 158.56 - Partition records.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 25 Indians 1 2011-04-01 2011-04-01 false Partition records. 158.56 Section 158.56 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR LAND AND WATER OSAGE LANDS § 158.56 Partition records. Upon completion of an action in partition, a copy of the judgment roll showing schedule of costs...

  8. 25 CFR 158.56 - Partition records.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Partition records. 158.56 Section 158.56 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR LAND AND WATER OSAGE LANDS § 158.56 Partition records. Upon completion of an action in partition, a copy of the judgment roll showing schedule of costs...

  9. Oxygen Fugacity of the Martian Mantle From Pyroxene/Melt Partitioning of REE

    NASA Technical Reports Server (NTRS)

    Musselwhite, D. S.; Jones, J. H.

    2003-01-01

    This study is part of an ongoing effort to calibrate the pyroxene/melt REE oxybarometer for conditions relevant to the martian meteorites. Redox variations have been reported among the shergottites. Wadhwa used the Eu and Gd augite/melt partitioning experiments of McKay, designed for the LEW86010 angrite, to infer a range of fo2 for the shergottites. Others inferred fo2 using equilibria between Fe-Ti oxides. There is fairly good agreement between the Fe-Ti oxide determinations and the estimates from Eu anomalies in terms of which meteorites are more or less oxidized. The Eu anomaly technique and the Fe-Ti oxide technique both essentially show the same trend, with Shergotty and Zagami being the most oxidized and QUE94201 and DaG 476 being the most reduced. Thus, the variation in fo2 appears to be both real and substantive. However, although the redox trends indicated by the two techniques are similar, there is as much as two log unit offset between the results of three researchers. One explanation for this offset is that the Eu calibration used for the shergottites was actually designed for the LEW86010 angrite, a silica-undersaturated basalt whose pyroxene (diopside) compositions are rather extreme. To correct this, experiments have been conducted on the redox relationship of Eu partitioning relative to Sm and Gd for pyroxene/melt compositions more relevant to Martian meteorites. We report here preliminary results for experiments on pigeonite/melt partitioning as a function of fO2.

  10. Structural and vibrational properties of α-MoO3 from van der Waals corrected density functional theory calculations

    NASA Astrophysics Data System (ADS)

    Ding, Hong; Ray, Keith G.; Ozolins, Vidvuds; Asta, Mark

    2012-01-01

    Structural and vibrational properties of α-MoO3 are studied employing two recently proposed methodologies for incorporating van der Waals (vdW) contributions in density functional theory (DFT) based calculations. The DFT-D2 [S. Grimme, J. Comput. Chem.JCCHDD0192-865110.1002/jcc.20495 27, 1787 (2006)] and optB88 vdW-DFT [J. Klimeš , J. Phys.: Condens. MatterPRBMDO0953-898410.1088/0953-8984/22/2/022201 22, 022201 (2010)] methods are shown to give rise to increased accuracy in predicted lattice parameters, relative to conventional DFT methods. Calculated vibrational frequencies agree with measurements to within 5% and 10% for modes involving bonded and nonbonded interactions in this compound, respectively.

  11. Hierarchical radial basis function networks and local polynomial un-warping for X-ray image intensifier distortion correction: a comparison with global techniques.

    PubMed

    Cerveri, P; Forlani, C; Pedotti, A; Ferrigno, G

    2003-03-01

    Global polynomial (GP) methods have been widely used to correct geometric image distortion of small-size (up to 30 cm) X-ray image intensifiers (XRIIs). This work confirms that this kind of approach is suitable for 40 cm XRIIs (now increasingly used). Nonetheless, two local methods, namely 3rd-order local un-warping polynomials (LUPs) and hierarchical radial basis function (HRBF) networks are proposed as alternative solutions. Extensive experimental tests were carried out to compare these methods with classical low-order local polynomial and GP techniques, in terms of residual error (RMSE) measured at points not used for parameter estimation. Simulations showed that the LUP and HRBF methods had accuracies comparable with that attained using GP methods. In detail, the LUP method (0.353 microm) performed worse than HRBF (0.348 microm) only for small grid spacing (15 x 15 control points); the accuracy of both HRBF (0.157 microm) and LUP (0.160 microm) methods was little affected by local distortions (30 x 30 control points); weak local distortions made the GP method poorer (0.320 microm). Tests on real data showed that LUP and HRBF had accuracies comparable with that of GP for both 30 cm (GP: 0.238 microm; LUP: 0.240 microm; HRBF: 0.238 microm) and 40 cm (GP: 0.164 microm; LUP: 0.164 microm; HRBF: 0.164 microm) XRIIs. The LUP-based distortion correction was implemented in real time for image correction in digital tomography applications.

  12. Lowest excited states and optical absorption spectra of donor-acceptor copolymers for organic photovoltaics: a new picture emerging from tuned long-range corrected density functionals.

    PubMed

    Pandey, Laxman; Doiron, Curtis; Sears, John S; Brédas, Jean-Luc

    2012-11-01

    Polymers with low optical gaps are of importance to the organic photovoltaics community due to their potential for harnessing a large portion of the solar energy spectrum. The combination along their backbones of electron-rich and electron-deficient fragments contributes to the presence of low-lying excited states that are expected to display significant charge-transfer character. While conventional hybrid functionals are known to provide unsatisfactory results for charge-transfer excitations at the time-dependent DFT level, long-range corrected (LRC) functionals have been reported to give improved descriptions in a number of systems. Here, we use such LRC functionals, considering both tuned and default range-separation parameters, to characterize the absorption spectra of low-optical-gap systems of interest. Our results indicate that tuned LRC functionals lead to simulated optical-absorption properties in good agreement with experimental data. Importantly, the lowest-lying excited states (excitons) are shown to present a much more localized nature than initially anticipated.

  13. Can Multiconfigurational Self-Consistent Field Theory and Density Functional Theory Correctly Predict the Ground State of Metal-Metal-Bonded Complexes?

    PubMed

    Carlson, Rebecca K; Odoh, Samuel O; Tereniak, Stephen J; Lu, Connie C; Gagliardi, Laura

    2015-09-01

    The electronic structure of a diiron (FeFe) complex with strong metal-metal interaction and those of analogous complexes (CoCo, CoMn, CoFe, and FeMn) with much weaker metal-metal bonding are investigated with wave function-based methods and density functional theory. The delocalization and bonding between the metal centers in the diiron complex is only fully captured after inclusion of the complete set of 3d and 4d orbitals in the active space, a situation best suited for restricted active space (RAS) approaches. Truncation of the included set of 4d orbitals results in inappropriate localization of some 3d orbitals, incorrect description of the ground spin state as well as wrong spin state energetics, as compared to experiment. Using density functional theory, some local functionals are able to predict the correct ground spin states, and describe the chemical bonding and structural properties of all the metal-metal complexes considered in this work. In contrast, the introduction of some exact exchange results in increased localization of 3d orbitals and wrong spin state energetics, a situation that is particularly troublesome for the diiron complex.

  14. MacMahon's conjecture on symmetric plane partitions

    PubMed Central

    Andrews, George E.

    1977-01-01

    In 1898, P. A. MacMahon conjectured that the generating function for symmetric plane partitions with at most s rows and each part at most j has an especially simple closed form. An outline of the proof of this conjecture is given here. PMID:16592386

  15. Orientation and velocity dependence of the nonequilibrium partition coefficient

    NASA Technical Reports Server (NTRS)

    Beatty, K. M.; Jackson, K. A.

    1995-01-01

    Monte Carlo simulations based on a Spin-1 Ising Model for binary alloys have been used to investigate the non-equilibrium partition coefficient (k(sub neq)) as a function of solid-liquid interface velocity and orientation. In simulations of Si with a second component k(sub neq) is greater in the [111] direction than the [100] direction in agreement with experimental results reported by Azlz et al. The simulated partition coefficient scales with the square of the step velocity divided by the diffusion coefficient of the secondary component in the liquid.

  16. Simultaneous determination of penicillin G salts by infrared spectroscopy: Evaluation of combining orthogonal signal correction with radial basis function-partial least squares regression

    NASA Astrophysics Data System (ADS)

    Talebpour, Zahra; Tavallaie, Roya; Ahmadi, Seyyed Hamid; Abdollahpour, Assem

    2010-09-01

    In this study, a new method for the simultaneous determination of penicillin G salts in pharmaceutical mixture via FT-IR spectroscopy combined with chemometrics was investigated. The mixture of penicillin G salts is a complex system due to similar analytical characteristics of components. Partial least squares (PLS) and radial basis function-partial least squares (RBF-PLS) were used to develop the linear and nonlinear relation between spectra and components, respectively. The orthogonal signal correction (OSC) preprocessing method was used to correct unexpected information, such as spectral overlapping and scattering effects. In order to compare the influence of OSC on PLS and RBF-PLS models, the optimal linear (PLS) and nonlinear (RBF-PLS) models based on conventional and OSC preprocessed spectra were established and compared. The obtained results demonstrated that OSC clearly enhanced the performance of both RBF-PLS and PLS calibration models. Also in the case of some nonlinear relation between spectra and component, OSC-RBF-PLS gave satisfactory results than OSC-PLS model which indicated that the OSC was helpful to remove extrinsic deviations from linearity without elimination of nonlinear information related to component. The chemometric models were tested on an external dataset and finally applied to the analysis commercialized injection product of penicillin G salts.

  17. Functional representation for the born-oppenheimer diagonal correction and born-huang adiabatic potential energy surfaces for isotopomers of H3.

    PubMed

    Mielke, Steven L; Schwenke, David W; Schatz, George C; Garrett, Bruce C; Peterson, Kirk A

    2009-04-23

    Multireference configuration interaction (MRCI) calculations of the Born-Oppenheimer diagonal correction (BODC) for H(3) were performed at 1397 symmetry-unique configurations using the Handy-Yamaguchi-Schaefer approach; isotopic substitution leads to 4041 symmetry-unique configurations for the DH(2) mass combination. These results were then fit to a functional form that permits calculation of the BODC for any combination of isotopes. Mean unsigned fitting errors on a test grid of configurations not included in the fitting process were 0.14, 0.12, and 0.65 cm(-1) for the H(3), DH(2), and MuH(2) isotopomers, respectively. This representation can be combined with any Born-Oppenheimer potential energy surface (PES) to yield Born-Huang (BH) PESs; herein, we choose the CCI potential energy surface, the uncertainties of which ( approximately 0.01 kcal/mol) are much smaller than the magnitude of the BODC. Fortran routines to evaluate these BH surfaces are provided. Variational transition state theory calculations are presented comparing thermal rate constants for reactions on the BO and BH surfaces to provide an initial estimate of the significance of the diagonal correction for the dynamics. PMID:19290604

  18. Expression and Function of Ccbe1 in the Chick Early Cardiogenic Regions Are Required for Correct Heart Development

    PubMed Central

    Correia, Elizabeth; Inácio, José Manuel; Belo, José António

    2014-01-01

    During the course of a differential screen to identify transcripts specific for chick heart/hemangioblast precursor cells, we have identified Ccbe1 (Collagen and calcium-binding EGF-like domain 1). While the importance of Ccbe1 for the development of the lymphatic system is now well demonstrated, its role in cardiac formation remained unknown. Here we show by whole-mount in situ hybridization analysis that cCcbe1 mRNA is initially detected in early cardiac progenitors of the two bilateral cardiogenic fields (HH4), and at later stages on the second heart field (HH9-18). Furthermore, cCcbe1 is expressed in multipotent and highly proliferative cardiac progenitors. We characterized the role of cCcbe1 during early cardiogenesis by performing functional studies. Upon morpholino-induced cCcbe1 knockdown, the chick embryos displayed heart malformations, which include aberrant fusion of the heart fields, leading to incomplete terminal differentiation of the cardiomyocytes. cCcbe1 overexpression also resulted in severe heart defects, including cardia bifida. Altogether, our data demonstrate that although cardiac progenitors cells are specified in cCcbe1 morphants, the migration and proliferation of cardiac precursors cells are impaired, suggesting that cCcbe1 is a key gene during early heart development. PMID:25545279

  19. Effect of feeding Murraya koeingii and Brassica juncea diet on [correction] kidney functions and glucose levels in streptozotocin diabetic mice.

    PubMed

    Grover, J K; Yadav, S P; Vats, V

    2003-03-01

    Purpose of the study was to investigate the effects of daily oral feeding 15% of powdered leaves of Murraya koeingii (MK) (commonly called as Curry patta) and 10% powder of seeds of Brassica juncea (BJ) (commonly called as Rai) for 60 days on serum glucose concentrations and kidney functions in streptozotocin (STZ; 100mg/kg) diabetic rats. Serum glucose levels, body weight, urine volume, serum creatinine, and urinary albumin (UAE) levels were monitored on day 0, 10, 25, 40, and 70 of the experiment. After 60 days of STZ administration, urine volume per day and UAE levels were significantly higher (P<0.0005) in diabetic controls (DC) as compared to normal controls (NC). Although feeding of the MK/BJ showed a trend towards improvement in most of the parameters, results were not statistically different from the DC except in serum creatinine values in BJ-fed rats on day 70. Thus, these plants can be best utilized by promoting them as preferable food adjuvants for diabetic patients.

  20. Specific 13C functional pathways as diagnostic targets in gastroenterology breath-tests: tricks for a correct interpretation.

    PubMed

    Pizzoferrato, M; Del Zompo, F; Mangiola, F; Lopetuso, L R; Petito, V; Cammarota, G; Gasbarrini, A; Scaldaferri, F

    2013-01-01

    Breath tests are non-invasive, non-radioactive, safe, simple and effective tests able to determine significant metabolic alterations due to specific diseases or lack of specific enzymes. Carbon isotope (13)C, the stable-non radioactive isotope of carbon, is the most used substrate in breath testing, in which (13)C/(12)C ratio is measured and expressed as a delta value, a differences between readings and a fixed standard. (13)C/(12)C ratio is measured with isotope ratio mass spectrometry or non-dispersive isotope-selective infrared spectrometer and generally there is a good agreement between these techniques in the isotope ratio estimation. (13)C/(12)C ratio can be expressed as static measurement (like delta over baseline in urea breath test) or as dynamic measurement as percent dose recovery, but more dosages are necessary. (13)C Breath-tests are involved in many fields of interest within gastroenterology, such as detection of Helicobacter pylori infection, study of gastric emptying, assessment of liver and exocrine pancreatic functions, determination of oro-caecal transit time, evaluation of absorption and to a lesser extend detection of bacterial overgrowth. The use of every single test in a clinical setting is vary depending on accuracy and substrate costs. This review is meant to present (13)C the meaning of (13)C/(12)C ratio and static and dynamic measure and, finally, the instruments dedicated to its use in gastroenterology. A brief presentation of (13)C breath tests in gastroenterology is also provided. PMID:24443068

  1. Effects of the partitioning of diffuse and direct solar radiation on satellite-based modeling of crop gross primary production

    NASA Astrophysics Data System (ADS)

    Xin, Qinchuan; Gong, Peng; Suyker, Andrew E.; Si, Yali

    2016-08-01

    Modeling crop gross primary production (GPP) is critical to understanding the carbon dynamics of agro-ecosystems. Satellite-based studies have widely used production efficiency models (PEM) to estimate cropland GPP, wherein light use efficiency (LUE) is a key model parameter. One factor that has not been well considered in many PEMs is that canopy LUE could vary with illumination conditions. This study investigates how the partitioning of diffuse and direct solar radiation influences cropland GPP using both flux tower and satellite data. The field-measured hourly LUE under cloudy conditions was 1.50 and 1.70 times higher than that under near clear-sky conditions for irrigated corn and soybean, respectively. We applied a two-leaf model to simulate the canopy radiative transfer process, where modeled photosynthetically active radiation (PAR) absorbed by canopy agreed with tower measurements (R2 = 0.959 and 0.914 for corn and soybean, respectively). Derived canopy LUE became similar after accounting for the impact of light saturation on leaf photosynthetic capacity under varied illumination conditions. The impacts of solar radiation partitioning on satellite-based modeling of crop GPP was examined using vegetation indices (VI) derived from MODIS data. Consistent with the field modeling results, the relationship between daily GPP and PAR × VI under varied illumination conditions showed different patterns in terms of regression slope and intercept. We proposed a function to correct the influences of direct and diffuse radiation partitioning and the explained variance of flux tower GPP increased in all experiments. Our results suggest that the non-linear response of leaf photosynthesis to light absorption contributes to higher canopy LUE on cloudy days than on clear days. We conclude that accounting for the impacts of solar radiation partitioning is necessary for modeling crop GPP on a daily or shorter basis.

  2. Choosing a density functional for modeling adsorptive hydrogen storage: reference quantum mechanical calculations and a comparison of dispersion-corrected density functionals.

    PubMed

    Kocman, Mikuláš; Jurečka, Petr; Dubecký, Matúš; Otyepka, Michal; Cho, Yeonchoo; Kim, Kwang S

    2015-03-01

    Hydrogen storage in carbonaceous materials and their derivatives is currently a widely investigated topic. The rational design of novel adsorptive materials is often attempted with the help of computational chemistry tools, in particular density functional theory (DFT). However, different exchange-correlation functionals provide a very wide range of hydrogen binding energies. The aim of this article is to offer high level QM reference data based on coupled-cluster singles and doubles calculations with perturbative triple excitations, CCSD(T), and a complete basis set limit estimate that can be used to assess the accuracy of various DFT-based predictions. For one complex, the CCSD(T) result is verified against diffusion quantum Monte Carlo calculations. Reference binding curves are calculated for two model compounds representing weak and strong hydrogen adsorption: coronene (-4.7 kJ mol(-1) per H2), and coronene modified with boron and lithium (-14.3 kJ mol(-1)). The reference data are compared to results obtained with widely used density functionals including pure DFT, M06, DFT-D3, PBE-TS, PBE + MBD, optB88-vdW, vdW-DF, vdW-DF2 and VV10. We find that whereas DFT-D3 shows excellent results for weak hydrogen adsorption on coronene, most of the less empirical density based dispersion functionals except VV10 overestimate this interaction. On the other hand, some of the less empirical density based dispersion functionals better describe stronger binding in the more polar coroB2Li22H2 complex which is one of realistic models for high-capacity hydrogen storage materials. Our results may serve as a guide for choosing suitable DFT methods for quickly evaluating hydrogen binding potential and as a reference for assessing the accuracy of the previously published DFT results.

  3. Twisted sectors from plane partitions

    NASA Astrophysics Data System (ADS)

    Datta, Shouvik; Gaberdiel, Matthias R.; Li, Wei; Peng, Cheng

    2016-09-01

    Twisted sectors arise naturally in the bosonic higher spin CFTs at their free points, as well as in the associated symmetric orbifolds. We identify the coset representations of the twisted sector states using the description of W_{∞} representations in terms of plane partitions. We confirm these proposals by a microscopic null-vector analysis, and by matching the excitation spectrum of these representations with the orbifold prediction.

  4. Ferrous iron partitioning in the lower mantle

    NASA Astrophysics Data System (ADS)

    Muir, Joshua M. R.; Brodholt, John P.

    2016-08-01

    We used density functional theory (DFT) to examine the partitioning of ferrous iron between periclase and bridgmanite under lower mantle conditions. To study the effects of the three major variables - pressure, temperature and concentration - these have been varied from 0 to 150 GPa, from 1000 to 4000 K and from 0 to 100% total iron content. We find that increasing temperature increases KD, increasing iron concentration decreases KD, while pressure can both increase and decrease KD. We find that KD decreases slowly from about 0.32 to 0.06 with depth under lower mantle conditions. We also find that KD increases sharply to 0.15 in the very lowermost mantle due to the strong temperature increases near the CMB. Spin transitions have a large effect on the activity of ferropericlase which causes KD to vary with pressure in a peak-like fashion. Despite the apparently large changes in KD through the mantle, this actually results in relatively small changes in total iron content in the two phases, with XFefp ranging from about 0.20 to 0.35, before decreasing again to about 0.28 at the CMB, and XFebd has a pretty constant value of about 0.04-0.07 throughout the lower mantle. For the very high Fe concentrations suggested for ULVZs, Fe partitions very strongly into ferropericlase.

  5. A Robust Computational Method for Coupled Liquid-liquid Phase Separation and Gas-particle Partitioning Predictions of Multicomponent Aerosols

    NASA Astrophysics Data System (ADS)

    Zuend, A.; Di Stefano, A.

    2014-12-01

    Providing efficient and reliable model predictions for the partitioning of atmospheric aerosol components between different phases (gas, liquids, solids) is a challenging problem. The partitioning of water, various semivolatile organic components, inorganic acids, bases, and salts, depends simultaneously on the chemical properties and interaction effects among all constituents of a gas + aerosol system. The effects of hygroscopic particle growth on the water contents and physical states of potentially two or more liquid and/or solid aerosol phases in turn may significantly affect multiphase chemistry, the direct effect of aerosols on climate, and the ability of specific particles to act as cloud condensation or ice nuclei. Considering the presence of a liquid-liquid phase separation in aerosol particles, which typically leads to one phase being enriched in rather hydrophobic compounds and the other phase enriched in water and dissolved electrolytes, adds a high degree of complexity to the goal of predicting the gas-particle partitioning of all components. Coupled gas-particle partitioning and phase separation methods are required to correctly account for the phase behaviour of aerosols exposed to varying environmental conditions, such as changes to relative humidity. We present new theoretical insights and a substantially improved algorithm for the reliable prediction of gas-particle partitioning at thermodynamic equilibrium based on the Aerosol Inorganic-Organic Mixtures Functional groups Activity Coefficients (AIOMFAC) model. We introduce a new approach for the accurate prediction of the phase distribution of multiple inorganic ions between two liquid phases, constrained by charge balance, and the coupling of the liquid-liquid equilibrium model to a robust gas-particle partitioning algorithm. Such coupled models are useful for exploring the range of environmental conditions leading to complete or incomplete miscibility of aerosol constituents which will affect

  6. Magnetic properties and vapochromic reversible guest-induced transformation in a bispyrazolato copper(II) polymer: an experimental and dispersion-corrected density functional theory study.

    PubMed

    Bencini, Alessandro; Casarin, Maurizio; Forrer, Daniel; Franco, Lorenzo; Garau, Federica; Masciocchi, Norberto; Pandolfo, Luciano; Pettinari, Claudio; Ruzzi, Marco; Vittadini, Andrea

    2009-05-01

    Dispersion-corrected density functional theory (DFT-D) calculations, Electron Spin Resonance spectroscopy (EPR), and variable temperature magnetic moment measurements were used to investigate the structure and the electronic/magnetic properties of bispyrazolato-copper(II) coordination polymer and of its hydration product. The Cu(II) ions are antiferromagnetically coupled through the sigma system of the pyrazolate rings in both compounds. Theoretical electron density maps reveal that water molecules interact simultaneously and to a comparable extent with two Cu(II) centers (through the electronegative O end) and two pyrazolate rings (through the partly positively charged H atoms), which is compatible with the observed internuclear distances. DFT-D calculations indicate that low kinetic barriers are involved in the rearrangement of the host structure.

  7. Effects of functional orthodontic appliances in the correction of a primary anterior crossbite--changes in craniofacial morphology and tongue position.

    PubMed

    Onodera, Kieko; Niikuni, Naoko; Yanagisawa, Munemitsu; Nakajima, Ichiro

    2006-08-01

    Chin caps have been used for the correction of primary anterior crossbites, but previous studies of the treatment effects have highlighted problems such as pressure on the temporomandibular joint (TMJ). Therefore, to reduce pressure on the TMJ, a functional orthodontic appliance, the Yanagisawa Class III (YC3) shield was developed to improve the overjet in the primary dentition. The aim of this study was to determine the treatment effects of the YC3 in correcting a primary anterior crossbite compared with a chin cap. The pre- and post-treatment lateral cephalograms of 10 patients (5 male, 5 females) and 10 treated with a YC3 (5 males, 5 females) were compared in relation to craniofacial morphology and tongue position [the YC3 was used from 51 months of age +/- 7 months to 74 months of age +/- 12 months (i.e. for 23 +/- 9 months) and the chin cap from 53 months of age +/- 2 months to 75 months of age +/- 1 month (i.e. for 22 +/- 5 months)]. A Mann-Whitney U-test was used to determine any statistical differences. The YC3 group showed significantly higher values for gonial angle and U1 to SN (P < 0.05), and significantly lower values for interincisal and tongue position (P < 0.05), compared with the chin cap group. The results indicate that the use of the YC3 not only improves overjet, but also changes the tongue position. The findings also suggest that the YC3 results in functional effects on the skeletal system during the mid-growth period.

  8. Some Remarks on the Theory of Element Partitioning

    NASA Astrophysics Data System (ADS)

    Karato, S. I.

    2015-12-01

    Element partitioning is probably the most important concept in geochemistry. However some fundamental issues on element partitioning are poorly understood or misinterpreted or misused. In this presentation, I will discuss two issues. First, the dependence of (trace) element partitioning on the properties of trace element has been understood incompletely (or incorrectly). A strain energy model is a good approximation, but in all previous models, only the influence of the size of trace element is considered. As a result, the influence of "stiffness" of the trace element was ignored and the physical meaning of elastic constants in the theory was vaguely described as "site-elasticity". I developed a modified model in which the influence of the stiffness of the trace element is included with the correct boundary conditions. The incorporation of the influence of stiffness of trace element is critical particularly in a case where the trace element is soft, e.g., a case of noble gas. The new model provides better explanation of the observed element partitioning. Second, the influence of selective dissolution of a trace element in the melt is often ignored. It is well known that the solubility of noble gas in the melt strongly depends on its atomic size. In contrast, the dependence of trace element solubility on its size is not well known but usually ignored. I developed a conceptual model to explain why noble gas solubility is strongly size dependent but not for the solubility of other charged trace elements. These two shortcomings in the previous models are serious when the partitioning of noble gas elements is considered. Some applications of these models will be discussed including the behavior of the noble gases during melting and solidification and the evaluation of water content and its influence on the rheological properties of the lithosphere.

  9. Metal/Silicate Partitioning at High Pressures and Temperatures

    NASA Technical Reports Server (NTRS)

    Shofner, G.; Campbell, A.; Danielson, L.; Righter, K.; Rahman, Z.

    2010-01-01

    The behavior of siderophile elements during metal-silicate segregation, and their resulting distributions provide insight into core formation processes. Determination of partition coefficients allows the calculation of element distributions that can be compared to established values of element abundances in the silicate (mantle) and metallic (core) portions of the Earth. Moderately siderophile elements, including W, are particularly useful in constraining core formation conditions because they are sensitive to variations in T, P, oxygen fugacity (fO2), and silicate composition. To constrain the effect of pressure on W metal/silicate partitioning, we performed experiments at high pressures and temperatures using a multi anvil press (MAP) at NASA Johnson Space Center and laser-heated diamond anvil cells (LHDAC) at the University of Maryland. Starting materials consisted of natural peridotite mixed with Fe and W metals. Pressure conditions in the MAP experiments ranged from 10 to 16 GPa at 2400 K. Pressures in the LHDAC experiments ranged from 26 to 58 GPa, and peak temperatures ranged up to 5000 K. LHDAC experimental run products were sectioned by focused ion beam (FIB) at NASA JSC. Run products were analyzed by electron microprobe using wavelength dispersive spectroscopy. Liquid metal/liquid silicate partition coefficients for W were calculated from element abundances determined by microprobe analyses, and corrected to a common fO2 condition of IW-2 assuming +4 valence for W. Within analytical uncertainties, W partitioning shows a flat trend with increasing pressure from 10 to 16 GPa. At higher pressures, W becomes more siderophile, with an increase in partition coefficient of approximately 0.5 log units.

  10. Correction of Distortion in Flattened Representations of the Cortical Surface Allows Prediction of V1-V3 Functional Organization from Anatomy

    PubMed Central

    Benson, Noah C.; Butt, Omar H.; Brainard, David H.; Aguirre, Geoffrey K.

    2014-01-01

    Several domains of neuroscience offer map-like models that link location on the cortical surface to properties of sensory representation. Within cortical visual areas V1, V2, and V3, algebraic transformations can relate position in the visual field to the retinotopic representation on the flattened cortical sheet. A limit to the practical application of this structure-function model is that the cortex, while topologically a two-dimensional surface, is curved. Flattening of the curved surface to a plane unavoidably introduces local geometric distortions that are not accounted for in idealized models. Here, we show that this limitation is overcome by correcting the geometric distortion induced by cortical flattening. We use a mass-spring-damper simulation to create a registration between functional MRI retinotopic mapping data of visual areas V1, V2, and V3 and an algebraic model of retinotopy. This registration is then applied to the flattened cortical surface anatomy to create an anatomical template that is linked to the algebraic retinotopic model. This registered cortical template can be used to accurately predict the location and retinotopic organization of these early visual areas from cortical anatomy alone. Moreover, we show that prediction accuracy remains when extrapolating beyond the range of data used to inform the model, indicating that the registration reflects the retinotopic organization of visual cortex. We provide code for the mass-spring-damper technique, which has general utility for the registration of cortical structure and function beyond the visual cortex. PMID:24676149

  11. Cohesive properties of noble metals by van der Waals-corrected density functional theory: Au, Ag, and Cu as case studies

    NASA Astrophysics Data System (ADS)

    Ambrosetti, Alberto; Silvestrelli, Pier Luigi

    2016-07-01

    The cohesive energy, equilibrium lattice constant, and bulk modulus of Au, Ag, and Cu noble metals are computed by different van der Waals (vdW)-corrected density functional theory (DFT) methods, including vdW-DF, vdW-DF2, vdW-DF-cx, rVV10, and PBE-D. Two specifically designed methods are also developed in order to effectively include dynamical screening effects: the DFT/vdW-WF2p method, based on the generation of maximally localized Wannier functions, and the RPAp scheme (in two variants), based on a single-oscillator model of the localized electron response. Comparison with results obtained without explicit inclusion of van der Waals effects, such as with the local density approximation (LDA), PBE, PBEsol, or the hybrid PBE0 functional, elucidates the importance of a suitable description of screened van der Waals interactions even in the case of strong metal bonding. Many-body effects are also quantitatively evaluated within the RPAp approach.

  12. Barometric and Earth Tide Correction

    SciTech Connect

    Toll, Nathaniel J.

    2005-11-10

    BETCO corrects for barometric and earth tide effects in long-term water level records. A regression deconvolution method is used ot solve a series of linear equations to determine an impulse response function for the well pressure head. Using the response function, a pressure head correction is calculated and applied.

  13. Computer program for calculating and fitting thermodynamic functions

    NASA Technical Reports Server (NTRS)

    Mcbride, Bonnie J.; Gordon, Sanford

    1992-01-01

    A computer program is described which (1) calculates thermodynamic functions (heat capacity, enthalpy, entropy, and free energy) for several optional forms of the partition function, (2) fits these functions to empirical equations by means of a least-squares fit, and (3) calculates, as a function of temperture, heats of formation and equilibrium constants. The program provides several methods for calculating ideal gas properties. For monatomic gases, three methods are given which differ in the technique used for truncating the partition function. For diatomic and polyatomic molecules, five methods are given which differ in the corrections to the rigid-rotator harmonic-oscillator approximation. A method for estimating thermodynamic functions for some species is also given.

  14. Unsupervised hierarchical partitioning of hyperspectral images: application to marine algae identification

    NASA Astrophysics Data System (ADS)

    Chen, B.; Chehdi, K.; De Oliveria, E.; Cariou, C.; Charbonnier, B.

    2015-10-01

    In this paper a new unsupervised top-down hierarchical classification method to partition airborne hyperspectral images is proposed. The unsupervised approach is preferred because the difficulty of area access and the human and financial resources required to obtain ground truth data, constitute serious handicaps especially over large areas which can be covered by airborne or satellite images. The developed classification approach allows i) a successive partitioning of data into several levels or partitions in which the main classes are first identified, ii) an estimation of the number of classes automatically at each level without any end user help, iii) a nonsystematic subdivision of all classes of a partition Pj to form a partition Pj+1, iv) a stable partitioning result of the same data set from one run of the method to another. The proposed approach was validated on synthetic and real hyperspectral images related to the identification of several marine algae species. In addition to highly accurate and consistent results (correct classification rate over 99%), this approach is completely unsupervised. It estimates at each level, the optimal number of classes and the final partition without any end user intervention.

  15. Thermodynamic approaches using group contribution methods to model partitioning of semi-volatile organic compounds on atmospheric particulate matter: Temperature, humidity, and composition of aerosols

    NASA Astrophysics Data System (ADS)

    Jang, Myoseon

    The partitioning of organic compounds between particulate matter and the gas phase is strongly influenced by temperature, water vapor concentration, the chemical composition of particles, and the amount of organic material in particles. To describe the partitioning of semi-volatile organic compounds (SOCs) between the gas phase and particles (G/P), a partitioning constant, Kp, has been estimated from experimental measurements and theory. Because the true or observed Kp of SOCs determined from a given particle medium includes the activity coefficient term, the linearity between log Kp and the liquid (or subcooled liquid) vapor pressure, log pLo must be corrected by the activity coefficients of individual compounds. To calculate activity coefficients in different particle liquid media such as wood combustion, diesel combustion exhaust, and the secondary aerosols from α-pinene-ozone reaction, thermodynamic models (Hildebrand-Hansen cohesive energy density and UNIFAC) which use an additive group contribution method were used. Humidity effects on the G/P partitioning of the different types of semi-volatile organic compounds (SOCs) in the organic layer of different particles, were studied. The equilibrated water uptake in the organic layer of chemically different particles was computed from the activity coefficient of water in the organic liquid layer of an aerosol and the ambient relative humidity (RH). It was concluded that the humidity effect on partitioning was most important for hydrophobic compounds in polar aerosols and this effect was significant. Secondary aerosols from the α-pinene reaction with ozone were characterized using derivation methods. Products were identified by using instrumental techniques such as GC/CI-MS-ECD, GC/EI-MS-ECD, and GC/FT-IR. For oxy functional groups such as acids, ketones and aldehydes, derivatization was performed using fluorinated reagents to reinforce the analytical power on GC development: O- (2,3,4,5,6-pentafluorobenzyl

  16. Cylindric partitions, {{\\boldsymbol{ W }}}_{r} characters and the Andrews-Gordon-Bressoud identities

    NASA Astrophysics Data System (ADS)

    Foda, O.; Welsh, T. A.

    2016-04-01

    We study the Andrews-Gordon-Bressoud (AGB) generalisations of the Rogers-Ramanujan q-series identities in the context of cylindric partitions. We recall the definition of r-cylindric partitions, and provide a simple proof of Borodin’s product expression for their generating functions, that can be regarded as a limiting case of an unpublished proof by Krattenthaler. We also recall the relationships between the r-cylindric partition generating functions, the principal characters of {\\hat{{sl}}}r algebras, the {{\\boldsymbol{ M }}}r r,r+d minimal model characters of {{\\boldsymbol{ W }}}r algebras, and the r-string abaci generating functions, providing simple proofs for each. We then set r = 2, and use two-cylindric partitions to re-derive the AGB identities as follows. Firstly, we use Borodin’s product expression for the generating functions of the two-cylindric partitions with infinitely long parts, to obtain the product sides of the AGB identities, times a factor {(q;q)}∞ -1, which is the generating function of ordinary partitions. Next, we obtain a bijection from the two-cylindric partitions, via two-string abaci, into decorated versions of Bressoud’s restricted lattice paths. Extending Bressoud’s method of transforming between restricted paths that obey different restrictions, we obtain sum expressions with manifestly non-negative coefficients for the generating functions of the two-cylindric partitions which contains a factor {(q;q)}∞ -1. Equating the product and sum expressions of the same two-cylindric partitions, and canceling a factor of {(q;q)}∞ -1 on each side, we obtain the AGB identities.

  17. Van Der Waals-Corrected Density Functional Theory Simulation of Adsorption Processes on Noble-Metal Surfaces: Xe on Ag(111), Au(111), and Cu(111)

    NASA Astrophysics Data System (ADS)

    Silvestrelli, Pier Luigi; Ambrosetti, Alberto

    2016-10-01

    The DFT/vdW-WF2s1 method based on the generation of localized Wannier functions, recently developed to include the van der Waals interactions in the density functional theory and describe adsorption processes on metal surfaces by taking metal-screening effects into account, is applied to the case of the interaction of Xe with noble-metal surfaces, namely Ag(111), Au(111), and Cu(111). The study is also repeated by adopting the DFT/vdW-QHO-WF variant relying on the quantum harmonic oscillator model which describes well many body effects. Comparison of the computed equilibrium binding energies and distances, and the C_3 coefficients characterizing the adatom-surface van der Waals interactions, with available experimental and theoretical reference data shows that the methods perform well and elucidates the importance of properly including screening effects. The results are also compared with those obtained by other vdW-corrected DFT schemes, including PBE-D, vdW-DF, vdW-DF2, rVV10, and by the simpler local density approximation and semi-local (PBE) generalized gradient approximation approaches.

  18. A Density Functional Theory Based Protocol to Compute the Redox Potential of Transition Metal Complex with the Correction of Pseudo-Counterion: General Theory and Applications.

    PubMed

    Matsui, Toru; Kitagawa, Yasutaka; Shigeta, Yasuteru; Okumura, Mitsutaka

    2013-07-01

    We propose an accurate scheme to evaluate the redox potential of a wide variety of transition metal complexes by adding a charge-dependent correction term for a counterion around the charged complexes, which is based on Generalized Born theory, to the solvation energy. The mean absolute error (MAE) toward experimental redox potentials of charged complexes is considerably reduced from 0.81 V (maximum error 1.22 V) to 0.22 V (maximum error 0.50 V). We found a remarkable exchange-correlation functional dependence on the results rather than the basis set ones. The combination of Wachters+f (for metal) and 6-31++G(d,p) (for other atoms) with the B3LYP functional gives the least MAE 0.15 V for the test complexes. This scheme is applicable to other solvents, and heavier transition metal complexes such as M1(CO)5(pycn) (M1 = Cr, Mo, W), M2(mnt)2 (M2 = Ni, Pd, Pt), and M3(bpy)3 (M3 = Fe, Ru, Os) with the same quality.

  19. AAV-mediated intramuscular delivery of myotubularin corrects the myotubular myopathy phenotype in targeted murine muscle and suggests a function in plasma membrane homeostasis.

    PubMed

    Buj-Bello, Anna; Fougerousse, Françoise; Schwab, Yannick; Messaddeq, Nadia; Spehner, Danièle; Pierson, Christopher R; Durand, Muriel; Kretz, Christine; Danos, Olivier; Douar, Anne-Marie; Beggs, Alan H; Schultz, Patrick; Montus, Marie; Denèfle, Patrice; Mandel, Jean-Louis

    2008-07-15

    Myotubular myopathy (XLMTM, OMIM 310400) is a severe congenital muscular disease due to mutations in the myotubularin gene (MTM1) and characterized by the presence of small myofibers with frequent occurrence of central nuclei. Myotubularin is a ubiquitously expressed phosphoinositide phosphatase with a muscle-specific role in man and mouse that is poorly understood. No specific treatment exists to date for patients with myotubular myopathy. We have constructed an adeno-associated virus (AAV) vector expressing myotubularin in order to test its therapeutic potential in a XLMTM mouse model. We show that a single intramuscular injection of this vector in symptomatic Mtm1-deficient mice ameliorates the pathological phenotype in the targeted muscle. Myotubularin replacement in mice largely corrects nuclei and mitochondria positioning in myofibers and leads to a strong increase in muscle volume and recovery of the contractile force. In addition, we used this AAV vector to overexpress myotubularin in wild-type skeletal muscle and get insight into its localization and function. We show that a substantial proportion of myotubularin associates with the sarcolemma and I band, including triads. Myotubularin overexpression in muscle induces the accumulation of packed membrane saccules and presence of vacuoles that contain markers of sarcolemma and T-tubules, suggesting that myotubularin is involved in plasma membrane homeostasis of myofibers. This study provides a proof-of-principle that local delivery of an AAV vector expressing myotubularin can improve the motor capacities of XLMTM muscle and represents a novel approach to study myotubularin function in skeletal muscle.

  20. Liquid structures of water, methanol, and hydrogen fluoride at ambient conditions from first principles molecular dynamics simulations with a dispersion corrected density functional.

    PubMed

    McGrath, Matthew J; Kuo, I-Feng William; Siepmann, J Ilja

    2011-11-28

    Using first principles molecular dynamics simulations in the isobaric-isothermal ensemble (T = 300 K, p = 1 atm) with the Becke-Lee-Yang-Parr exchange/correlation functional and a dispersion correction due to Grimme, the hydrogen bonding networks of pure liquid water, methanol, and hydrogen fluoride are probed. Although an accurate density is found for water with this level of electronic structure theory, the average liquid densities for both hydrogen fluoride and methanol are overpredicted by 50 and 25%, respectively. The radial distribution functions indicate somewhat overstructured liquid phases for all three compounds. The number of hydrogen bonds per molecule in water is about twice as high as for methanol and hydrogen fluoride, though the ratio of cohesive energy over number of hydrogen bonds is lower for water. An analysis of the hydrogen-bonded aggregates revealed the presence of mostly linear chains in both hydrogen fluoride and methanol, with a few stable rings and chains spanning the simulation box in the case of hydrogen fluoride. Only an extremely small fraction of smaller clusters was found for water, indicating that its hydrogen bond network is significantly more extensive. A special form of water with on average about two hydrogen bonds per molecule yields a hydrogen-bonding environment significantly different from the other two compounds.

  1. On some trees having partition dimension four

    NASA Astrophysics Data System (ADS)

    Ida Bagus Kade Puja Arimbawa, K.; Baskoro, Edy Tri

    2016-02-01

    In 1998, G. Chartrand, E. Salehi and P. Zhang introduced the notion of partition dimension of a graph. Since then, the study of this graph parameter has received much attention. A number of results have been obtained to know the values of partition dimensions of various classes of graphs. However, for some particular classes of graphs, finding of their partition dimensions is still not completely solved, for instances a class of general tree. In this paper, we study the properties of trees having partition dimension 4. In particular, we show that, for olive trees O(n), its partition dimension is equal to 4 if and only if 8 ≤ n ≤ 17. We also characterize all centipede trees having partition dimension 4.

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

    PubMed

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

    2008-12-01

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

  3. Chemical amplification based on fluid partitioning in an immiscible liquid

    DOEpatents

    Anderson, Brian L.; Colston, Bill W.; Elkin, Christopher J.

    2010-09-28

    A system for nucleic acid amplification of a sample comprises partitioning the sample into partitioned sections and performing PCR on the partitioned sections of the sample. Another embodiment of the invention provides a system for nucleic acid amplification and detection of a sample comprising partitioning the sample into partitioned sections, performing PCR on the partitioned sections of the sample, and detecting and analyzing the partitioned sections of the sample.

  4. An Efficient Algorithm for Partitioning and Authenticating Problem-Solutions of eLeaming Contents

    ERIC Educational Resources Information Center

    Dewan, Jahangir; Chowdhury, Morshed; Batten, Lynn

    2013-01-01

    Content authenticity and correctness is one of the important challenges in eLearning as there can be many solutions to one specific problem in cyber space. Therefore, the authors feel it is necessary to map problems to solutions using graph partition and weighted bipartite matching. This article proposes an efficient algorithm to partition…

  5. The dependence of the lipid bilayer membrane: buffer partition coefficient of pentobarbitone on pH and lipid composition.

    PubMed Central

    Miller, K W; Yu, S C

    1977-01-01

    1 The membrane/buffer partition coefficient of [14C]-pentobarbitone has been determined as a function of the lipid composition of bilayer membranes. 2 A new technique based on ultrafiltration gave comparable results to conventional techniques but required less time for equilbration. 3 The membrane/buffer coefficient was independent of pentobarbitone concentration in the range studies. 4 The apparent partition coefficient varied with pH and was a linear function of the degree of dissociation of pentobarbition. 5 Both the charged and uncharged forms of pentobarbitone partitioned into the membrane, the latter to a much greater extent than the former. 6 At low pH the highest partition coefficient observed was in egg phosphatidylcholine bilayer membranes. 7 Incorporation of cholesterol or phosphatidic acid into phosphatidylcholine membranes greatly reduced the partition coefficient. 8 High pressures do not greatly change these partition coefficients. PMID:21013

  6. Mass partitioning effects in diffusion transport.

    PubMed

    Kojic, Milos; Milosevic, Miljan; Wu, Suhong; Blanco, Elvin; Ferrari, Mauro; Ziemys, Arturas

    2015-08-28

    Frequent mass exchange takes place in a heterogeneous environment among several phases, where mass partitioning may occur at the interface of phases. Analytical and computational methods for diffusion do not usually incorporate molecule partitioning masking the true picture of mass transport. Here we present a computational finite element methodology to calculate diffusion mass transport with a partitioning phenomenon included and the analysis of the effects of partitioning. Our numerical results showed that partitioning controls equilibrated mass distribution as expected from analytical solutions. The experimental validation of mass release from drug-loaded nanoparticles showed that partitioning might even dominate in some cases with respect to diffusion itself. The analysis of diffusion kinetics in the parameter space of partitioning and diffusivity showed that partitioning is an extremely important parameter in systems, where mass diffusivity is fast and that the concentration of nanoparticles can control payload retention inside nanoparticles. The computational and experimental results suggest that partitioning and physiochemical properties of phases play an important, if not crucial, role in diffusion transport and should be included in the studies of mass transport processes.

  7. Mass partitioning effects in diffusion transport.

    PubMed

    Kojic, Milos; Milosevic, Miljan; Wu, Suhong; Blanco, Elvin; Ferrari, Mauro; Ziemys, Arturas

    2015-08-28

    Frequent mass exchange takes place in a heterogeneous environment among several phases, where mass partitioning may occur at the interface of phases. Analytical and computational methods for diffusion do not usually incorporate molecule partitioning masking the true picture of mass transport. Here we present a computational finite element methodology to calculate diffusion mass transport with a partitioning phenomenon included and the analysis of the effects of partitioning. Our numerical results showed that partitioning controls equilibrated mass distribution as expected from analytical solutions. The experimental validation of mass release from drug-loaded nanoparticles showed that partitioning might even dominate in some cases with respect to diffusion itself. The analysis of diffusion kinetics in the parameter space of partitioning and diffusivity showed that partitioning is an extremely important parameter in systems, where mass diffusivity is fast and that the concentration of nanoparticles can control payload retention inside nanoparticles. The computational and experimental results suggest that partitioning and physiochemical properties of phases play an important, if not crucial, role in diffusion transport and should be included in the studies of mass transport processes. PMID:26204522

  8. Computer code for controller partitioning with IFPC application: A user's manual

    NASA Technical Reports Server (NTRS)

    Schmidt, Phillip H.; Yarkhan, Asim

    1994-01-01

    A user's manual for the computer code for partitioning a centralized controller into decentralized subcontrollers with applicability to Integrated Flight/Propulsion Control (IFPC) is presented. Partitioning of a centralized controller into two subcontrollers is described and the algorithm on which the code is based is discussed. The algorithm uses parameter optimization of a cost function which is described. The major data structures and functions are described. Specific instructions are given. The user is led through an example of an IFCP application.

  9. A CORRECTION.

    PubMed

    Johnson, D

    1940-03-22

    IN a recently published volume on "The Origin of Submarine Canyons" the writer inadvertently credited to A. C. Veatch an excerpt from a submarine chart actually contoured by P. A. Smith, of the U. S. Coast and Geodetic Survey. The chart in question is Chart IVB of Special Paper No. 7 of the Geological Society of America entitled "Atlantic Submarine Valleys of the United States and the Congo Submarine Valley, by A. C. Veatch and P. A. Smith," and the excerpt appears as Plate III of the volume fist cited above. In view of the heavy labor involved in contouring the charts accompanying the paper by Veatch and Smith and the beauty of the finished product, it would be unfair to Mr. Smith to permit the error to go uncorrected. Excerpts from two other charts are correctly ascribed to Dr. Veatch. PMID:17839404

  10. A CORRECTION.

    PubMed

    Johnson, D

    1940-03-22

    IN a recently published volume on "The Origin of Submarine Canyons" the writer inadvertently credited to A. C. Veatch an excerpt from a submarine chart actually contoured by P. A. Smith, of the U. S. Coast and Geodetic Survey. The chart in question is Chart IVB of Special Paper No. 7 of the Geological Society of America entitled "Atlantic Submarine Valleys of the United States and the Congo Submarine Valley, by A. C. Veatch and P. A. Smith," and the excerpt appears as Plate III of the volume fist cited above. In view of the heavy labor involved in contouring the charts accompanying the paper by Veatch and Smith and the beauty of the finished product, it would be unfair to Mr. Smith to permit the error to go uncorrected. Excerpts from two other charts are correctly ascribed to Dr. Veatch.

  11. Partitioning of Nb, Mo, Ba, Ce, Pb, Th and U between immiscible carbonate and silicate liquids: Evaluating the effects of P2O5,F, and carbonate composition

    NASA Technical Reports Server (NTRS)

    Jones, J. H.; Walker, D.

    1993-01-01

    Previously we have reported carbonate liq./silicate liq. partition coefficients (D) for a standard suite of trace elements (Nb, Mo, Ba, Ce, Pb, Th, and U) and Ra and Pa as well. In brief, we have found that immiscible liquid partitioning is a strong function of temperature. As the critical temperature of the carbonate-silicate solvus is approached, all partition coefficients approach unity. Additionally, for the overwhelming majority of the partitioning elements, InD is a linear function of 'ionic field strength,' z/r, where z is the charge of the partitioned cation and r is its ionic radius.

  12. Equilibrium absorptive partitioning theory between multiple aerosol particle modes

    NASA Astrophysics Data System (ADS)

    Crooks, Matthew; Connolly, Paul; Topping, David; McFiggans, Gordon

    2016-10-01

    An existing equilibrium absorptive partitioning model for calculating the equilibrium gas and particle concentrations of multiple semi-volatile organics within a bulk aerosol is extended to allow for multiple involatile aerosol modes of different sizes and chemical compositions. In the bulk aerosol problem, the partitioning coefficient determines the fraction of the total concentration of semi-volatile material that is in the condensed phase of the aerosol. This work modifies this definition for multiple polydisperse aerosol modes to account for multiple condensed concentrations, one for each semi-volatile on each involatile aerosol mode. The pivotal assumption in this work is that each aerosol mode contains an involatile constituent, thus overcoming the potential problem of smaller particles evaporating completely and then condensing on the larger particles to create a monodisperse aerosol at equilibrium. A parameterisation is proposed in which the coupled non-linear system of equations is approximated by a simpler set of equations obtained by setting the organic mole fraction in the partitioning coefficient to be the same across all modes. By perturbing the condensed masses about this approximate solution a correction term is derived that accounts for many of the removed complexities. This method offers a greatly increased efficiency in calculating the solution without significant loss in accuracy, thus making it suitable for inclusion in large-scale models.

  13. Investigation of the pressure dependent thermodynamic and elastic properties of 1,3,5-triamino-2,4,6-trinitrobenzene using dispersion corrected density functional theory

    SciTech Connect

    Rykounov, A. A.

    2015-06-07

    The influence of pressure on the thermodynamic, structural, and elastic properties of the 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) molecular crystal at T = 0 is systematically studied. Calculations are carried out using density functional theory methods in a plane wave basis set with dispersion corrections for the exchange-correlation part of total energy, and ultrasoft pseudopotentials. The equilibrium unit cell parameters, the cold compression curve in the pressure range of 0–50 GPa and the sound speeds are computed. The effect of finite pressure on the molecular structure of TATB is elucidated from the analysis of relative changes in the intra- and intermolecular geometrical parameters. For the first time, the full set of elastic constants of this crystal at zero and non-zero pressures is determined from ab initio calculations. The resulted structural, elastic, and acoustic properties of TATB are shown to be in a good agreement with available experimental and theoretical data.

  14. Broad-based nutritional supplementation in 3xTg mice corrects mitochondrial function and indicates sex-specificity in response to Alzheimer's disease intervention.

    PubMed

    Wolf, Andrew B; Braden, B Blair; Bimonte-Nelson, Heather; Kusne, Yael; Young, Nicole; Engler-Chiurazzi, Elizabeth; Garcia, Alexandra N; Walker, Douglas G; Moses, Guna S D; Tran, Hung; LaFerla, Frank; Lue, LihFen; Emerson Lombardo, Nancy; Valla, Jon

    2012-01-01

    Nutrition has been highlighted as a potential factor in Alzheimer's disease (AD) risk and decline and has been investigated as a therapeutic target. Broad-based combination diet therapies have the potential to simultaneously effect numerous protective and corrective processes, both directly (e.g., neuroprotection) and indirectly (e.g., improved vascular health). Here we administered either normal mouse chow with a broad-based nutritional supplement or mouse chow alone to aged male and female 3xTg mice and wildtype (WT) controls. After approximately 4 months of feeding, mice were given a battery of cognitive tasks and then injected with a radiolabeled glucose analog. Brains were assessed for differences in regional glucose uptake and mitochondrial cytochrome oxidase activity, AD pathology, and inflammatory markers. Supplementation induced behavioral changes in the 3xTg, but not WT, mice, and the mode of these changes was influenced by sex. Subsequent analyses indicated that differential response to supplementation by male and female 3xTg mice highlighted brain regional strategies for the preservation of function. Several regions involved have been shown to mediate responses to steroid hormones, indicating a mechanism for sex-based vulnerability. Thus, these findings may have broad implications for the human response to future therapeutics.

  15. A fast iterative convolution weighting approach for gridding-based direct Fourier three-dimensional reconstruction with correction for the contrast transfer function.

    PubMed

    Abrishami, V; Bilbao-Castro, J R; Vargas, J; Marabini, R; Carazo, J M; Sorzano, C O S

    2015-10-01

    We describe a fast and accurate method for the reconstruction of macromolecular complexes from a set of projections. Direct Fourier inversion (in which the Fourier Slice Theorem plays a central role) is a solution for dealing with this inverse problem. Unfortunately, the set of projections provides a non-equidistantly sampled version of the macromolecule Fourier transform in the single particle field (and, therefore, a direct Fourier inversion) may not be an optimal solution. In this paper, we introduce a gridding-based direct Fourier method for the three-dimensional reconstruction approach that uses a weighting technique to compute a uniform sampled Fourier transform. Moreover, the contrast transfer function of the microscope, which is a limiting factor in pursuing a high resolution reconstruction, is corrected by the algorithm. Parallelization of this algorithm, both on threads and on multiple CPU's, makes the process of three-dimensional reconstruction even faster. The experimental results show that our proposed gridding-based direct Fourier reconstruction is slightly more accurate than similar existing methods and presents a lower computational complexity both in terms of time and memory, thereby allowing its use on larger volumes. The algorithm is fully implemented in the open-source Xmipp package and is downloadable from http://xmipp.cnb.csic.es.

  16. Does oral supplementation of a fermented papaya preparation correct respiratory burst function of innate immune cells in type 2 diabetes mellitus patients?

    PubMed

    Dickerson, Ryan; Banerjee, Jaideep; Rauckhorst, Adam; Pfeiffer, Douglas R; Gordillo, Gayle M; Khanna, Savita; Osei, Kwame; Roy, Sashwati

    2015-02-01

    Fermented papaya preparation (FPP) is a nutritional supplement reported to act as an antioxidant by scavenging reactive oxygen species (ROS) and removing "bad ROS," while inducing "respiratory burst" production of necessary "good ROS." We sought to investigate the safety of oral administration of FPP (9 g/day, 6 weeks) to T2D patients with regard to its effect on the hyperglycemia status of these patients. Peripheral blood was collected during a baseline visit, followed by subsequent collections both during and after supplementation. Induced "respiratory burst" ROS production was measured at each visit in addition to fasting blood glucose, lipid profile, glycated hemoglobin (HbA1c), and lipid/protein peroxidation. Oral FPP supplementation induced "respiratory burst" in peripheral blood mononuclear cells while not influencing other blood parameters studied. When human monocytic THP-1 cells were supplemented with sugar-based FPP, cellular ATP and NADPH concentrations were increased while matched glucose alone did not produce similar effects, suggesting a glucose-independent component of FPP to be responsible for increasing cellular energetics. THP-1 cells supplemented with FPP also exhibited higher mitochondrial membrane potential (Δψm) and oxygen consumption as compared with cells treated with glucose alone. Taken together, our observations lead to the hypothesis that FPP corrects inducible "respiratory burst" function in type 2 diabetes patients.

  17. Functional properties of bone marrow derived multipotent mesenchymal stromal cells are altered in heart failure patients, and could be corrected by adjustment of expansion strategies

    PubMed Central

    Dmitrieva, Renata I.; Revittser, Alla V.; Klukina, Maria A.; Sviryaev, Yuri V.; Korostovtseva, Ludmila S.; Kostareva, Anna A.; Zaritskey, Andrey Yu.; Shlyakhto, Evgeny V.

    2015-01-01

    Background: Bone marrow multipotent mesenchymal stromal cells (BM-MMSC) considered as a prospective substrate for cell therapy applications, however adult stem cells could be affected by donor-specific factors: age, gender, medical history. Our aim was to investigate how HF affects the functional properties of BM-MMSC. Materials and methods: BM-MMSC from 10 healthy donors (HD), and 16 donors with chronic HF were evaluated for proliferative activity, ability to differentiate, replicative senescence, expression of genes that affect regeneration and fibrosis. The effect of culturing conditions on efficiency of BM-MMSC expansion was determined. Results: HF-derived BM-MMSC demonstrated early decrease of proliferative activity and upregulation of genes that control both, regeneration and fibrosis: Tgf-β pathway, synthesis of ECM, remodeling enzymes, adhesion molecules. We assume that these effects were related to increase of frequency of myofibroblast-like CD146+/SMAα+ CFU-F in HF samples; (ii) low seeding density and hypoxia resulted in predominant purification and expansion of CD146+/SMAα- CFU-Fs. (iii) the activity of NPs system was downregulated in HF BM-MMSC; Conclusions: downregulation of NP signaling in combination with upregulation of Tgf-β pathway in BM-MMSC would result in pro-fibrotic phenotype and make these cells non-effective for therapeutic applications; the corrections in culturing strategy resulted in 23-27 increase of expansion efficiency. PMID:25606985

  18. Successes and failures of Hubbard-corrected density functional theory. The case of Mg doped LiCoO2

    SciTech Connect

    Santana Palacio, Juan A.; Kim, Jeongnim; Kent, Paul R.; Reboredo, Fernando A.

    2014-10-28

    We have evaluated the successes and failures of the Hubbard-corrected density functional theory approach to study Mg doping of LiCoO2. We computed the effect of the U parameter on the energetic, geometric, and electronic properties of two possible doping mechanisms: (1) substitution of Mg onto a Co (or Li) site with an associated impurity state and (2) formation of impurity-state-free complexes of substitutional Mg and point defects in LiCoO2. We find that formation of impurity states results in changes on the valency of Co in LiCoO2. Variation of the Co U shifts the energy of the impurity state, resulting in energetic, geometric, and electronic properties that depend significantly on the specific value of U. In contrast, the properties of the impurity-state-free complexes are insensitive to U. These results identify reasons for the strong dependence on the doping properties on the chosen value of U and for the overall difficulty of achieving agreement with the experimentally known energetic and electronic properties of doped transition metal oxides such as LiCoO2.

  19. A fast iterative convolution weighting approach for gridding-based direct Fourier three-dimensional reconstruction with correction for the contrast transfer function.

    PubMed

    Abrishami, V; Bilbao-Castro, J R; Vargas, J; Marabini, R; Carazo, J M; Sorzano, C O S

    2015-10-01

    We describe a fast and accurate method for the reconstruction of macromolecular complexes from a set of projections. Direct Fourier inversion (in which the Fourier Slice Theorem plays a central role) is a solution for dealing with this inverse problem. Unfortunately, the set of projections provides a non-equidistantly sampled version of the macromolecule Fourier transform in the single particle field (and, therefore, a direct Fourier inversion) may not be an optimal solution. In this paper, we introduce a gridding-based direct Fourier method for the three-dimensional reconstruction approach that uses a weighting technique to compute a uniform sampled Fourier transform. Moreover, the contrast transfer function of the microscope, which is a limiting factor in pursuing a high resolution reconstruction, is corrected by the algorithm. Parallelization of this algorithm, both on threads and on multiple CPU's, makes the process of three-dimensional reconstruction even faster. The experimental results show that our proposed gridding-based direct Fourier reconstruction is slightly more accurate than similar existing methods and presents a lower computational complexity both in terms of time and memory, thereby allowing its use on larger volumes. The algorithm is fully implemented in the open-source Xmipp package and is downloadable from http://xmipp.cnb.csic.es. PMID:26094203

  20. Dispersion-Corrected Density Functional Theory Investigations of Structural and Electronic Properties of Bulk MoS2: Effect of Uniaxial Strain.

    PubMed

    Nguyen, Chuong V; Hieu, Nguyen N; Nguyen, Duong T

    2015-12-01

    Strain-dependent structural and electronic properties of MoS2 materials are investigated using first principles calculations. The structural and electronic band structures of the MoS2 with relaxed unit cells are optimized and calculated by the dispersion-corrected density functional theory (DFT-D2). Calculations within the local density approximation (LDA) and GGA using PAW potentials were also performed for specific cases for the purpose of comparison. The effect of strain on the band gap and the dependence of formation energy on strain of MoS2 are also studied and discussed using the DFT-D2 method. In bulk MoS2, the orbitals shift towards the higher/lower energy area when strain is applied along the z/x direction, respectively. The energy splitting of Mo4d states is in the range from 0 to 2 eV, which is due to the reduction of the electronic band gap of MoS2.

  1. Asymmetric partitioning of transfected DNA during mammalian cell division

    PubMed Central

    Wang, Xuan; Le, Nhung; Denoth-Lippuner, Annina; Barral, Yves; Kroschewski, Ruth

    2016-01-01

    Foreign DNA molecules and chromosomal fragments are generally eliminated from proliferating cells, but we know little about how mammalian cells prevent their propagation. Here, we show that dividing human and canine cells partition transfected plasmid DNA asymmetrically, preferentially into the daughter cell harboring the young centrosome. Independently of how they entered the cell, most plasmids clustered in the cytoplasm. Unlike polystyrene beads of similar size, these clusters remained relatively immobile and physically associated to endoplasmic reticulum-derived membranes, as revealed by live cell and electron microscopy imaging. At entry of mitosis, most clusters localized near the centrosomes. As the two centrosomes split to assemble the bipolar spindle, predominantly the old centrosome migrated away, biasing the partition of the plasmid cluster toward the young centrosome. Down-regulation of the centrosomal proteins Ninein and adenomatous polyposis coli abolished this bias. Thus, we suggest that DNA clustering, cluster immobilization through association to the endoplasmic reticulum membrane, initial proximity between the cluster and centrosomes, and subsequent differential behavior of the two centrosomes together bias the partition of plasmid DNA during mitosis. This process leads to their progressive elimination from the proliferating population and might apply to any kind of foreign DNA molecule in mammalian cells. Furthermore, the functional difference of the centrosomes might also promote the asymmetric partitioning of other cellular components in other mammalian and possibly stem cells. PMID:27298340

  2. Do Psychological Sex Differences Reflect Evolutionary Bisexual Partitioning?

    PubMed

    Trofimova, Irina

    2015-01-01

    This article analyzes sex differences in communicative and exploratory abilities and mental disabilities from the rarely discussed perspective of sex differences in the shape of phenotypic distributions. The article reviews the most consistent findings related to such differences and compares them with the evolutionary theory of sex (ETS). The ETS considers sexual dimorphism as a functional specialization of a species into 2 partitions: variational and conservational. The analysis suggests that male superiority in risk and sensation seeking and physical abilities; higher rates of psychopathy, dyslexia, and autism; and higher birth and accidental death rates reflects the systemic variational function of the male sex. Female superiority in verbal abilities, lawfulness, socialization, empathy, and agreeableness is presented as a reflection of the systemic conservational function of the female sex. From this perspective psychological sex differences in communicative and exploratory abilities might not just be an accidental result of sexual selection or labor distribution in early humans. It might reflect a global functional differentiation tendency within a species to expand its phenotypic diversity and at the same time to conserve beneficial features in the species' behavior. The article also offers an addition to the ETS by suggesting that the male sex (variable partition) plays an evolutionary role in pruning of the redundant excesses in a species' bank of beneficial characteristics despite resistance from the conservational partition. PMID:26721176

  3. Identifying Cognitive States Using Regularity Partitions

    PubMed Central

    2015-01-01

    Functional Magnetic Resonance (fMRI) data can be used to depict functional connectivity of the brain. Standard techniques have been developed to construct brain networks from this data; typically nodes are considered as voxels or sets of voxels with weighted edges between them representing measures of correlation. Identifying cognitive states based on fMRI data is connected with recording voxel activity over a certain time interval. Using this information, network and machine learning techniques can be applied to discriminate the cognitive states of the subjects by exploring different features of data. In this work we wish to describe and understand the organization of brain connectivity networks under cognitive tasks. In particular, we use a regularity partitioning algorithm that finds clusters of vertices such that they all behave with each other almost like random bipartite graphs. Based on the random approximation of the graph, we calculate a lower bound on the number of triangles as well as the expectation of the distribution of the edges in each subject and state. We investigate the results by comparing them to the state of the art algorithms for exploring connectivity and we argue that during epochs that the subject is exposed to stimulus, the inspected part of the brain is organized in an efficient way that enables enhanced functionality. PMID:26317983

  4. Ethanol and Water Adsorption on Transition-Metal 13-Atom Clusters: A Density Functional Theory Investigation within van der Waals Corrections.

    PubMed

    Zibordi-Besse, Larissa; Tereshchuk, Polina; Chaves, Anderson S; Da Silva, Juarez L F

    2016-06-23

    Transition-metal (TM) nanoparticles supported on oxides or carbon black have attracted much attention as potential catalysts for ethanol steam reforming reactions for hydrogen production. To improve the performance of nanocatalysts, a fundamental understanding of the interaction mechanism between water and ethanol with finite TM particles is required. In this article, we employed first-principles density functional theory with van der Waals (vdW) corrections to investigate the interaction of ethanol and water with TM13 clusters, where TM = Ni, Cu, Pd, Ag, Pt, and Au. We found that both water and ethanol bind via the anionic O atom to onefold TM sites, while at higher-energy structures, ethanol binds also via the H atom from the CH2 group to the TM sites, which can play an important role at real catalysts. The putative global minimum TM13 configurations are only slightly affected upon the adsorption of water or ethanol; however, for few systems, the compact higher-energy icosahedron structure changes its configuration upon ethanol or water adsorption. That is, those configurations are only shallow local minimums in the phase space. Except few deviations, we found similar trends for the magnitude of the adsorption energies of water and ethanol, that is, Ni13 > Pt13 > Pd13 and Cu13 > Au13 > Ag13, which is enhanced by the addition of the vdW correction (i.e., from 4% to 62%); however, the trend is the same. We found that the magnitude of the adsorption energy increases by shifting the center of gravity of the d-states toward the highest occupied molecular orbital. On the basis of the Mulliken and Hirshfeld charge analysis, as well as electron density differences, we identified the location of the charge redistribution and a tiny charge transfer (from 0.01 e to 0.19 e) from the molecules to the TM13 clusters. Our vibrational analysis indicates the red shifts in the OH modes upon binding of both water and ethanol molecules to the TM13 clusters, suggesting a weakening of

  5. Ethanol and Water Adsorption on Transition-Metal 13-Atom Clusters: A Density Functional Theory Investigation within van der Waals Corrections.

    PubMed

    Zibordi-Besse, Larissa; Tereshchuk, Polina; Chaves, Anderson S; Da Silva, Juarez L F

    2016-06-23

    Transition-metal (TM) nanoparticles supported on oxides or carbon black have attracted much attention as potential catalysts for ethanol steam reforming reactions for hydrogen production. To improve the performance of nanocatalysts, a fundamental understanding of the interaction mechanism between water and ethanol with finite TM particles is required. In this article, we employed first-principles density functional theory with van der Waals (vdW) corrections to investigate the interaction of ethanol and water with TM13 clusters, where TM = Ni, Cu, Pd, Ag, Pt, and Au. We found that both water and ethanol bind via the anionic O atom to onefold TM sites, while at higher-energy structures, ethanol binds also via the H atom from the CH2 group to the TM sites, which can play an important role at real catalysts. The putative global minimum TM13 configurations are only slightly affected upon the adsorption of water or ethanol; however, for few systems, the compact higher-energy icosahedron structure changes its configuration upon ethanol or water adsorption. That is, those configurations are only shallow local minimums in the phase space. Except few deviations, we found similar trends for the magnitude of the adsorption energies of water and ethanol, that is, Ni13 > Pt13 > Pd13 and Cu13 > Au13 > Ag13, which is enhanced by the addition of the vdW correction (i.e., from 4% to 62%); however, the trend is the same. We found that the magnitude of the adsorption energy increases by shifting the center of gravity of the d-states toward the highest occupied molecular orbital. On the basis of the Mulliken and Hirshfeld charge analysis, as well as electron density differences, we identified the location of the charge redistribution and a tiny charge transfer (from 0.01 e to 0.19 e) from the molecules to the TM13 clusters. Our vibrational analysis indicates the red shifts in the OH modes upon binding of both water and ethanol molecules to the TM13 clusters, suggesting a weakening of

  6. Assimilate partitioning during reproductive growth

    SciTech Connect

    Finazzo, S.F.; Davenport, T.L.

    1987-04-01

    Leaves having various phyllotactic relationships to fruitlets were labeled for 1 hour with 10/sub r/Ci of /sup 14/CO/sub 2/. Fruitlets were also labeled. Fruitlets did fix /sup 14/CO/sub 2/. Translocation of radioactivity from the peel into the fruit occurred slowly and to a limited extent. No evidence of translocation out of the fruitlets was observed. Assimilate partitioning in avocado was strongly influenced by phyllotaxy. If a fruit and the labeled leaf had the same phyllotaxy then greater than 95% of the radiolabel was present in this fruit. When the fruit did not have the same phyllotaxy as the labeled leaf, the radiolabel distribution was skewed with 70% of the label going to a single adjacent position. Avocado fruitlets exhibit uniform labeling throughout a particular tissue. In avocado, assimilates preferentially move from leaves to fruits with the same phyllotaxy.

  7. Trace element partition coefficient in ionic crystals.

    PubMed

    Nagasawa, H

    1966-05-01

    Partition coefficient monovalent trace ions between liquids and either solid NaNO(2) or KCl were determined. The isotropic elastic model of ionic crystals was used for calculating the energy change caused by the ionic substitutions. The observed values of partition coefficients in KCl good agreement with calculate values.

  8. [On the partition of acupuncture academic schools].

    PubMed

    Yang, Pengyan; Luo, Xi; Xia, Youbing

    2016-05-01

    Nowadays extensive attention has been paid on the research of acupuncture academic schools, however, a widely accepted method of partition of acupuncture academic schools is still in need. In this paper, the methods of partition of acupuncture academic schools in the history have been arranged, and three typical methods of"partition of five schools" "partition of eighteen schools" and "two-stage based partition" are summarized. After adeep analysis on the disadvantages and advantages of these three methods, a new method of partition of acupuncture academic schools that is called "three-stage based partition" is proposed. In this method, after the overall acupuncture academic schools are divided into an ancient stage, a modern stage and a contemporary stage, each schoolis divided into its sub-school category. It is believed that this method of partition can remedy the weaknesses ofcurrent methods, but also explore a new model of inheritance and development under a different aspect through thedifferentiation and interaction of acupuncture academic schools at three stages.

  9. Building Ecology and Partition Design. Technical Bulletin.

    ERIC Educational Resources Information Center

    Maryland State Dept. of Education, Baltimore.

    This bulletin is intended as a resource for school system facility planners and architects who design schools. Ways in which decision makers can incorporate environmental concerns in the design of school buildings are detailed. Focus is on the design of interior partition systems. Partition systems in schools serve several purposes; they define…

  10. Isoperimetric graph partitioning for image segmentation.

    PubMed

    Grady, Leo; Schwartz, Eric L

    2006-03-01

    Spectral graph partitioning provides a powerful approach to image segmentation. We introduce an alternate idea that finds partitions with a small isoperimetric constant, requiring solution to a linear system rather than an eigenvector problem. This approach produces the high quality segmentations of spectral methods, but with improved speed and stability.

  11. Generalized Enhanced Multivariance Product Representation for Data Partitioning: Constancy Level

    SciTech Connect

    Tunga, M. Alper; Demiralp, Metin

    2011-09-14

    Enhanced Multivariance Product Representation (EMPR) method is used to represent multivariate functions in terms of less-variate structures. The EMPR method extends the HDMR expansion by inserting some additional support functions to increase the quality of the approximants obtained for dominantly or purely multiplicative analytical structures. This work aims to develop the generalized form of the EMPR method to be used in multivariate data partitioning approaches. For this purpose, the Generalized HDMR philosophy is taken into consideration to construct the details of the Generalized EMPR at constancy level as the introductory steps and encouraging results are obtained in data partitioning problems by using our new method. In addition, to examine this performance, a number of numerical implementations with concluding remarks are given at the end of this paper.

  12. Parallel hypergraph partitioning for scientific computing.

    SciTech Connect

    Heaphy, Robert; Devine, Karen Dragon; Catalyurek, Umit; Bisseling, Robert; Hendrickson, Bruce Alan; Boman, Erik Gunnar

    2005-07-01

    Graph partitioning is often used for load balancing in parallel computing, but it is known that hypergraph partitioning has several advantages. First, hypergraphs more accurately model communication volume, and second, they are more expressive and can better represent nonsymmetric problems. Hypergraph partitioning is particularly suited to parallel sparse matrix-vector multiplication, a common kernel in scientific computing. We present a parallel software package for hypergraph (and sparse matrix) partitioning developed at Sandia National Labs. The algorithm is a variation on multilevel partitioning. Our parallel implementation is novel in that it uses a two-dimensional data distribution among processors. We present empirical results that show our parallel implementation achieves good speedup on several large problems (up to 33 million nonzeros) with up to 64 processors on a Linux cluster.

  13. Cell partition in two phase polymer systems

    NASA Technical Reports Server (NTRS)

    Brooks, D. E.

    1979-01-01

    Aqueous phase-separated polymer solutions can be used as support media for the partition of biological macromolecules, organelles and cells. Cell separations using the technique have proven to be extremely sensitive to cell surface properties but application of the systems are limited to cells or aggregates which do not significantly while the phases are settling. Partition in zero g in principle removes this limitation but an external driving force must be applied to induce the phases to separate since their density difference disappears. We have recently shown that an applied electric field can supply the necessary driving force. We are proposing to utilize the NASA FES to study field-driven phase separation and cell partition on the ground and in zero g to help define the separation/partition process, with the ultimate goal being to develop partition as a zero g cell separation technique.

  14. Partitioning of Eu between augite and a highly spiked martian basalt composition as a function of oxygen fugacity (IW-1 to QFM): Determination of Eu[superscript 2+]/Eu[superscript 3+] ratios by XANES

    SciTech Connect

    Karner, J.M.; Papike, J.J.; Sutton, S.R.; Burger, P.V.; Shearer, C.K.; Le, L.; Newville, M.; Choi, Y.

    2010-03-16

    We have determined D{sub Eu} between augite and melt in samples that crystallized from a highly spiked martian basalt composition at four f{sub O{sub 2}} conditions. D{sub Eu} augite/melt shows a steady increase with f{sub O{sub 2}} from 0.086 at IW-1 to 0.274 at IW+3.5. This increase is because Eu{sup 3+} is more compatible than Eu{sup 2+} in the pyroxene structure; thus increasing f{sub O{sub 2}} leads to greater Eu{sup 3+}/Eu{sup 2+} in the melt and more Eu (total) can partition into the crystallizing pyroxene. This interpretation is supported by direct determinations of Eu valence state by XANES, which show a steady increase of Eu{sup 3+}/Eu{sup 2+} with increasing f{sub O{sub 2}} in both pyroxene (0.38 to 14.6) and glass (0.20 to 12.6) in the samples. Also, pyroxene Eu{sup 3+}/Eu{sup 2+} is higher than that of adjacent glass in all the samples, which verifies that Eu{sup 3+} is more compatible than Eu{sup 2+} in the pyroxene structure. Combining partitioning data with XANES data allows for the calculation of specific valence state D-values for augite/melt where D{sub Eu{sup 3+}} = 0.28 and D{sub Eu{sup 2+}} = 0.07.

  15. Dense Subgraph Partition of Positive Hypergraphs.

    PubMed

    Liu, Hairong; Latecki, Longin Jan; Yan, Shuicheng

    2015-03-01

    In this paper, we present a novel partition framework, called dense subgraph partition (DSP), to automatically, precisely and efficiently decompose a positive hypergraph into dense subgraphs. A positive hypergraph is a graph or hypergraph whose edges, except self-loops, have positive weights. We first define the concepts of core subgraph, conditional core subgraph, and disjoint partition of a conditional core subgraph, then define DSP based on them. The result of DSP is an ordered list of dense subgraphs with decreasing densities, which uncovers all underlying clusters, as well as outliers. A divide-and-conquer algorithm, called min-partition evolution, is proposed to efficiently compute the partition. DSP has many appealing properties. First, it is a nonparametric partition and it reveals all meaningful clusters in a bottom-up way. Second, it has an exact and efficient solution, called min-partition evolution algorithm. The min-partition evolution algorithm is a divide-and-conquer algorithm, thus time-efficient and memory-friendly, and suitable for parallel processing. Third, it is a unified partition framework for a broad range of graphs and hypergraphs. We also establish its relationship with the densest k-subgraph problem (DkS), an NP-hard but fundamental problem in graph theory, and prove that DSP gives precise solutions to DkS for all kin a graph-dependent set, called critical k-set. To our best knowledge, this is a strong result which has not been reported before. Moreover, as our experimental results show, for sparse graphs, especially web graphs, the size of critical k-set is close to the number of vertices in the graph. We test the proposed partition framework on various tasks, and the experimental results clearly illustrate its advantages.

  16. Use of partition coefficients in flow-limited physiologically-based pharmacokinetic modeling

    PubMed Central

    Thompson, Matthew D.; Beard, Daniel A.; Wu, Fan

    2012-01-01

    Permeability-limited two-subcompartment and flow-limited, well-stirred tank tissue compartment models are routinely used in physiologically-based pharmacokinetic modeling. Here, the permeability-limited two-subcompartment model is used to derive a general flow-limited case of a two-subcompartment model with the well-stirred tank being a specific case where tissue fractional blood volume approaches zero. The general flow-limited two-subcompartment model provides a clear distinction between two partition coefficients typically used in PBPK: a biophysical partition coefficient and a well-stirred partition coefficient. Case studies using diazepam and cotinine demonstrate that, when the well-stirred tank is used with a priori predicted biophysical partition coefficients, simulations overestimate or underestimate total organ drug concentration relative to flow-limited two-subcompartment model behavior in tissues with higher fractional blood volumes. However, whole-body simulations show predicted drug concentrations in plasma and lower fractional blood volume tissues are relatively unaffected. These findings point to the importance of accurately determining tissue fractional blood volume for flow-limited PBPK modeling. Simulations using biophysical and well-stirred partition coefficients optimized with flow-limited two-subcompartment and well-stirred models, respectively, lead to nearly identical fits to tissue drug distribution data. Therefore, results of whole-body PBPK modeling with diazepam and cotinine indicate both flow-limited models are appropriate PBPK tissue models as long as the correct partition coefficient is used: the biophysical partition coefficient is for use with two-subcompartment models and the well-stirred partition coefficient is for use with the well-stirred tank model. PMID:22639356

  17. Correction of defective CFTR/ENaC function and tightness of cystic fibrosis airway epithelium by amniotic mesenchymal stromal (stem) cells.

    PubMed

    Carbone, Annalucia; Castellani, Stefano; Favia, Maria; Diana, Anna; Paracchini, Valentina; Di Gioia, Sante; Seia, Manuela; Casavola, Valeria; Colombo, Carla; Conese, Massimo

    2014-08-01

    Cystic fibrosis (CF) is caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, with most of the mortality given by the lung disease. Human amniotic mesenchymal stromal (stem) cells (hAMSCs) hold great promise for regenerative medicine in the field of lung disease; however, their potential as therapeutics for CF lung disease has not been fully explored. In the present study, hAMSCs were analysed in co-cultures on Transwell filters with CF immortalized airway epithelial cells (CFBE41o- line) at different ratios to exploit their potency to resume basic defects associated with CF. The results show that F-actin content was increased in co-cultures as compared with CF cells and actin was reorganized to form stress fibres. Confocal microscopy studies revealed that co-cultures had a tendency of increased expression of occludin and ZO-1 at the intercellular borders, paralleled by a decrease in dextran permeability, suggestive of more organized tight junctions (TJs). Spectrofluorometric analysis of CFTR function demonstrated that hAMSC-CFBE co-cultures resumed chloride transport, in line with the appearance of the mature Band C of CFTR protein by Western blotting. Moreover, hAMSC-CFBE co-cultures, at a 1:5 ratio, showed a decrease in fluid absorption, as opposed to CFBE cell monolayers that displayed a great rate of fluid resorption from the apical side. Our data show that human amniotic MSCs can be used in co-culture with CF respiratory epithelial cells to model their engraftment into the airways and have the potential to resume a tight epithelium with partial correction of the CF phenotype.

  18. Correction of defective CFTR/ENaC function and tightness of cystic fibrosis airway epithelium by amniotic mesenchymal stromal (stem) cells.

    PubMed

    Carbone, Annalucia; Castellani, Stefano; Favia, Maria; Diana, Anna; Paracchini, Valentina; Di Gioia, Sante; Seia, Manuela; Casavola, Valeria; Colombo, Carla; Conese, Massimo

    2014-08-01

    Cystic fibrosis (CF) is caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, with most of the mortality given by the lung disease. Human amniotic mesenchymal stromal (stem) cells (hAMSCs) hold great promise for regenerative medicine in the field of lung disease; however, their potential as therapeutics for CF lung disease has not been fully explored. In the present study, hAMSCs were analysed in co-cultures on Transwell filters with CF immortalized airway epithelial cells (CFBE41o- line) at different ratios to exploit their potency to resume basic defects associated with CF. The results show that F-actin content was increased in co-cultures as compared with CF cells and actin was reorganized to form stress fibres. Confocal microscopy studies revealed that co-cultures had a tendency of increased expression of occludin and ZO-1 at the intercellular borders, paralleled by a decrease in dextran permeability, suggestive of more organized tight junctions (TJs). Spectrofluorometric analysis of CFTR function demonstrated that hAMSC-CFBE co-cultures resumed chloride transport, in line with the appearance of the mature Band C of CFTR protein by Western blotting. Moreover, hAMSC-CFBE co-cultures, at a 1:5 ratio, showed a decrease in fluid absorption, as opposed to CFBE cell monolayers that displayed a great rate of fluid resorption from the apical side. Our data show that human amniotic MSCs can be used in co-culture with CF respiratory epithelial cells to model their engraftment into the airways and have the potential to resume a tight epithelium with partial correction of the CF phenotype. PMID:24894806

  19. Linear Time Vertex Partitioning on Massive Graphs

    PubMed Central

    Mell, Peter; Harang, Richard; Gueye, Assane

    2016-01-01

    The problem of optimally removing a set of vertices from a graph to minimize the size of the largest resultant component is known to be NP-complete. Prior work has provided near optimal heuristics with a high time complexity that function on up to hundreds of nodes and less optimal but faster techniques that function on up to thousands of nodes. In this work, we analyze how to perform vertex partitioning on massive graphs of tens of millions of nodes. We use a previously known and very simple heuristic technique: iteratively removing the node of largest degree and all of its edges. This approach has an apparent quadratic complexity since, upon removal of a node and adjoining set of edges, the node degree calculations must be updated prior to choosing the next node. However, we describe a linear time complexity solution using an array whose indices map to node degree and whose values are hash tables indicating the presence or absence of a node at that degree value. This approach also has a linear growth with respect to memory usage which is surprising since we lowered the time complexity from quadratic to linear. We empirically demonstrate linear scalability and linear memory usage on random graphs of up to 15000 nodes. We then demonstrate tractability on massive graphs through execution on a graph with 34 million nodes representing Internet wide router connectivity. PMID:27336059

  20. Improved initialisation of model-based clustering using Gaussian hierarchical partitions

    PubMed Central

    Scrucca, Luca; Raftery, Adrian E.

    2015-01-01

    Initialisation of the EM algorithm in model-based clustering is often crucial. Various starting points in the parameter space often lead to different local maxima of the likelihood function and, so to different clustering partitions. Among the several approaches available in the literature, model-based agglomerative hierarchical clustering is used to provide initial partitions in the popular mclust R package. This choice is computationally convenient and often yields good clustering partitions. However, in certain circumstances, poor initial partitions may cause the EM algorithm to converge to a local maximum of the likelihood function. We propose several simple and fast refinements based on data transformations and illustrate them through data examples. PMID:26949421