Science.gov

Sample records for corrected partition function

  1. Quantum corrections to Bekenstein-Hawking black hole entropy and gravity partition functions

    NASA Astrophysics Data System (ADS)

    Bytsenko, A. A.; Tureanu, A.

    2013-08-01

    Algebraic aspects of the computation of partition functions for quantum gravity and black holes in AdS3 are discussed. We compute the sub-leading quantum corrections to the Bekenstein-Hawking entropy. It is shown that the quantum corrections to the classical result can be included systematically by making use of the comparison with conformal field theory partition functions, via the AdS3/CFT2 correspondence. This leads to a better understanding of the role of modular and spectral functions, from the point of view of the representation theory of infinite-dimensional Lie algebras. Besides, the sum of known quantum contributions to the partition function can be presented in a closed form, involving the Patterson-Selberg spectral function. These contributions can be reproduced in a holomorphically factorized theory whose partition functions are associated with the formal characters of the Virasoro modules. We propose a spectral function formulation for quantum corrections to the elliptic genus from supergravity states.

  2. Partition function corrections. [vibration-rotation interaction coupling in diatomic molecules

    NASA Technical Reports Server (NTRS)

    1976-01-01

    The vibration-rotation interaction coupling in diatomic molecules is analyzed and first-order expressions for the energy levels are deduced. Corrections to the partition function to account for this coupling are derived. The effects of long-range intermolecular forces due to induced dipole-induced dipole interactions, dipole-induced dipole interactions, charge-dipole interactions, and charge-charge interactions are considered. London's quantized oscillator model of the induced dipole-induced dipole interaction is developed. The partition function including effects of such dispersion forces is derived and is shown to lead to the virial equation of state. For a model combining the hard sphere and long-range attractive type potentials, this is found to lead to the van der Waals equation of state. The equation of state near the critical point is presented in reduced form (thermodynamic variables expressed in units of critical point values). Finally, approximate corrections to the electronic partition functions are derived to account for perturbations of excited electronic states induced by neighboring neutral particles, heavy ions, and fast electron collisions.

  3. 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.

  4. Rotational partition functions for linear molecules

    NASA Astrophysics Data System (ADS)

    McDowell, Robin S.

    1988-01-01

    An accurate closed-form expression for the rotational partition function of linear polyatomic molecules in 1Sigma electronic states is derived, including the effect of nuclear spin (significant at very low temperatures) and of quartic and sextic centrifugal distortion terms (significant at moderate and high temperatures). The proper first-order quantum correction to the classical rigid-rotator partition function is shown to yield Qr = about 1/beta exp beta/3, where beta is defined as hcB / kT and B is the rotational constant in per cm; for beta of 0.2 or greater additional power-series terms in beta are necessary. Comparison between the results of this treatment and exact summations are made for HCN and C2H2 at temperatures from 2 to 5000 K, including separate evaluation of the conributions of nuclear spin and centrifugal distortion.

  5. Partition function of interacting calorons ensemble

    NASA Astrophysics Data System (ADS)

    Deldar, S.; Kiamari, M.

    2016-01-01

    We present a method for computing the partition function of a caloron ensemble taking into account the interaction of calorons. We focus on caloron-Dirac string interaction and show that the metric that Diakonov and Petrov offered, works well in the limit where this interaction occurs. We suggest computing the correlation function of two polyakov loops by applying Ewald's method.

  6. Some comments on molecular partition functions

    SciTech Connect

    Sharp, C.M.

    1987-03-01

    In models of cool stellar atmospheres where molecules are important, molecular spectroscopic data can be used to calculate partition functions, from which equilibrium constants hence abundances can be obtained. In this report, it is shown that simple analytic approximations can be used to calculate very easily the partition functions of diatomic molecules, and comparisons are made for the two particularly important astrophysical molecules, H/sub 2/ and CO, with other work where the partition functions are calculated by explicitly summing over a very large number of energy levels. It is found that these analytic approximations give excellent agreement with more detailed calculations and are certainly adequate for many purposes. This method is very convenient, as only a few spectroscopic constants are needed, and the analytic formulae are very easily evaluated.

  7. Rotational partition functions for symmetric-top molecules

    NASA Astrophysics Data System (ADS)

    McDowell, Robin S.

    1990-08-01

    An improved expression is found for the rotational partition functions of symmetric-top molecules. The expression includes the effect of nuclear spin for molecules of C(3v) symmetry. The effect that centrifugal distortion of the rotating molecules has on these rigid-rotator formulations is considered. The nuclear-spin correction is generalized to symmetric-top molecules of other symmetries. The treatment is extended to nonplanar molecules that exhibit inversion doubling, with particular attention given to NH3.

  8. GPS/INS integration by functional partitioning

    NASA Astrophysics Data System (ADS)

    Diesel, John W.

    It is shown that a GPS/INS system integrated by functional partitioning can satisfy all of the RTCA navigation requirements and goals. This is accomplished by accurately calibrating the INS using GPS after the inertial instruments are thermally stabilized and by exploiting the very slow subsequent error growth in the INS information. In this way, autonomous integrity monitoring can be achieved using only existing or presently planned systems.

  9. Wigner expansions for partition functions of nonrelativistic and relativistic oscillator systems

    NASA Technical Reports Server (NTRS)

    Zylka, Christian; Vojta, Guenter

    1993-01-01

    The equilibrium quantum statistics of various anharmonic oscillator systems including relativistic systems is considered within the Wigner phase space formalism. For this purpose the Wigner series expansion for the partition function is generalized to include relativistic corrections. The new series for partition functions and all thermodynamic potentials yield quantum corrections in terms of powers of h(sup 2) and relativistic corrections given by Kelvin functions (modified Hankel functions) K(sub nu)(mc(sup 2)/kT). As applications, the symmetric Toda oscillator, isotonic and singular anharmonic oscillators, and hindered rotators, i.e. oscillators with cosine potential, are addressed.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. A Recursive Method for Calculating Certain Partition Functions.

    ERIC Educational Resources Information Center

    Woodrum, Luther; And Others

    1978-01-01

    Describes a simple recursive method for calculating the partition function and average energy of a system consisting of N electrons and L energy levels. Also, presents an efficient APL computer program to utilize the recursion relation. (Author/GA)

  17. Pure Partition Functions of Multiple SLEs

    NASA Astrophysics Data System (ADS)

    Kytölä, Kalle; Peltola, Eveliina

    2016-08-01

    Multiple Schramm-Loewner Evolutions (SLE) are conformally invariant random processes of several curves, whose construction by growth processes relies on partition functions—Möbius covariant solutions to a system of second order partial differential equations. In this article, we use a quantum group technique to construct a distinguished basis of solutions, which conjecturally correspond to the extremal points of the convex set of probability measures of multiple SLEs.

  18. Pure Partition Functions of Multiple SLEs

    NASA Astrophysics Data System (ADS)

    Kytölä, Kalle; Peltola, Eveliina

    2016-05-01

    Multiple Schramm-Loewner Evolutions (SLE) are conformally invariant random processes of several curves, whose construction by growth processes relies on partition functions—Möbius covariant solutions to a system of second order partial differential equations. In this article, we use a quantum group technique to construct a distinguished basis of solutions, which conjecturally correspond to the extremal points of the convex set of probability measures of multiple SLEs.

  19. Line defects and 5d instanton partition functions

    NASA Astrophysics Data System (ADS)

    Kim, Hee-Cheol

    2016-03-01

    We consider certain line defect operators in five-dimensional SUSY gauge theories, whose interaction with the self-dual instantons is described by 1d ADHM-like gauged quantum mechanics constructed by Tong and Wong. The partition function in the presence of these operators is known to be a generating function of BPS Wilson loops in skew symmetric tensor representations of the gauge group. We calculate the partition function and explicitly prove that it is a finite polynomial of the defect mass parameter x, which is an essential property of the defect operator and the Wilson loop generating function. The relation between the line defect partition function and the qq-character defined by N . Nekrasov is briefly discussed.

  20. 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.

  1. Quantum mechanical single molecule partition function from path integral Monte Carlo simulations.

    PubMed

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

    2006-06-21

    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. PMID:16821901

  2. 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.

  3. 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.

  4. Partition zeta functions, multifractal spectra, and tapestries of complex dimensions

    NASA Astrophysics Data System (ADS)

    Ellis, Kate E.; Lapidus, Michel L.; MacKenzie, Michael C.; Rock, John A.

    2015-03-01

    For a Borel measure and a sequence of partitions on the unit interval, we define a multifractal spectrum based on coarse Hölder regularity. Specifically, the coarse Hölder regularity values attained by a given measure and with respect to a sequence of partitions generate a sequence of lengths (or rather, scales) which in turn define certain Dirichlet series, called the partition zeta functions. The abscissae of convergence of these functions define a multifractal spectrum whose concave envelope is the (geometric) Hausdorff multifractal spectrum which follows from a certain type of Moran construction. We discuss at some length the important special case of self-similar measures associated with weighted iterated function systems and, in particular, certain multinomial measures. Moreover, our multifractal spectrum is shown to extend to a tapestry of complex dimensions for a specific case of atomic measures.

  5. 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.

  6. The rotational partition function of the symmetric top and the effect of K doubling thereon

    NASA Astrophysics Data System (ADS)

    Martin, J. M. L.; François, J. P.; Gijbels, R.

    1991-12-01

    McDowell's earlier derivation of the partition function for a nonrigid symmetric top has been extended with a fourth-order correction for centrifugal distortion and correction terms for K doubling. Comparison with direct numerical summation (including K-doubling effects) indicates that the inclusion of the fourth-oder term is necessary to ensure high accuracy in the computed enthalpy function and heat capacity above 2000 K, as well as that the effect of K doubling is very small at practical temperatures. The only effect of any practical importance is that of d2 for molecules with fourfold symmetry: the present approximate expressions represent this effect quite well.

  7. Marginal Consistency: Upper-Bounding Partition Functions over Commutative Semirings.

    PubMed

    Werner, Tomás

    2015-07-01

    Many inference tasks in pattern recognition and artificial intelligence lead to partition functions in which addition and multiplication are abstract binary operations forming a commutative semiring. By generalizing max-sum diffusion (one of convergent message passing algorithms for approximate MAP inference in graphical models), we propose an iterative algorithm to upper bound such partition functions over commutative semirings. The iteration of the algorithm is remarkably simple: change any two factors of the partition function such that their product remains the same and their overlapping marginals become equal. In many commutative semirings, repeating this iteration for different pairs of factors converges to a fixed point when the overlapping marginals of every pair of factors coincide. We call this state marginal consistency. During that, an upper bound on the partition function monotonically decreases. This abstract algorithm unifies several existing algorithms, including max-sum diffusion and basic constraint propagation (or local consistency) algorithms in constraint programming. We further construct a hierarchy of marginal consistencies of increasingly higher levels and show than any such level can be enforced by adding identity factors of higher arity (order). Finally, we discuss instances of the framework for several semirings, including the distributive lattice and the max-sum and sum-product semirings. PMID:26352452

  8. 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.

  9. 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.

  10. Orbifolds, defects and sphere partition function

    NASA Astrophysics Data System (ADS)

    Hosomichi, Kazuo

    2016-02-01

    Gauge theories in the presence of codimension two vortex defects are known to be related to the theories on orbifolds. By using this relation we study the localized path integrals of 2D {N}=(2,2) SUSY gauge theories with point-like vortex defects. We present a formula for the correlation functions of vortex defects inserted at the north and the south poles of squashed spheres. For Abelian gauge theories the correlators are locally constant as functions of the parameters of the defect, but exhibit discontinuity at some threshold values determined from the R-charges of the matter multiplets. For non-Abelian gauge groups the correlators depend non-trivially on the types of gauge symmetry breaking due to the defects.

  11. 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.

  12. Identification of plasmid partition function in coryneform bacteria

    SciTech Connect

    Kurusu, Yasurou; Satoh, Yukie; Inui, Masayuki; Kohama, Keiko; Kobayashi, Miki; Terasawa, Masato; Yukawa, Hideaki )

    1991-03-01

    The authors have identified and characterized a partition function that is required for stable maintenance of plasmids in the coryneform bacteria Brevibacterium flavum MJ233 and Corynebacterium glutamicum ATCC 31831. This function is localized to a HindIII-NspV fragment (673 bp) adjacent to the replication region of the plasmid, named pBY503, from Brevibacterium stationis IFO 12144. The function was independent of copy number control and was not associated directly with plasmid replication functions. This fragment was able to stabilize the unstable plasmids in cis but not in trans.

  13. 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

  14. Factorized domain wall partition functions in trigonometric vertex models

    NASA Astrophysics Data System (ADS)

    Foda, O.; Wheeler, M.; Zuparic, M.

    2007-10-01

    We obtain factorized domain wall partition functions for two sets of trigonometric vertex models: (1) the N-state Deguchi Akutsu models, for N \\in \\{2, 3, 4\\} (and conjecture the result for all N>=5), and (2) the sl(r+1|s+1) Perk Schultz models, for \\{r, s \\in \\mathbb {N}\\} , where (given the symmetries of these models) the result is independent of {r,s}.

  15. 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.

  16. 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.

  17. 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.

  18. Analysis of Partition Functions for Metallocenes: Ferrocene, Ruthenocene, and Osmocene.

    PubMed

    Ferreira da Cunha, T; Calderini, D; Skouteris, D

    2016-07-14

    We present a calculation of the torsional potential of the three metallocenes of the iron group, that is, ferrocene, ruthenocene, and osmocene, calculated with the GAUSSIAN program suite. Both a variational method (through computation of the exact energy levels) and our Chebyshev imaginary time propagation method are used to calculate the hindered rotation partition function, demonstrating the efficiency of the Chebyshev scheme. The transition from a semirigid through a hindered rotor to the free rotor regime is demonstrated, and the effect of the hindered rotation (as opposed to a harmonic) treatment on the thermodynamics of metallocenes is demonstrated. PMID:27003631

  19. 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.

  20. Functional analysis of the yeast plasmid partition locus STB

    PubMed Central

    Murray, James A. H.; Cesareni, Gianni

    1986-01-01

    Derivatives of the yeast 2μ plasmid with the cis-acting locus STB (also called REP3) are stably maintained if two plasmid-encoded proteins are present in trans. There are conflicting reports of both the extent of STB and its possible involvement in plasmid partition or copy number control. We have resolved the controversy by constructing 2µ derivatives with a conditional STB function, and showing that when STB is inactivated plasmids become concentrated in a small fraction of the population although the total number of plasmids remains unaltered. Moreover we show that STB consists of two functionally distinct domains which we call STB-proximal and STB-distal relative to the origin of replication. Although STB-proximal is sufficient for proper partitioning, this function is severely disrupted by active transcription from neighbouring sequences. STB-distal is important to protect STB-proximal and ORI from such transcription, and can be effeciently replaced by a 94-bp terminator fragment in an orientation-dependent manner. We find that STB-distal contains an additional element which depresses transcription from upstream promoters. We also describe the phenomenon of replicaton inhibition which we believe can exlain the anomalous instability of some yeast plasmids. ImagesFig. 4.Fig. 5.Fig. 6.Fig. 7. PMID:16453734

  1. Improved estimation of solubility and partitioning through correction of UNIFAC-derived activity coefficients

    SciTech Connect

    Banerjee, S.; Howard, P.H.

    1988-07-01

    Octanol-water partition coefficients (K/sub ow/) of 75 compounds ranging over 9 orders of magnitude are correlated by log K/sub ow/ = -0.40 + 0.73 log (..gamma../sub W/)/sub U/ -0.39 log (..gamma../sub 0/)/sub U/ (r = 0.98), where (..gamma..//sub W/)/sub U/ and (..gamma../sub 0/)/sub U/ are UNIFAC-derived activity coefficients in water and octanol, respectively. The constants 0.73 and -0.39 are obtained empirically and are intended to compensate for group nonadditivity. Correction factors of similar magnitude are obtained in independent correlations of water solubility with (..gamma../sub W/)/sub U/ and of octanol solubility with (..gamma../sub 0/)/sub U/, thereby confirming the validity of the approach.

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

    PubMed Central

    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

  3. 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.

  4. The grand partition function of dilute biregular solutions

    NASA Astrophysics Data System (ADS)

    Nagamori, Meguru; Ito, Kimihisa; Tokuda, Motonori

    1994-10-01

    It has been demonstrated that the grand partition function (GPF) of biregular solutions contains in one single equation such thermodynamic principles as Henry's law, Raoult's law, the Gibbs-Duhem relation, Raoultian activity coefficients and their finite power series, Wagner's rec-iprocity, Schenck-Frohberg-Steinmetz's interchange, Lupis-Elliott's additivity, Mori-Morooka's disparity, and Darken's quadratic formalism. The logarithm of the Raoultian activity coefficient of species i, In γi should not be expressed by the Taylor series expansion, lest its truncation infringe the Gibbs-Duhem equation. The GPF methodology establishes that In γi, is not a vector but a scalar point function, free from any path dependence. While Darken's quadratic formalism employs three parameters to describe a ternary solution, the present biregularity approximation offers an alternative using seven empirical parameters, in case better accuracy is needed.

  5. 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

  6. Exact Potts model partition functions on ladder graphs

    NASA Astrophysics Data System (ADS)

    Shrock, Robert

    2000-08-01

    We present exact calculations of the partition function Z of the q-state Potts model and its generalization to real q, for arbitrary temperature on n-vertex ladder graphs, i.e., strips of the square lattice with width Ly=2 and arbitrary length Lx, with free, cyclic, and Möbius longitudinal boundary conditions. These partition functions are equivalent to Tutte/Whitney polynomials for these graphs. The free energy is calculated exactly for the infinite-length limit of these ladder graphs and the thermodynamics is discussed. By comparison with strip graphs of other widths, we analyze how the singularities at the zero-temperature critical point of the ferromagnet on infinite-length, finite-width strips depend on the width. We point out and study the following noncommutativity at certain special values q s: lim n→∞ limq→q s Z 1/n≠ limq→q s limn→∞ Z 1/n. It is shown that the Potts antiferromagnet on both the infinite-length line and ladder graphs with cyclic or Möbius boundary conditions exhibits a phase transition at finite temperature if 0< q<2, but with unphysical properties, including negative specific heat and non-existence, in the low-temperature phase, of an n→∞ limit for thermodynamic functions that is independent of boundary conditions. Considering the full generalization to arbitrary complex q and temperature, we determine the singular locus B in the corresponding C2 space, arising as the accumulation set of partition function zeros as n→∞. In particular, we study the connection with the T=0 limit of the Potts antiferromagnet where B reduces to the accumulation set of chromatic zeros. Certain properties of the complex-temperature phase diagrams are shown to exhibit close connections with those of the model on the square lattice, showing that exact solutions on infinite-length strips provide a way of gaining insight into these complex-temperature phase diagrams.

  7. 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.

  8. 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.

  9. The asymptotic asymmetric-top rotational partition function

    NASA Astrophysics Data System (ADS)

    Watson, James K. G.

    The high-temperature asymptotic expansion of the rotational partition function of a rigid asymmetric-top molecule can be written in the form where g is the mean nuclear statistical weight and gζ is a nuclear statistical weight factor associated with the principal axis ζ. The asymptotic expansion of Q', which is calculated by two different methods, is expressed in the formulation of McDowell as where tMPH1377_images Here, α, β and γ are the dimensionless temperature-reduced rotational constants hcA/kT, hcB/kT and hcC/kT, and each sum is over the three cyclic permutations of (α, β, γ). For the Q'ζ, the principal asymptotic approximations tMPH1377_images are obtained, confirming results in the 1955 dissertation of Woolley.

  10. 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

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. A general approach to association using cluster partition functions

    NASA Astrophysics Data System (ADS)

    Hendriks, E. M.; Walsh, J.; van Bergen, A. R. D.

    1997-06-01

    A systematic and fundamental approach to associating mixtures is presented. It is shown how the thermodynamic functions may be computed starting from a partition function based on the cluster concept such as occurs in chemical theory. The theory provides a basis for and an extension of the existing chemical theory of (continuous) association. It is applicable to arbitrary association schemes. Analysis of separate cases is not necessary. The assumptions that were made to allow the development were chosen such as to make the principle of reactivity valid. It is this same principle that links various theories: the chemical theory of continuous association, the lattice fluid hydrogen bonding model, and first-order perturbation theory. The equivalence between these theories in appropriate limits is shown in a general and rigorous way. The theory is believed to provide a practical framework for engineering modeling work. Binary interaction parameters can be incorporated. The association scheme is accounted for by a set of generic equations, which should facilitate robust implementation in computer programs.

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

    SciTech Connect

    Mosquera, Martín A.; Wasserman, Adam; Department of Physics, Purdue University, West Lafayette, Indiana 47907

    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.

  18. 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)

  19. A partitioned correlation function interaction approach for describing electron correlation in atoms

    NASA Astrophysics Data System (ADS)

    Verdebout, S.; Rynkun, P.; Jönsson, P.; Gaigalas, G.; Froese Fischer, C.; Godefroid, M.

    2013-04-01

    The traditional multiconfiguration Hartree-Fock (MCHF) and configuration interaction (CI) methods are based on a single orthonormal orbital basis. For atoms with many closed core shells, or complicated shell structures, a large orbital basis is needed to saturate the different electron correlation effects such as valence, core-valence and correlation within the core shells. The large orbital basis leads to massive configuration state function (CSF) expansions that are difficult to handle, even on large computer systems. We show that it is possible to relax the orthonormality restriction on the orbital basis and break down the originally very large calculations into a series of smaller calculations that can be run in parallel. Each calculation determines a partitioned correlation function (PCF) that accounts for a specific correlation effect. The PCFs are built on optimally localized orbital sets and are added to a zero-order multireference (MR) function to form a total wave function. The expansion coefficients of the PCFs are determined from a low dimensional generalized eigenvalue problem. The interaction and overlap matrices are computed using a biorthonormal transformation technique (Verdebout et al 2010 J. Phys. B: At. Mol. Phys. 43 074017). The new method, called partitioned correlation function interaction (PCFI), converges rapidly with respect to the orbital basis and gives total energies that are lower than the ones from ordinary MCHF and CI calculations. The PCFI method is also very flexible when it comes to targeting different electron correlation effects. Focusing our attention on neutral lithium, we show that by dedicating a PCF to the single excitations from the core, spin- and orbital-polarization effects can be captured very efficiently, leading to highly improved convergence patterns for hyperfine parameters compared with MCHF calculations based on a single orthogonal radial orbital basis. By collecting separately optimized PCFs to correct the MR

  20. LETTER: The partition function of the trigonometric SOS model with a reflecting end

    NASA Astrophysics Data System (ADS)

    Filali, G.; Kitanine, N.

    2010-06-01

    We compute the partition function of the trigonometric SOS model with one reflecting end and domain wall type boundary conditions. We show that in this case, instead of the sum of determinants obtained by Rosengren for the SOS model on a square lattice without reflection, the partition function can be represented as a single Izergin determinant. This result is crucial for the study of the Bethe vectors of the spin chains with non-diagonal boundary terms.

  1. 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.

  2. 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.

  3. 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. PMID:25053308

  4. 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.

  5. 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.

  6. Methane high-temperature partition function from contact transformations and variational calculations

    NASA Astrophysics Data System (ADS)

    Nikitin, A. V.; Krishna, B. M.; Rey, M.; Tashkun, S. A.; Tyute, Vl. G.

    2015-12-01

    The temperature dependence of the methane 12CH4 partition function was investigated up to T=3000 K. The ro-vibrational energy levels were calculated using high-order contact transformation (CT) method that permitted building accurate effective Hamiltonian models for highly excited vibration-rotation states from the molecular potential energy surface. Comparisons with variational calculations using large basis sets as well as convergence and extrapolation issues are discussed. The accuracy of the present calculations for the methane partition function was estimated as 1-2% at 2000 K. This estimated error is considerably smaller than the difference with other calculations available in the literature.

  7. Partition function of N={2}^{ast } SYM on a large four-sphere

    NASA Astrophysics Data System (ADS)

    Hollowood, Timothy J.; Kumar, S. Prem

    2015-12-01

    We examine the partition function of N={2}^{ast } supersymmetric SU( N) Yang-Mills theory on the four-sphere in the large radius limit. We point out that the large radius partition function, at fixed N, is computed by saddle-points lying on walls of marginal stability on the Coulomb branch of the theory on {R}^4 . For N an even (odd) integer and θ YM = 0( π), these include a point of maximal degeneration of the Donagi-Witten curve to a torus where BPS dyons with electric charge [N/2] become massless. We argue that the dyon singularity is the lone saddle-point in the SU(2) theory, while for SU( N) with N > 2, we characterize potentially competing saddle-points by obtaining the relations between the Seiberg-Witten periods at such points. Using Nekrasov's instanton partition function, we solve for the maximally degenerate saddle-point and obtain its free energy as a function of g YM and N, and show that the results are "large- N exact". In the large- N theory our results provide analytical expressions for the periods/eigenvalues at the maximally degenerate saddle-point, precisely matching previously known formulae following from the correspondence between N={2}^{ast } theory and the elliptic Calogero-Moser integrable model. The maximally singular point ceases to be a saddle-point of the partition function above a critical value of the coupling, in agreement with the recent findings of Russo and Zarembo.

  8. NITROGEN AND CO2 AFFECT REGROWTH AND BIOMASS PARTITIONING DIFFERENTLY IN FORAGES OF THREE FUNCTIONAL GROUPS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Little work has been done to assess the impact of elevated C02 on responses of forages to defoliation. This study examines regrowth, biomass partitioning, and labile C and N metabolites in three functional plant-types: a C3 grass [Pascopyrum smithii (Rydb.) A. Love], a C4 grass [Bouteloua gracilis ...

  9. Script N = 8 dyon partition function and walls of marginal stability

    NASA Astrophysics Data System (ADS)

    Sen, Ashoke

    2008-07-01

    We construct the partition function of 1/8 BPS dyons in type II string theory on T6 from counting of microstates of a D1-D5 system in Taub-NUT space. Our analysis extends the earlier ones by Shih, Strominger and Yin and by Pioline by taking into account the walls of marginal stability on which a 1/8 BPS dyon can decay into a pair of half-BPS dyons. Across these walls the dyon spectrum changes discontinuously, and as a result the spectrum is not manifestly invariant under S-duality transformation of the charges. However the partition function is manifestly S-duality invariant and takes the same form in all domains of the moduli space separated by walls of marginal stability, the spectra in different domains being obtained by choosing different integration contours along which we carry out the Fourier transform of the partition function. The jump in the spectrum across a wall of marginal stability, calculated from the behaviour of the partition function at an appropriate pole, reproduces the expected wall crossing formula.

  10. The hypergeometric series for the partition function of the 2D Ising model

    NASA Astrophysics Data System (ADS)

    Viswanathan, G. M.

    2015-07-01

    In 1944 Onsager published the formula for the partition function of the Ising model for the infinite square lattice. He was able to express the internal energy in terms of a special function, but he left the free energy as a definite integral. Seven decades later, the partition function and free energy have yet to be written in closed form, even with the aid of special functions. Here we evaluate the definite integral explicitly, using hypergeometric series. Let β denote the reciprocal temperature, J the coupling and f the free energy per spin. We prove that - β f = \\ln(2 \\cosh 2K) - κ2 ~ {_4F_3} \\big[~ 1,~1,~3/2,~3/2 ~~~2,~2,~2 ;16 κ2 ~\\big] ~ , where pFq is the generalized hypergeometric function, K = βJ, and 2κ = tanh 2K sech 2K.

  11. 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.

  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. Calculation of converged rovibrational energies and partition function for methane using vibrational-rotational configuration interaction.

    PubMed

    Chakraborty, Arindam; Truhlar, Donald G; Bowman, Joel M; Carter, Stuart

    2004-08-01

    The rovibration partition function of CH4 was calculated in the temperature range of 100-1000 K using well-converged energy levels that were calculated by vibrational-rotational configuration interaction using the Watson Hamiltonian for total angular momenta J = 0-50 and the MULTIMODE computer program. The configuration state functions are products of ground-state occupied and virtual modals obtained using the vibrational self-consistent field method. The Gilbert and Jordan potential energy surface was used for the calculations. The resulting partition function was used to test the harmonic oscillator approximation and the separable-rotation approximation. The harmonic oscillator, rigid-rotator approximation is in error by a factor of 2.3 at 300 K, but we also propose a separable-rotation approximation that is accurate within 2% from 100 to 1000 K. PMID:15260761

  14. The Orthogonally Partitioned EM Algorithm: Extending the EM Algorithm for Algorithmic Stability and Bias Correction Due to Imperfect Data.

    PubMed

    Regier, Michael D; Moodie, Erica E M

    2016-05-01

    We propose an extension of the EM algorithm that exploits the common assumption of unique parameterization, corrects for biases due to missing data and measurement error, converges for the specified model when standard implementation of the EM algorithm has a low probability of convergence, and reduces a potentially complex algorithm into a sequence of smaller, simpler, self-contained EM algorithms. We use the theory surrounding the EM algorithm to derive the theoretical results of our proposal, showing that an optimal solution over the parameter space is obtained. A simulation study is used to explore the finite sample properties of the proposed extension when there is missing data and measurement error. We observe that partitioning the EM algorithm into simpler steps may provide better bias reduction in the estimation of model parameters. The ability to breakdown a complicated problem in to a series of simpler, more accessible problems will permit a broader implementation of the EM algorithm, permit the use of software packages that now implement and/or automate the EM algorithm, and make the EM algorithm more accessible to a wider and more general audience. PMID:27227718

  15. Missing mass approximations for the partition function of stimulus driven Ising models

    PubMed Central

    Haslinger, Robert; Ba, Demba; Galuske, Ralf; Williams, Ziv; Pipa, Gordon

    2013-01-01

    Ising models are routinely used to quantify the second order, functional structure of neural populations. With some recent exceptions, they generally do not include the influence of time varying stimulus drive. Yet if the dynamics of network function are to be understood, time varying stimuli must be taken into account. Inclusion of stimulus drive carries a heavy computational burden because the partition function becomes stimulus dependent and must be separately calculated for all unique stimuli observed. This potentially increases computation time by the length of the data set. Here we present an extremely fast, yet simply implemented, method for approximating the stimulus dependent partition function in minutes or seconds. Noting that the most probable spike patterns (which are few) occur in the training data, we sum partition function terms corresponding to those patterns explicitly. We then approximate the sum over the remaining patterns (which are improbable, but many) by casting it in terms of the stimulus modulated missing mass (total stimulus dependent probability of all patterns not observed in the training data). We use a product of conditioned logistic regression models to approximate the stimulus modulated missing mass. This method has complexity of roughly O(LNNpat) where is L the data length, N the number of neurons and Npat the number of unique patterns in the data, contrasting with the O(L2N) complexity of alternate methods. Using multiple unit recordings from rat hippocampus, macaque DLPFC and cat Area 18 we demonstrate our method requires orders of magnitude less computation time than Monte Carlo methods and can approximate the stimulus driven partition function more accurately than either Monte Carlo methods or deterministic approximations. This advance allows stimuli to be easily included in Ising models making them suitable for studying population based stimulus encoding. PMID:23898262

  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. 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.

  18. A growth walk model for estimating the canonical partition function of interacting self-avoiding walk.

    PubMed

    Narasimhan, S L; Krishna, P S R; Ponmurugan, M; Murthy, K P N

    2008-01-01

    We have explained in detail why the canonical partition function of interacting self-avoiding walk (ISAW) is exactly equivalent to the configurational average of the weights associated with growth walks, such as the interacting growth walk (IGW), if the average is taken over the entire genealogical tree of the walk. In this context, we have shown that it is not always possible to factor the density of states out of the canonical partition function if the local growth rule is temperature dependent. We have presented Monte Carlo results for IGWs on a diamond lattice in order to demonstrate that the actual set of IGW configurations available for study is temperature dependent even though the weighted averages lead to the expected thermodynamic behavior of ISAW. PMID:18190183

  19. Atomic charges, dipole moments, and Fukui functions using the Hirshfeld partitioning of the electron density.

    PubMed

    De Proft, F; Van Alsenoy, C; Peeters, A; Langenaeker, W; Geerlings, P

    2002-09-01

    In the Hirshfeld partitioning of the electron density, the molecular electron density is decomposed in atomic contributions, proportional to the weight of the isolated atom density in the promolecule density, constructed by superimposing the isolated atom electron densities placed on the positions the atoms have in the molecule. A maximal conservation of the information of the isolated atoms in the atoms-in-molecules is thereby secured. Atomic charges, atomic dipole moments, and Fukui functions resulting from the Hirshfeld partitioning of the electron density are computed for a large series of molecules. In a representative set of organic and hypervalent molecules, they are compared with other commonly used population analysis methods. The expected bond polarities are recovered, but the charges are much smaller compared to other methods. Condensed Fukui functions for a large number of molecules, undergoing an electrophilic or a nucleophilic attack, are computed and compared with the HOMO and LUMO densities, integrated over the Hirshfeld atoms in molecules. PMID:12116389

  20. QCD at nonzero density and canonical partition functions with Wilson fermions

    SciTech Connect

    Alexandru, Andrei; Wenger, Urs

    2011-02-01

    We present a reduction method for Wilson-Dirac fermions with nonzero chemical potential which generates a dimensionally reduced fermion matrix. The size of the reduced fermion matrix is independent of the temporal lattice extent and the dependence on the chemical potential is factored out. As a consequence the reduced matrix allows a simple evaluation of the Wilson fermion determinant for any value of the chemical potential and hence the exact projection to the canonical partition functions.

  1. 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.

  2. The ratios of partition functions at different temperatures - Sensitivity to potential energy shape II

    NASA Astrophysics Data System (ADS)

    Buchowiecki, Marcin

    2016-05-01

    The ratios of partition functions at different temperatures are calculated and its dependence on potential energy shape is analyzed. The role of anharmonicity and non-rigidity of rotations is discussed in the context of the angular frequency and the shape of potential energy curve. A role of inflection point of potential energy curve for the quality of rigid rotor harmonic oscillator and rigid rotor Morse oscillator is elucidated.

  3. Analysis of chromatin attachment and partitioning functions of bovine papillomavirus type 1 E2 protein.

    PubMed

    Abroi, Aare; Ilves, Ivar; Kivi, Sirje; Ustav, Mart

    2004-02-01

    Recent studies have suggested that the tethering of viral genomes to host cell chromosomes could provide one of the ways to achieve their nuclear retention and partitioning during extrachromosomal maintenance in dividing cells. The data we present here provide firm evidence that the partitioning of the bovine papillomavirus type 1 (BPV1) genome is dependent on the chromatin attachment process mediated by viral E2 protein and its multiple binding sites. On the other hand, the attachment of E2 and the E2-mediated tethering of reporter plasmids to host chromosomes are not necessarily sufficient for efficient partitioning, suggesting that additional E2-dependent activities might be involved in the latter process. The activity of E2 protein in chromatin attachment and partitioning is more sensitive to the point mutations in the N-terminal domain than its transactivation and replication initiation functions. Therefore, at least part of the interactions of the E2 N-terminal domain with its targets during the chromatin attachment and partitioning processes are likely to involve specific receptors not involved in transactivation and replication activities of the protein. The mutational analysis also indicates that the binding of E2 to chromatin is not achieved through interaction of linear N-terminal subsequences of the E2 protein with putative receptors. Instead, the composite surface elements of the N-terminal domain build up the receptor-binding surface of E2. In this regard, the interaction of BPV1 E2 with its chromosomal targets clearly differs from the interactions of LANA1 protein from Kaposi's sarcoma-associated human herpesvirus and EBNA1 from Epstein-Barr virus with their specific receptors. PMID:14747575

  4. The Functional Illiterate: Is Correctional Education Doing Its Job?

    ERIC Educational Resources Information Center

    Loeffler, Cynthia A.; Martin, Thomas C.

    A study researched the existence of established Adult Basic Education (ABE) curricula for incarcerated adult inmate/students in state correctional education programs, specifically the functionally illiterate. All 50 State Departments of Corrections were surveyed by questionnaire; 44 responded. ABE was a basis for curricula according to 37.6% of…

  5. 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.

  6. 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.

  7. Applanation pressure function in Goldmann tonometry and its correction.

    PubMed

    Śródka, Wiesław

    2013-01-01

    So far applanation tonometry has not worked out any theoretical basis for correcting the result of intraocular pressure measurement carried out on a cornea with noncalibration dimensions by means of the Goldmann tonometer. All the tables of instrument reading corrections for cornea thickness or cornea curvature radius are based exclusively on measurements. This paper represents an attempt at creating a mechanical description of corneal apex deformation in Goldmann applanation tonometry. The functional dependence between intraocular pressure and the pressure exerted on the corneal apex by the tonometer was determined from a biomechanical model. Numerical GAT simulations, in which this function was also interrelated with the cornea's curvature radius and thickness were run and a constitutive equation for applanation tonometry, i.e. a full analytical description of intraocular pressure as a function of the above variables, was derived on this basis. The correction factors were defined and an algorithm for correcting the measured pressure was formulated. The presented formalism puts the results of experimental tonometry in new light. Analytical correction factors need not to come exclusively from measurements. A geometric interdependence between them and their dependence on pressure have been revealed. The theoretical description of applanation tonometry contained in the constitutive equation consists of a pressure function developed for a cornea with calibration dimensions and a coefficient correcting this calibration function, dependent exclusively on the cornea's actual thickness and curvature radius. The calibration function is a generalization of the Imbert-Fick law. PMID:24215153

  8. Relativistic and binding energy corrections to heavy quark fragmentation functions

    SciTech Connect

    Yusuf, M.A.; Bashir, A.

    1997-11-01

    We calculate the fragmentation function for a charm quark to decay inclusively into S-wave charmonium states, including relativistic and binding energy corrections in powers of the quark relative velocity v. We also use these fragmentation functions to estimate their contribution to the production rate of {eta}{sub c} and J/{psi} in Z{sup 0} decay. These corrections contribute about 38{percent} to the integrated c{r_arrow}J/{psi}+X fragmentation. For {eta}{sub c}, these corrections are found to be small. {copyright} {ital 1997} {ital The American Physical Society}

  9. 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.

  10. 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).

  11. Semiclassical partition function for strings dual to Wilson loops with small cusps in ABJM

    NASA Astrophysics Data System (ADS)

    Aguilera-Damia, Jeremías; Correa, Diego H.; Silva, Guillermo A.

    2015-03-01

    We compute the 1-loop partition function for strings in , whose worldsheets end along a line with small cusp angles in the boundary of AdS. We obtain these 1-loop results in terms of the vacuum energy for on-shell modes. Our results verify the proposal by Lewkowycz and Maldacena in arXiv:1312.5682 for the exact Bremsstrahlung function up to the next to leading order in the strong coupling expansion. The agreement is observed for cusps distorting either the 1/2 BPS or the 1/6 BPS Wilson line.

  12. High temperature partition functions and thermodynamic data for ammonia and phosphine

    NASA Astrophysics Data System (ADS)

    Sousa-Silva, Clara; Hesketh, Nicholas; Yurchenko, Sergei N.; Hill, Christian; Tennyson, Jonathan

    2014-07-01

    The total internal partition function of ammonia (14NH3) and phosphine (31PH3) are calculated as a function of temperature by explicit summation of 153 million (for PH3) and 7.5 million (for NH3) theoretical rotation-vibrational energy levels. High accuracy estimates are obtained for the specific heat capacity, Cp, the Gibbs enthalpy function, gef, the Helmholtz function, hcf, and the entropy, S, of gas phase molecules as a function of temperature. In order to reduce the computational costs associated with the high rotational excitations, only the A-symmetry energy levels are used above a certain threshold of the total angular momentum number J. With this approach levels are summed up to dissociation energy for values of Jmax=45 and 100 for ammonia (Emax=41 051 cm-1) and phosphine (Emax=28 839.7 cm-1), respectively. Estimates of the partition function are converged for all temperatures considered for phosphine and below 3000 K for ammonia. All other thermodynamic properties are converged to at least 2000 K for ammonia and fully converged for phosphine.

  13. 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.

  14. 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.

  15. 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

  16. 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

    2015-01-01

    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

  17. 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.

  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. PMID:25467186

  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. Partition function for a two dimensional plasma in the random phase approximation

    NASA Technical Reports Server (NTRS)

    Seyler, C. E., Jr.

    1974-01-01

    The partition function for a two-dimensional plasma is evaluated within the random phase approximation. The periodic boundary conditions are fully taken into account by including the periodic image interactions. In the guiding-center limit, the negative temperature threshold energy is evaluated, and a value different from previous calculations results. When an identical random phase evaluated, and a value different from previous calculations results. When an identical random phase evaluation is applied to the finite gyroradius plasma, the Salzberg-Prager-May equation of state is recovered.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

    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.

  3. 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.

  4. Inner products of Bethe states as partial domain wall partition functions

    NASA Astrophysics Data System (ADS)

    Kostov, Ivan; Matsuo, Yutaka

    2012-10-01

    We study the inner product of Bethe states in the inhomogeneous periodic XXX spin-1/2 chain of length L, which is given by the Slavnov determinant formula. We show that the inner product of an on-shell M -magnon state with a generic M -magnon state is given by the same expression as the inner product of a 2 M -magnon state with a vacuum descendent. The second inner product is proportional to the partition function of the six-vertex model on a rectangular L × 2 M grid, with partial domain-wall boundary conditions.

  5. 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.

  6. 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

  7. Partition Equilibrium

    NASA Astrophysics Data System (ADS)

    Feldman, Michal; Tennenholtz, Moshe

    We introduce partition equilibrium and study its existence in resource selection games (RSG). In partition equilibrium the agents are partitioned into coalitions, and only deviations by the prescribed coalitions are considered. This is in difference to the classical concept of strong equilibrium according to which any subset of the agents may deviate. In resource selection games, each agent selects a resource from a set of resources, and its payoff is an increasing (or non-decreasing) function of the number of agents selecting its resource. While it has been shown that strong equilibrium exists in resource selection games, these games do not possess super-strong equilibrium, in which a fruitful deviation benefits at least one deviator without hurting any other deviator, even in the case of two identical resources with increasing cost functions. Similarly, strong equilibrium does not exist for that restricted two identical resources setting when the game is played repeatedly. We prove that for any given partition there exists a super-strong equilibrium for resource selection games of identical resources with increasing cost functions; we also show similar existence results for a variety of other classes of resource selection games. For the case of repeated games we identify partitions that guarantee the existence of strong equilibrium. Together, our work introduces a natural concept, which turns out to lead to positive and applicable results in one of the basic domains studied in the literature.

  8. Inferring Functional Interaction and Transition Patterns via Dynamic Bayesian Variable Partition Models

    PubMed Central

    Zhang, Jing; Li, Xiang; Li, Cong; Lian, Zhichao; Huang, Xiu; Zhong, Guocheng; Zhu, Dajiang; Li, Kaiming; Jin, Changfeng; Hu, Xintao; Han, Junwei; Guo, Lei; Hu, Xiaoping; Li, Lingjiang; Liu, Tianming

    2014-01-01

    Multivariate connectivity and functional dynamics have been of wide interest in the neuroimaging field, and a variety of methods have been developed to study functional interactions and dynamics. In contrast, the temporal dynamic transitions of multivariate functional interactions among brain networks, in particular, in resting state, have been much less explored. This paper presents a novel dynamic Bayesian variable partition model (DBVPM) that simultaneously considers and models multivariate functional interactions and their dynamics via a unified Bayesian framework. The basic idea is to detect the temporal boundaries of piecewise quasi-stable functional interaction patterns, which are then modeled by representative signature patterns and whose temporal transitions are characterized by finite-state transition machines. Results on both simulated and experimental datasets demonstrated the effectiveness and accuracy of the DBVPM in dividing temporally transiting functional interaction patterns. The application of DBVPM on a post-traumatic stress disorder (PTSD) dataset revealed substantially different multivariate functional interaction signatures and temporal transitions in the default mode and emotion networks of PTSD patients, in comparison with those in healthy controls. This result demonstrated the utility of DBVPM in elucidating salient features that cannot be revealed by static pair-wise functional connectivity analysis. PMID:24222313

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

    PubMed Central

    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.; Consortium, ReproGen; Purcell, Shaun; Stahl, Eli; Lindstrom, Sara; Perry, John R. B.; Okada, Yukinori; Raychaudhuri, Soumya; Daly, Mark; Patterson, Nick; Neale, Benjamin M.; Price, Alkes L.

    2015-01-01

    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 results 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 body mass index, age at menarche, educational attainment, and smoking behavior. PMID:26414678

  10. Joint multifractal analysis based on the partition function approach: analytical analysis, numerical simulation and empirical application

    NASA Astrophysics Data System (ADS)

    Xie, Wen-Jie; Jiang, Zhi-Qiang; Gu, Gao-Feng; Xiong, Xiong; Zhou, Wei-Xing

    2015-10-01

    Many complex systems generate multifractal time series which are long-range cross-correlated. Numerous methods have been proposed to characterize the multifractal nature of these long-range cross correlations. However, several important issues about these methods are not well understood and most methods consider only one moment order. We study the joint multifractal analysis based on partition function with two moment orders, which was initially invented to investigate fluid fields, and derive analytically several important properties. We apply the method numerically to binomial measures with multifractal cross correlations and bivariate fractional Brownian motions without multifractal cross correlations. For binomial multifractal measures, the explicit expressions of mass function, singularity strength and multifractal spectrum of the cross correlations are derived, which agree excellently with the numerical results. We also apply the method to stock market indexes and unveil intriguing multifractality in the cross correlations of index volatilities.

  11. 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.

  12. Semantics and correctness proofs for programs with partial functions

    SciTech Connect

    Yakhnis, A.; Yakhnis, V.

    1996-09-01

    This paper presents a portion of the work on specification, design, and implementation of safety-critical systems such as reactor control systems. A natural approach to this problem, once all the requirements are captured, would be to state the requirements formally and then either to prove (preferably via automated tools) that the system conforms to spec (program verification), or to try to simultaneously generate the system and a mathematical proof that the requirements are being met (program derivation). An obstacle to this is frequent presence of partially defined operations within the software and its specifications. Indeed, the usual proofs via first order logic presuppose everywhere defined operations. Recognizing this problem, David Gries, in ``The Science of Programming,`` 1981, introduced the concept of partial functions into the mainstream of program correctness and gave hints how his treatment of partial functions could be formalized. Still, however, existing theorem provers and software verifiers have difficulties in checking software with partial functions, because of absence of uniform first order treatment of partial functions within classical 2-valued logic. Several rigorous mechanisms that took partiality into account were introduced [Wirsing 1990, Breu 1991, VDM 1986, 1990, etc.]. However, they either did not discuss correctness proofs or departed from first order logic. To fill this gap, the authors provide a semantics for software correctness proofs with partial functions within classical 2-valued 1st order logic. They formalize the Gries treatment of partial functions and also cover computations of functions whose argument lists may be only partially available. An example is nuclear reactor control relying on sensors which may fail to deliver sense data. This approach is sufficiently general to cover correctness proofs in various implementation languages.

  13. 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

  14. 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

  15. Minimal energy ensemble Monte Carlo algorithm for the partition function of fermions coupled to classical fields

    NASA Astrophysics Data System (ADS)

    Grzybowski, Przemysław R.; Czekaj, Łukasz; Nogala, Mariusz; Ścibior, Adam; Chhajlany, Ravindra W.

    2016-06-01

    Models of noninteracting fermions coupled to auxiliary classical fields are relevant to the understanding of a wide variety of problems in many-body physics, e.g., the description of manganites, diluted magnetic semiconductors, or strongly interacting electrons on lattices. We present a flat-histogram Monte Carlo algorithm that simulates a statistical ensemble that allows one to directly acquire the partition function at all temperatures for such systems. The defining feature of the algorithm is that it utilizes the complete thermodynamic information from the full energy spectrum of noninteracting fermions available during sampling of the configuration space of the classical fields. We benchmark the method for the classical Ising and Potts models in two dimensions, as well as the Falicov-Kimball model describing itinerant electrons interacting with heavy ions.

  16. Two-loop partition function in the planar plane-wave matrix model

    NASA Astrophysics Data System (ADS)

    Spradlin, Marcus; Van Raamsdonk, Mark; Volovich, Anastasia

    2004-12-01

    We perform two independent calculations of the two-loop partition function for the 't Hooft large N limit of the plane-wave matrix model, conjectured to be dual to the decoupled little string theory of a single spherical type IIA NS5-brane. The first is via a direct two-loop path-integral calculation in the matrix model, while the second employs the one-loop dilatation operator of four-dimensional N = 4 Yang-Mills theory truncated to the SU (2 | 4) subsector. We find precise agreement between the results of the two calculations. Various polynomials appearing in the result have rather special properties, possibly related to the large symmetry algebra of the theory or to integrability.

  17. 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).

  18. Singularities of the Partition Function for the Ising Model Coupled to 2D Quantum Gravity

    NASA Astrophysics Data System (ADS)

    Ambjørn, J.; Anagnostopoulos, K. N.; Magnea, U.

    We study the zeros in the complex plane of the partition function for the Ising model coupled to 2D quantum gravity for complex magnetic field and real temperature, and for complex temperature and real magnetic field, respectively. We compute the zeros by using the exact solution coming from a two-matrix model and by Monte-Carlo simulations of Ising spins on dynamical triangulations. We present evidence that the zeros form simple one-dimensional curves in the complex plane, and that the critical behaviour of the system is governed by the scaling of the distribution of the singularities near the critical point. Despite the small size of the systems studied, we can obtain a reasonable estimate of the (known) critical exponents.

  19. Twists of Plücker Coordinates as Dimer Partition Functions

    NASA Astrophysics Data System (ADS)

    Marsh, R. J.; Scott, J. S.

    2016-02-01

    The homogeneous coordinate ring of the Grassmannian Gr k, n has a cluster structure defined in terms of planar diagrams known as Postnikov diagrams. The cluster corresponding to such a diagram consists entirely of Plücker coordinates. We introduce a twist map on Gr k, n , related to the Berenstein-Fomin-Zelevinsky-twist, and give an explicit Laurent expansion for the twist of an arbitrary Plücker coordinate in terms of the cluster variables associated with a fixed Postnikov diagram. The expansion arises as a (scaled) dimer partition function of a weighted version of the bipartite graph dual to the Postnikov diagram, modified by a boundary condition determined by the Plücker coordinate. We also relate the twist map to a maximal green sequence.

  20. 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.

  1. 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.

  2. 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.

  3. Partition function, metastability, and kinetics of the escape transition for an ideal chain

    NASA Astrophysics Data System (ADS)

    Klushin, L. I.; Skvortsov, A. M.; Leermakers, F. A.

    2004-06-01

    An end-tethered polymer chain squeezed between two pistons undergoes an abrupt transition from a confined coil state to an inhomogeneous flower-like conformation partially escaped from the gap. We present a rigorous analytical theory for the equilibrium and kinetic aspects of this phenomenon for a Gaussian chain. Applying the analogy with the problem of the adsorption of an ideal chain constrained by one of its ends, we obtain a closed analytical expression for the exact partition function. Various equilibrium thermodynamic characteristics (the fraction of imprisoned segments, the average compression, and lateral forces) are calculated as a function of the piston separation. The force versus separation curve is studied in two complementary statistical ensembles, the constant force and the constant confinement width ones. The differences in these force curves are significant in the transition region for large systems, but disappear for small systems. The effects of metastability are analyzed by introducing the Landau free energy as a function of the chain stretching, which serves as the order parameter. The phase diagram showing the binodal and two spinodal lines is presented. We obtain the barrier heights between the stable and metastable states in the free energy landscape. The mean first passage time, i.e., the lifetime of the metastable coil and flower states, is estimated on the basis of the Fokker-Planck formalism. Equilibrium analytical theory for a Gaussian chain is complemented by numerical calculations for a lattice freely jointed chain model.

  4. Hierarchical partitioning of metazoan protein conservation profiles provides new functional insights.

    PubMed

    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

  5. Scattering corrections in neutron radiography using point scattered functions

    NASA Astrophysics Data System (ADS)

    Kardjilov, N.; de Beer, F.; Hassanein, R.; Lehmann, E.; Vontobel, P.

    2005-04-01

    Scattered neutrons cause distortions and blurring in neutron radiography pictures taken at small distances between the investigated object and the detector. This defines one of the most significant problems in quantitative neutron radiography. The quantification of strong scattering materials such as hydrogenous materials—water, oil, plastic, etc.—with a high precision is very difficult due to the scattering effect in the radiography images. The scattering contribution in liquid test samples (H 2O, D 2O and a special type oil ISOPAR L) at different distances between the samples and the detector, the so-called Point Scattered Function (PScF), was calculated with the help of MCNP-4C Monte Carlo code. Corrections of real experimental data were performed using the calculated PScF. Some of the results as well as the correction algorithm will be presented.

  6. 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

  7. 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.

  8. 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.

  9. Corrections Regarding the Impedance of Distance Functions for Several g(d) Functions

    ERIC Educational Resources Information Center

    Beaman, Jay

    1976-01-01

    Five functions were introduced for modeling travel behavior in the Beaman article "Distance and the 'Reaction' to Distance as a Function of Distance" published in Vol. 6, No. 3 of "Journal of Leisure Research" with the graphs of the functions printed incorrectly. This is a corrected version. (MM)

  10. 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.

  11. Structural properties of Potts model partition functions and chromatic polynomials for lattice strips

    NASA Astrophysics Data System (ADS)

    Chang, Shu-Chiuan; Shrock, Robert

    2001-07-01

    The q-state Potts model partition function (equivalent to the Tutte polynomial) for a lattice strip of fixed width Ly and arbitrary length Lx has the form Z(G,q,v)=∑ j=1N Z,G,λ c Z,G,j(λ Z,G,j) L x, where v is a temperature-dependent variable. The special case of the zero-temperature antiferromagnet ( v=-1) is the chromatic polynomial P( G, q). Using coloring and transfer matrix methods, we give general formulas for C X,G=∑ j=1N X,G,λ c X,G,j for X= Z, P on cyclic and Möbius strip graphs of the square and triangular lattice. Combining these with a general expression for the (unique) coefficient cZ, G, j of degree d in q: c (d)=U 2d( q/2) , where Un( x) is the Chebyshev polynomial of the second kind, we determine the number of λZ, G, j's with coefficient c( d) in Z( G, q, v) for these cyclic strips of width Ly to be n Z(L y,d)=(2d+1)(L y+d+1) -1{2L y}/{L y-d } for 0⩽ d⩽ Ly and zero otherwise. For both cyclic and Möbius strips of these lattices, the total number of distinct eigenvalues λZ, G, j is calculated to be N Z,L y,λ = {2L y}/{L y}. Results are also presented for the analogous numbers nP( Ly, d) and NP, Ly, λ for P( G, q). We find that nP( Ly,0)= nP( Ly-1,1)= MLy-1 (Motzkin number), nZ( Ly,0)= CLy (the Catalan number), and give an exact expression for NP, Ly, λ. Our results for NZ, Ly, λ and NP, Ly, λ apply for both the cyclic and Möbius strips of both the square and triangular lattices; we also point out the interesting relations NZ, Ly, λ=2 NDA, tri, Ly and NP, Ly, λ=2 NDA, sq, Ly, where NDA, Λ, n denotes the number of directed lattice animals on the lattice Λ. We find the asymptotic growths NZ, Ly, λ∼ Ly-1/24 Ly and NP, Ly, λ∼ Ly-1/23 Ly as Ly→∞. Some general geometric identities for Potts model partition functions are also presented.

  12. 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.

  13. Maps of zeros of the grand canonical partition function in a statistical model of high energy collisions

    NASA Astrophysics Data System (ADS)

    Brambilla, M.; Giovannini, A.; Ugoccioni, R.

    2006-06-01

    Theorems on zeros of the truncated generating function in the complex plane are reviewed. When examined in the framework of a statistical model of high energy collisions based on the negative binomial (Pascal) multiplicity distribution, these results lead to maps of zeros of the grand canonical partition function which allow us to interpret in a novel way different classes of events in pp collisions at LHC c.m. energies.

  14. 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.

  15. 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.

  16. The correct renal function evaluation in patients with thyroid dysfunction.

    PubMed

    Simeoni, Mariadelina; Cerantonio, Annamaria; Pastore, Ida; Liguori, Rossella; Greco, Marta; Foti, Daniela; Gulletta, Elio; Brunetti, Antonio; Fuiano, Giorgio

    2016-05-01

    Thyroid dysfunction induces several renal derangements involving all nephron portions. Furthermore, dysthyroidism is a recognized risk factor associated with the development of chronic kidney disease. Current data, in fact, demonstrate that either subclinical or overt thyroid disease is associated with significant changes in creatinine, estimated glomerular filtration rate, measured glomerular filtration rate and Cystatin C. Herein, we systematically reviewed several relevant studies aiming at the identification of the most sensitive and specific parameter for the correct renal function evaluation in patients with thyroid dysfunction, that are usually treated as outpatients. Our systematic review indicates that estimated glomerular filtration rate, preferably with CKD-EPI equation, appears to be the most reliable and wieldy renal function parameter. Instead, Cystatin C should be better used in the grading of thyroid dysfunction severity. PMID:26511999

  17. 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.

  18. Functional Partitioning to Optimize End-to-End Performance on Many-core Architectures

    SciTech Connect

    Li, Min; Vazhkudai, Sudharshan S; Butt, Ali R; Meng, Fei; Ma, Xiaosong; Kim, Youngjae; Engelmann, Christian; Shipman, Galen M

    2010-01-01

    Scaling computations on emerging massive-core supercomputers is a daunting task, which coupled with the significantly lagging system I/O capabilities exacerbates applications end-to-end performance. The I/O bottleneck often negates potential performance benefits of assigning additional compute cores to an application. In this paper, we address this issue via a novel functional partitioning (FP) runtime environment that allocates cores to specific application tasks - checkpointing, de-duplication, and scientific data format transformation - so that the deluge of cores can be brought to bear on the entire gamut of application activities. The focus is on utilizing the extra cores to support HPC application I/O activities and also leverage solid-state disks in this context. For example, our evaluation shows that dedicating 1 core on an oct-core machine for checkpointing and its assist tasks using FP can improve overall execution time of a FLASH benchmark on 80 and 160 cores by 43.95% and 41.34%, respectively.

  19. Development of particle multiplicity distributions using a general form of the grand canonical partition function

    NASA Astrophysics Data System (ADS)

    Lee, S. J.; Mekjian, A. Z.

    2004-01-01

    Various phenomenological models of particle multiplicity distributions are discussed using a general form of a unified model which is based on the grand canonical partition function and Feynman's path integral approach to statistical processes. These models can be written as special cases of a more general distribution which has three control parameters which are a, x, z. The relation to these parameters to various physical quantities are discussed. A connection of the parameter a with Fisher's critical exponent τ is developed. Using this grand canonical approach, moments, cumulants and combinants are discussed and a physical interpretation of the combinants are given and their behavior connected to the critical exponent τ. Various physical phenomena such as hierarchical structure, void scaling relations, Koba-Nielson-Olesen or KNO scaling features, clan variables, and branching laws are shown in terms of this general approach. Several of these features which were previously developed in terms of the negative binomial distribution are found to be more general. Both hierarchical structure and void scaling relations depend on the Fisher exponent τ. Applications of our approach to the charged particle multiplicity distribution in jets of L3 and H1 data are given.

  20. 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

  1. 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

  2. The domain wall partition function for the Izergin-Korepin nineteen-vertex model at a root of unity

    NASA Astrophysics Data System (ADS)

    Garbali, A.

    2016-03-01

    We study the domain wall partition function Z N for the {{U}q}≤ft(A2(2)\\right) (Izergin-Korepin) integrable nineteen-vertex model on a square lattice of size N. Z N is a symmetric function of two sets of parameters: horizontal {{\\zeta}1},..,{{\\zeta}N} and vertical {{z}1},..,{{z}N} rapidities. For generic values of the parameter q we derive the recurrence relation for the domain wall partition function relating Z N+1 to {{P}N}{{Z}N} , where P N is the proportionality factor in the recurrence, which is a polynomial symmetric in two sets of variables {{\\zeta}1},..,{{\\zeta}N} and {{z}1},..,{{z}N} . After setting q={{\\text{e}}\\text{iπ /3}} the recurrence relation simplifies and we solve it in terms of a Jacobi-Trudi-like determinant of polynomials generated by P N .

  3. 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.

  4. Correction.

    PubMed

    2015-12-01

    In the article by Narayan et al (Narayan O, Davies JE, Hughes AD, Dart AM, Parker KH, Reid C, Cameron JD. Central aortic reservoir-wave analysis improves prediction of cardiovascular events in elderly hypertensives. Hypertension. 2015;65:629–635. doi: 10.1161/HYPERTENSIONAHA.114.04824), which published online ahead of print December 22, 2014, and appeared in the March 2015 issue of the journal, some corrections were needed.On page 632, Figure, panel A, the label PRI has been corrected to read RPI. In panel B, the text by the upward arrow, "10% increase in kd,” has been corrected to read, "10% decrease in kd." The corrected figure is shown below.The authors apologize for these errors. PMID:26558821

  5. 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

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

    NASA Astrophysics Data System (ADS)

    Mielke, Steven L.; Truhlar, Donald G.

    2016-01-01

    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.

  7. Resist charging effect correction function qualification for photomasks production

    NASA Astrophysics Data System (ADS)

    Sidorkin, Vadim; Finken, Michael; Wandel, Timo; Nakayamada, Noriaki; Cantrell, G. R.

    2014-10-01

    We quantitatively evaluate Nuflare's latest resist charging effect correction (CEC) model for advanced photomask production using e-beam lithography. Functionality of this CEC model includes the simulation of static and timedependent charging effects together with an improved calibration method. CEC model calibration is performed by polynomial fitting of image placement distortions induced by various beam scattering effects on a special test design with writing density variations. CEC model parameters can be fine tuned for different photomask blank materials facilitating resist charging compensation maps for different product layers. Application of this CEC model into production yields a significant reduction in photomask image placement (IP), as well as improving photomask overlay between critical neighbouring layers. The correlations between IP improvement facilitated by this CEC model and single mask parameters are presented and discussed. The layer design specifics, resist and blank materials, coupled with their required exposure parameters are observed to be the major influences on CEC model performance.

  8. Transfer Matrices and Partition-Function Zeros for Antiferromagnetic Potts Models VI. Square Lattice with Extra-Vertex Boundary Conditions

    NASA Astrophysics Data System (ADS)

    Salas, Jesús; Sokal, Alan D.

    2011-09-01

    We study, using transfer-matrix methods, the partition-function zeros of the square-lattice q-state Potts antiferromagnet at zero temperature (= square-lattice chromatic polynomial) for the boundary conditions that are obtained from an m× n grid with free boundary conditions by adjoining one new vertex adjacent to all the sites in the leftmost column and a second new vertex adjacent to all the sites in the rightmost column. We provide numerical evidence that the partition-function zeros are becoming dense everywhere in the complex q-plane outside the limiting curve {B}_{infty}(sq) for this model with ordinary (e.g. free or cylindrical) boundary conditions. Despite this, the infinite-volume free energy is perfectly analytic in this region.

  9. Potts model partition functions for self-dual families of strip graphs

    NASA Astrophysics Data System (ADS)

    Chang, Shu-Chiuan; Shrock, Robert

    2001-12-01

    We consider the q-state Potts model on families of self-dual strip graphs GD of the square lattice of width Ly and arbitrarily great length Lx, with periodic longitudinal boundary conditions. The general partition function Z and the T=0 antiferromagnetic special case P (chromatic polynomial) have the respective forms ∑ j=1 NF, Ly, λcF, Ly, j( λF, Ly, j) Lx, with F= Z, P. For arbitrary Ly, we determine (i) the general coefficient cF, Ly, j in terms of Chebyshev polynomials, (ii) the number nF( Ly, d) of terms with each type of coefficient, and (iii) the total number of terms NF, Ly, λ. We point out interesting connections between the nZ( Ly, d) and Temperley-Lieb algebras, and between the NF, Ly, λ and enumerations of directed lattice animals. Exact calculations of P are presented for 2⩽ Ly⩽4. In the limit of infinite length, we calculate the ground state degeneracy per site (exponent of the ground state entropy), W( q). Generalizing q from Z+ to C, we determine the continuous locus B in the complex q plane where W( q) is singular. We find the interesting result that for all Ly values considered, the maximal point at which B crosses the real q-axis, denoted qc, is the same, and is equal to the value for the infinite square lattice, qc=3. This is the first family of strip graphs of which we are aware that exhibits this type of universality of qc.

  10. Experimental Energy Levels and Partition Function of the 12C2 Molecule

    NASA Astrophysics Data System (ADS)

    Furtenbacher, Tibor; Szabó, István; Császár, Attila G.; Bernath, Peter F.; Yurchenko, Sergei N.; Tennyson, Jonathan

    2016-06-01

    The carbon dimer, the 12C2 molecule, is ubiquitous in astronomical environments. Experimental-quality rovibronic energy levels are reported for 12C2, based on rovibronic transitions measured for and among its singlet, triplet, and quintet electronic states, reported in 42 publications. The determination utilizes the Measured Active Rotational-Vibrational Energy Levels (MARVEL) technique. The 23,343 transitions measured experimentally and validated within this study determine 5699 rovibronic energy levels, 1325, 4309, and 65 levels for the singlet, triplet, and quintet states investigated, respectively. The MARVEL analysis provides rovibronic energies for six singlet, six triplet, and two quintet electronic states. For example, the lowest measurable energy level of the {{a}}{}3{{{\\Pi }}}{{u}} state, corresponding to the J = 2 total angular momentum quantum number and the F 1 spin-multiplet component, is 603.817(5) cm‑1. This well-determined energy difference should facilitate observations of singlet–triplet intercombination lines, which are thought to occur in the interstellar medium and comets. The large number of highly accurate and clearly labeled transitions that can be derived by combining MARVEL energy levels with computed temperature-dependent intensities should help a number of astrophysical observations as well as corresponding laboratory measurements. The experimental rovibronic energy levels, augmented, where needed, with ab initio variational ones based on empirically adjusted and spin–orbit coupled potential energy curves obtained using the Duo code, are used to obtain a highly accurate partition function, and related thermodynamic data, for 12C2 up to 4000 K.

  11. 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

  12. Partition function zeros for the Ising model on complete graphs and on annealed scale-free networks

    NASA Astrophysics Data System (ADS)

    Krasnytska, M.; Berche, B.; Holovatch, Yu; Kenna, R.

    2016-04-01

    We analyse the partition function of the Ising model on graphs of two different types: complete graphs, wherein all nodes are mutually linked and annealed scale-free networks for which the degree distribution decays as P(k) ˜ k -λ . We are interested in zeros of the partition function in the cases of complex temperature or complex external field (Fisher and Lee-Yang zeros respectively). For the model on an annealed scale-free network, we find an integral representation for the partition function which, in the case λ > 5, reproduces the zeros for the Ising model on a complete graph. For 3 < λ < 5 we derive the λ-dependent angle at which the Fisher zeros impact onto the real temperature axis. This, in turn, gives access to the λ-dependent universal values of the critical exponents and critical amplitudes ratios. Our analysis of the Lee-Yang zeros reveals a difference in their behaviour for the Ising model on a complete graph and on an annealed scale-free network when 3 < λ < 5. Whereas in the former case the zeros are purely imaginary, they have a non zero real part in latter case, so that the celebrated Lee-Yang circle theorem is violated.

  13. Correction

    NASA Astrophysics Data System (ADS)

    1995-04-01

    Seismic images of the Brooks Range, Arctic Alaska, reveal crustal-scale duplexing: Correction Geology, v. 23, p. 65 68 (January 1995) The correct Figure 4A, for the loose insert, is given here. See Figure 4A below. Corrected inserts will be available to those requesting copies of the article from the senior author, Gary S. Fuis, U.S. Geological Survey, 345 Middlefield Road, Menlo Park, CA 94025. Figure 4A. P-wave velocity model of Brooks Range region (thin gray contours) with migrated wide-angle reflections (heavy red lines) and migreated vertical-incidence reflections (short black lines) superimposed. Velocity contour interval is 0.25 km/s; 4,5, and 6 km/s contours are labeled. Estimated error in velocities is one contour interval. Symbols on faults shown at top are as in Figure 2 caption.

  14. Altitude-adjusted corrected geomagnetic coordinates: Definition and functional approximations

    NASA Astrophysics Data System (ADS)

    Shepherd, S. G.

    2014-09-01

    Analysis of the functional approximations used to transform between geographic and Altitude-Adjusted Corrected Geomagnetic (AACGM) coordinates reveals that errors of >50 km can occur in the auroral and polar regions. These errors are the result of efforts to better approximate AACGM coordinates near the magnetic equator and the South Atlantic Anomaly. In these regions AACGM coordinates are not defined and alternate coordinates have been used. This augmentation and emphasis on the solution in regions near the equator result in spherical harmonic approximating functions that are less accurate than need be in the auroral and polar regions. In response, a new set of spherical harmonic coefficients have been derived that better represent AACGM coordinates in these regions. These new AACGM coefficients are limited to below 2000 km in altitude in order to ensure accuracy. For altitudes above 2000 km, a magnetic field-line tracing solution is recommended. A software package developed to take advantage of the new AACGM coefficients provides the capability of tracing magnetic field lines at any altitude, for improved accuracy. In addition, linear interpolation between 5 year epochs is used to produce coordinates that vary smoothly over the entire period from 1965 to present. The intent of this work is to provide a more accurate procedure for determining AACGM coordinates in the auroral and polar regions for the study of magnetospheric and ionospheric processes.

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

    SciTech Connect

    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(AuPH{sub 3}){sub 4}]{sup +} 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.

  16. 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. PMID:24832312

  17. In silico analysis of division times of Escherichia coli populations as a function of the partitioning scheme of non-functional proteins

    PubMed Central

    Gupta, Abhishekh; Lloyd-Price, Jason; Ribeiro, Andre S.

    2015-01-01

    Abstract Recent evidence suggests that cells employ functionally asymmetric partitioning schemes in division to cope with aging. We explore various schemes in silico, with a stochastic model of Escherichia coli that includes gene expression, non-functional proteins generation, aggregation and polar retention, and molecule partitioning in division. The model is implemented in SGNS2, which allows stochastic, multi-delayed reactions within hierarchical, transient, interlinked compartments. After setting parameter values of non-functional proteins’ generation and effects that reproduce realistic intracellular and population dynamics, we investigate how the spatial organization of non-functional proteins affects mean division times of cell populations in lineages and, thus, mean cell numbers over time. We find that division times decrease for increasingly asymmetric partitioning. Also, increasing the clustering of non-functional proteins decreases division times. Increasing the bias in polar segregation further decreases division times, particularly if the bias favors the older pole and aggregates’ polar retention is robust. Finally, we show that the non-energy consuming retention of inherited non-functional proteins at the older pole via nucleoid occlusion is a source of functional asymmetries and, thus, is advantageous. Our results suggest that the mechanisms of intracellular organization of non-functional proteins, including clustering and polar retention, affect the vitality of E. coli populations. PMID:25318468

  18. Correction.

    PubMed

    2016-02-01

    Neogi T, Jansen TLTA, Dalbeth N, et al. 2015 Gout classification criteria: an American College of Rheumatology/European League Against Rheumatism collaborative initiative. Ann Rheum Dis 2015;74:1789–98. The name of the 20th author was misspelled. The correct spelling is Janitzia Vazquez-Mellado. We regret the error. PMID:26881284

  19. Correction.

    PubMed

    2016-02-01

    In the article by Guessous et al (Guessous I, Pruijm M, Ponte B, Ackermann D, Ehret G, Ansermot N, Vuistiner P, Staessen J, Gu Y, Paccaud F, Mohaupt M, Vogt B, Pechère-Bertschi A, Martin PY, Burnier M, Eap CB, Bochud M. Associations of ambulatory blood pressure with urinary caffeine and caffeine metabolite excretions. Hypertension. 2015;65:691–696. doi: 10.1161/HYPERTENSIONAHA.114.04512), which published online ahead of print December 8, 2014, and appeared in the March 2015 issue of the journal, a correction was needed.One of the author surnames was misspelled. Antoinette Pechère-Berstchi has been corrected to read Antoinette Pechère-Bertschi.The authors apologize for this error. PMID:26763012

  20. 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

  1. 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

  2. Correction

    NASA Astrophysics Data System (ADS)

    1998-12-01

    Alleged mosasaur bite marks on Late Cretaceous ammonites are limpet (patellogastropod) home scars Geology, v. 26, p. 947 950 (October 1998) This article had the following printing errors: p. 947, Abstract, line 11, “sepia” should be “septa” p. 947, 1st paragraph under Introduction, line 2, “creep” should be “deep” p. 948, column 1, 2nd paragraph, line 7, “creep” should be “deep” p. 949, column 1, 1st paragraph, line 1, “creep” should be “deep” p. 949, column 1, 1st paragraph, line 5, “19774” should be “1977)” p. 949, column 1, 4th paragraph, line 7, “in particular” should be “In particular” CORRECTION Mammalian community response to the latest Paleocene thermal maximum: An isotaphonomic study in the northern Bighorn Basin, Wyoming Geology, v. 26, p. 1011 1014 (November 1998) An error appeared in the References Cited. The correct reference appears below: Fricke, H. C., Clyde, W. C., O'Neil, J. R., and Gingerich, P. D., 1998, Evidence for rapid climate change in North America during the latest Paleocene thermal maximum: Oxygen isotope compositions of biogenic phosphate from the Bighorn Basin (Wyoming): Earth and Planetary Science Letters, v. 160, p. 193 208.

  3. Level distributions, partition functions, and rates of chirality changing processes for the torsional mode around O-O bonds

    NASA Astrophysics Data System (ADS)

    Bitencourt, Ana C. P.; Ragni, Mirco; Maciel, Glauciete S.; Aquilanti, Vincenzo; Prudente, Frederico V.

    2008-10-01

    In view of the particular attention recently devoted to hindered rotations, we have tested reduced kinetic energy operators to study the torsional mode around the O-O bond for H2O2 and for a series of its derivatives (HOOCl, HOOCN, HOOF, HOONO, HOOMe, HOOEt, MeOOMe, ClOOCl, FOOCl, FOOF, and FOONO), for which we had previously determined potential energy profiles along the dihedral ROOR ' angle [R,R'=H,F,Cl,CN,NO,Me (=CH3), Et (=C2H5)]. We have calculated level distributions as a function of temperature and partition functions for all systems. Specifically, for the H2O2 system we have used two procedures for the reduction in the kinetic energy operator to that of a rigid-rotor-like one and the calculated partition functions are compared with previous work. Quantum partition functions are evaluated both by quantum level state sums and by simple classical approximations. A semiclassical approach, using a linear approximation of the classical path and a quadratic Feynman-Hibbs approximation of Feynman path integral, introduced in previous work and here applied to the torsional mode, is shown to greatly improve the classical approximations. Further improvement is obtained by the explicit introduction of the dependence of the moment of inertia from the torsional angle. These results permit one to discuss the characteristic time for chirality changes for the investigated molecules either by quantum mechanical tunneling (dominating at low temperatures) or by transition state theory (expected to provide an estimate of racemization rates in the high energy limit).

  4. Real-time correction by optical tracking with integrated geometric distortion correction for reducing motion artifacts in functional MRI.

    PubMed

    Rotenberg, David; Chiew, Mark; Ranieri, Shawn; Tam, Fred; Chopra, Rajiv; Graham, Simon J

    2013-03-01

    Head motion artifacts are a major problem in functional MRI that limit its use in neuroscience research and clinical settings. Real-time scan-plane correction by optical tracking has been shown to correct slice misalignment and nonlinear spin-history artifacts; however, residual artifacts due to dynamic magnetic field nonuniformity may remain in the data. A recently developed correction technique, Phase Labeling for Additional Coordinate Encoding, can correct for absolute geometric distortion using only the complex image data from two echo planar images with slightly shifted k-space trajectories. An approach is presented that integrates Phase Labeling for Additional Coordinate Encoding into a real-time scan-plane update system by optical tracking, applied to a tissue-equivalent phantom undergoing complex motion and an functional MRI finger tapping experiment with overt head motion to induce dynamic field nonuniformity. Experiments suggest that such integrated volume-by-volume corrections are very effective at artifact suppression, with potential to expand functional MRI applications. PMID:22585554

  5. Variation in functional rooting depth and soil water partitioning along an elevational gradient in the southwestern U.S

    NASA Astrophysics Data System (ADS)

    Guo, J.; Hungate, B. A.; Kolb, T.; KOCH, G. W.

    2012-12-01

    In semi-arid environments, co-existing plant species may vary in rooting depth, reflecting functional differences in water sources. In mountains of the southwestern U.S., moisture availability increases with elevation and winter and summer precipitation inputs differ isotopically. Examining variation in functional rooting depth among different plant communities and seasons is important to understanding how these communities may respond to the predicted warming and drying of the Southwest. The goal of this study was to assess the water partitioning of the woody plant community along an elevational moisture gradient using water isotopes as a proxy for rooting depth. We hypothesized that spatial and temporal water partitioning would be greatest in low elevation, moisture-stressed sites and would decrease as moisture availability increases with elevation. Five plots were established in each of five biotic communities: upland Sonoran desert, pinyon-juniper woodland, ponderosa pine forest, mixed-conifer forest, and spruce-fir forest. Soils (surface, 20 cm, 40 cm) and stem samples of dominant woody perennials were sampled during the late spring dry season and in late summer following monsoon rains, water was extracted using a cryo-vacuum line, and δD and δ18O values were determined by off-axis cavity ringdown spectroscopy. Soil moisture content increased with elevation across all sites and increased with soil depth in the desert, pinyon-juniper, and ponderosa sites. The δD values differed significantly among species in the desert and the ponderosa forest communities (p=0.014 and 0.039 ), while no species differences in δD were found in the pinyon-juniper woodland or mixed-conifer forest. With the exception of the pinyon-juniper woodland, these data support our hypothesis that niche differentiation between species becomes less significant higher on the topographic moisture gradient, in the mixed-conifer forest. While spatial water partitioning mostly follows our

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. Computing the partition function and sampling for saturated secondary structures of RNA, with respect to the Turner energy model.

    PubMed

    Waldispühl, J; Clote, P

    2007-03-01

    An RNA secondary structure is saturated if no base pairs can be added without violating the definition of secondary structure. Here we describe a new algorithm, RNAsat, which for a given RNA sequence a, an integral temperature 0 partition function Z(k)(T)(a) = SigmaSepsilonSAT(k)(a) exp(-E(S)/RT), where the sum is over all saturated secondary structures of a which have exactly k base pairs, R is the universal gas constant and E(S) denotes the free energy with respect to the Turner nearest neighbor energy model. By dynamic programming, we compute Z(k)(T)simultaneously for all values of k in time O(n(5)) and space O(n(3)).Additionally, RNAsat computes the partition function Q(k)(T)(a) = SigmaSepsilonS(k)(a) exp(-E(S)/RT), where the sum is over all secondary structures of a which have k base pairs; the latter computation is performed simultaneously for all values of k in O(n(4)) time and O(n(3)) space. Lastly, using the partition function Z(k)(T) [resp. Q(k)(T)] with stochastic backtracking, RNAsat rigorously samples the collection of saturated secondary structures [resp. secondary structures] having k base pairs; for Q(k)(T) this provides a parametrized form of Sfold sampling (Ding and Lawrence, 2003). Using RNAsat, (i) we compute the ensemble free energy for saturated secondary structures having k base pairs, (ii) show cooperativity of the Turner model, (iii) demonstrate a temperature-dependent phase transition, (iv) illustrate the predictive advantage of RNAsat for precursor microRNA cel-mir-72 of C. elegans and for the pseudoknot PKB 00152 of Pseudobase (van Batenburg et al., 2001), (v) illustrate the RNA shapes (Giegerich et al., 2004) of sampled secondary structures [resp. saturated structures] having exactly k base pairs. A web server for RNAsat is under construction at bioinformatics.bc.edu/clotelab/RNAsat/. PMID:17456015

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. Transfer Matrices and Partition-Function Zeros for Antiferromagnetic Potts Models. III. Triangular-Lattice Chromatic Polynomial

    NASA Astrophysics Data System (ADS)

    Jacobsen, Jesper Lykke; Salas, Jesús; Sokal, Alan D.

    2003-09-01

    We study the chromatic polynomial P G ( q) for m× n triangular-lattice strips of widths m≤12P,9F (with periodic or free transverse boundary conditions, respectively) and arbitrary lengths n (with free longitudinal boundary conditions). The chromatic polynomial gives the zero-temperature limit of the partition function for the q-state Potts antiferromagnet. We compute the transfer matrix for such strips in the Fortuin-Kasteleyn representation and obtain the corresponding accumulation sets of chromatic zeros in the complex q-plane in the limit n→∞. We recompute the limiting curve obtained by Baxter in the thermodynamic limit m, n→∞ and find new interesting features with possible physical consequences. Finally, we analyze the isolated limiting points and their relation with the Beraha numbers.

  16. On using enriched cover function in the Partition-of-unity method for singular boundary-value problems

    NASA Astrophysics Data System (ADS)

    Liu, X.; Lee, C. K.; Fan, S. C.

    Amongst the various approaches of `meshless' method, the Partition-of-unity concept married with the traditional finite-element method, namely PUFEM, has emerged to be competitive in solving the boundary-value problems. It inherits most of the advantages from both techniques except that the beauty of being `meshless' vanishes. This paper presents an alternative approach to solve singular boundary-value problems. It follows the basic PUFEM procedures. The salient feature is to enhance the quality of the influence functions, either over one single nodal cover or multi-nodal-covers. In the vicinity of the singularity, available asymptotic analytical solution is employed to enrich the influence function. The beauty of present approach is that it facilitates easy replacement of the influence functions. In other words, it favors the `influence-function refinement' procedure in a bid to search for more accurate solutions. It is analogous to the `p-version refinement' in the traditional finite-element procedures. The present approach can yield very accurate solution without adopting refined meshes. As a result, the quantities around the singularity can be evaluated directly once the nodal values are solved. No additional post-processing is needed. Firstly, the formulation of the present PUFEM approach is described. Subsequently, illustrative examples show the application to three classical singular benchmark problems having various orders of singularity. Results obtained through mesh refinements, single-nodal-cover refinements or multi-nodal-cover refinements are compared.

  17. 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

  18. 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.

  19. Post-Secondary Correctional Education: Issues of Functional Illiteracy.

    ERIC Educational Resources Information Center

    Moke, Paul; Holloway, Jarrell

    1986-01-01

    This article examines the incidence of academic deficiency and functional illiteracy among offenders in a postsecondary prison education program. A descriptive analysis was conducted using aptitude test scores on reading, math, and language from 488 students in a medium security prison in Ohio. Results are presented and analyzed. (CT)

  20. 77 FR 1941 - Statement of Organization, Functions, and Delegations of Authority; Correction

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-12

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health Statement of Organization, Functions, and Delegations of Authority; Correction Correction In the Federal Register of January 6, 2012 (77 FR 797), the Department...

  1. 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

  2. Parent, Teacher, and Student Perspectives on How Corrective Lenses Improve Child Wellbeing and School Function.

    PubMed

    Dudovitz, Rebecca N; Izadpanah, Nilufar; Chung, Paul J; Slusser, Wendelin

    2016-05-01

    Objectives Up to 20 % of school-age children have a vision problem identifiable by screening, over 80 % of which can be corrected with glasses. While vision problems are associated with poor school performance, few studies describe whether and how corrective lenses affect academic achievement and health. Further, there are virtually no studies exploring how children with correctable visual deficits, their parents, and teachers perceive the connection between vision care and school function. Methods We conducted a qualitative evaluation of Vision to Learn (VTL), a school-based program providing free corrective lenses to low-income students in Los Angeles. Nine focus groups with students, parents, and teachers from three schools served by VTL explored the relationships between poor vision, receipt of corrective lenses, and school performance and health. Results Twenty parents, 25 teachers, and 21 students from three elementary schools participated. Participants described how uncorrected visual deficits reduced students' focus, perseverance, and class participation, affecting academic functioning and psychosocial stress; how receiving corrective lenses improved classroom attention, task persistence, and willingness to practice academic skills; and how serving students in school rather than in clinics increased both access to and use of corrective lenses. Conclusions for Practice Corrective lenses may positively impact families, teachers, and students coping with visual deficits by improving school function and psychosocial wellbeing. Practices that increase ownership and use of glasses, such as serving students in school, may significantly improve both child health and academic performance. PMID:26649878

  3. 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.

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

    SciTech Connect

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

    2011-10-01

    We perform a comprehensive analysis of target mass corrections to spin-averaged structure functions and asymmetries at next-to-leading order. Several different prescriptions for target mass corrections 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. Dispersion- and Exchange-Corrected Density Functional Theory for Sodium Ion Hydration.

    PubMed

    Soniat, Marielle; Rogers, David M; Rempe, Susan B

    2015-07-14

    A challenge in density functional theory is developing functionals that simultaneously describe intermolecular electron correlation and electron delocalization. Recent exchange-correlation functionals address those two issues by adding corrections important at long ranges: an atom-centered pairwise dispersion term to account for correlation and a modified long-range component of the electron exchange term to correct for delocalization. Here we investigate how those corrections influence the accuracy of binding free energy predictions for sodium-water clusters. We find that the dual-corrected ωB97X-D functional gives cluster binding energies closest to high-level ab initio methods (CCSD(T)). Binding energy decomposition shows that the ωB97X-D functional predicts the smallest ion-water (pairwise) interaction energy and larger multibody contributions for a four-water cluster than most other functionals - a trend consistent with CCSD(T) results. Also, ωB97X-D produces the smallest amounts of charge transfer and the least polarizable waters of the density functionals studied, which mimics the lower polarizability of CCSD. When compared with experimental binding free energies, however, the exchange-corrected CAM-B3LYP functional performs best (error <1 kcal/mol), possibly because of its parametrization to experimental formation enthalpies. For clusters containing more than four waters, "split-shell" coordination must be considered to obtain accurate free energies in comparison with experiment. PMID:26575733

  6. 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…

  7. Distinct Functional Constraints Partition Sequence Conservation in a cis-Regulatory Element

    PubMed Central

    Ruvinsky, Ilya

    2011-01-01

    Different functional constraints contribute to different evolutionary rates across genomes. To understand why some sequences evolve faster than others in a single cis-regulatory locus, we investigated function and evolutionary dynamics of the promoter of the Caenorhabditis elegans unc-47 gene. We found that this promoter consists of two distinct domains. The proximal promoter is conserved and is largely sufficient to direct appropriate spatial expression. The distal promoter displays little if any conservation between several closely related nematodes. Despite this divergence, sequences from all species confer robustness of expression, arguing that this function does not require substantial sequence conservation. We showed that even unrelated sequences have the ability to promote robust expression. A prominent feature shared by all of these robustness-promoting sequences is an AT-enriched nucleotide composition consistent with nucleosome depletion. Because general sequence composition can be maintained despite sequence turnover, our results explain how different functional constraints can lead to vastly disparate rates of sequence divergence within a promoter. PMID:21655084

  8. 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

  9. Evaluation of Range-Corrected Density Functionals for the Simulation of Pyridinium-Containing Molecular Crystals.

    PubMed

    Ruggiero, Michael T; Gooch, Jonathan; Zubieta, Jon; Korter, Timothy M

    2016-02-18

    The problem of nonlocal interactions in density functional theory calculations has in part been mitigated by the introduction of range-corrected functional methods. While promising solutions, the continued evaluation of range corrections in the structural simulations of complex molecular crystals is required to judge their efficacy in challenging chemical environments. Here, three pyridinium-based crystals, exhibiting a wide range of intramolecular and intermolecular interactions, are used as benchmark systems for gauging the accuracy of several range-corrected density functional techniques. The computational results are compared to low-temperature experimental single-crystal X-ray diffraction and terahertz spectroscopic measurements, enabling the direct assessment of range correction in the accurate simulation of the potential energy surface minima and curvatures. Ultimately, the simultaneous treatment of both short- and long-range effects by the ωB97-X functional was found to be central to its rank as the top performer in reproducing the complex array of forces that occur in the studied pyridinium solids. These results demonstrate that while long-range corrections are the most commonly implemented range-dependent improvements to density functionals, short-range corrections are vital for the accurate reproduction of forces that rapidly diminish with distance, such as quadrupole-quadrupole interactions. PMID:26814572

  10. 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

  11. Targeted Correction and Restored Function of the CFTR Gene in Cystic Fibrosis Induced Pluripotent Stem Cells

    PubMed Central

    Crane, Ana M.; Kramer, Philipp; Bui, Jacquelin H.; Chung, Wook Joon; Li, Xuan Shirley; Gonzalez-Garay, Manuel L.; Hawkins, Finn; Liao, Wei; Mora, Daniela; Choi, Sangbum; Wang, Jianbin; Sun, Helena C.; Paschon, David E.; Guschin, Dmitry Y.; Gregory, Philip D.; Kotton, Darrell N.; Holmes, Michael C.; Sorscher, Eric J.; Davis, Brian R.

    2015-01-01

    Summary Recently developed reprogramming and genome editing technologies make possible the derivation of corrected patient-specific pluripotent stem cell sources—potentially useful for the development of new therapeutic approaches. Starting with skin fibroblasts from patients diagnosed with cystic fibrosis, we derived and characterized induced pluripotent stem cell (iPSC) lines. We then utilized zinc-finger nucleases (ZFNs), designed to target the endogenous CFTR gene, to mediate correction of the inherited genetic mutation in these patient-derived lines via homology-directed repair (HDR). We observed an exquisitely sensitive, homology-dependent preference for targeting one CFTR allele versus the other. The corrected cystic fibrosis iPSCs, when induced to differentiate in vitro, expressed the corrected CFTR gene; importantly, CFTR correction resulted in restored expression of the mature CFTR glycoprotein and restoration of CFTR chloride channel function in iPSC-derived epithelial cells. PMID:25772471

  12. Targeted correction and restored function of the CFTR gene in cystic fibrosis induced pluripotent stem cells.

    PubMed

    Crane, Ana M; Kramer, Philipp; Bui, Jacquelin H; Chung, Wook Joon; Li, Xuan Shirley; Gonzalez-Garay, Manuel L; Hawkins, Finn; Liao, Wei; Mora, Daniela; Choi, Sangbum; Wang, Jianbin; Sun, Helena C; Paschon, David E; Guschin, Dmitry Y; Gregory, Philip D; Kotton, Darrell N; Holmes, Michael C; Sorscher, Eric J; Davis, Brian R

    2015-04-14

    Recently developed reprogramming and genome editing technologies make possible the derivation of corrected patient-specific pluripotent stem cell sources-potentially useful for the development of new therapeutic approaches. Starting with skin fibroblasts from patients diagnosed with cystic fibrosis, we derived and characterized induced pluripotent stem cell (iPSC) lines. We then utilized zinc-finger nucleases (ZFNs), designed to target the endogenous CFTR gene, to mediate correction of the inherited genetic mutation in these patient-derived lines via homology-directed repair (HDR). We observed an exquisitely sensitive, homology-dependent preference for targeting one CFTR allele versus the other. The corrected cystic fibrosis iPSCs, when induced to differentiate in vitro, expressed the corrected CFTR gene; importantly, CFTR correction resulted in restored expression of the mature CFTR glycoprotein and restoration of CFTR chloride channel function in iPSC-derived epithelial cells. PMID:25772471

  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. 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

  15. 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).

  16. NNLO corrections to inclusive semileptonic B decays in the shape-function region

    NASA Astrophysics Data System (ADS)

    Bell, Guido

    2009-05-01

    We compute 2-loop QCD corrections to the hard coefficient functions which arise in the factorization formula for B→Xℓν decays in the shape-function region. Our calculation provides the last missing piece required for a NNLO analysis of inclusive semileptonic B decays, which may significantly reduce the theoretical uncertainty in the extraction of the CKM matrix element |V|. Among the technical aspects, we find that the 2-loop hard coefficient functions are free of infrared singularities as predicted by the factorization framework. We perform a brief numerical analysis of the NNLO corrections and include a discussion on charm mass effects.

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

    PubMed Central

    Biek, D P; Shi, J

    1994-01-01

    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. Images PMID:8058752

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

    SciTech Connect

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

    2015-02-07

    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.

  20. Vortex Partition Functions, Wall Crossing and Equivariant Gromov-Witten Invariants

    NASA Astrophysics Data System (ADS)

    Bonelli, Giulio; Sciarappa, Antonio; Tanzini, Alessandro; Vasko, Petr

    2015-01-01

    In this paper we identify the problem of equivariant vortex counting in a (2,2) supersymmetric two dimensional quiver gauged linear sigma model with that of computing the equivariant Gromov-Witten invariants of the GIT quotient target space determined by the quiver. We provide new contour integral formulae for the and -functions encoding the equivariant quantum cohomology of the target space. Its chamber structure is shown to be encoded in the analytical properties of the integrand. This is explained both via general arguments and by checking several key cases. We show how several results in equivariant Gromov-Witten theory follow just by deforming the integration contour. In particular, we apply our formalism to compute Gromov-Witten invariants of the orbifold, of the Uhlembeck (partial) compactification of the moduli space of instantons on , and of A n and D n singularities both in the orbifold and resolved phases. Moreover, we analyse dualities of quantum cohomology rings of holomorphic vector bundles over Grassmannians, which are relevant to BPS Wilson loop algebrae.

  1. Perturbative O(αs) corrections to the correlation functions of light tetraquark currents

    NASA Astrophysics Data System (ADS)

    Groote, S.; Körner, J. G.; Niinepuu, D.

    2014-09-01

    We calculate the next-to-leading-order QCD corrections to the perturbative term in the operator product expansion of the spectral functions of light tetraquark currents. By using also configuration-space methods we keep the momentum-space four-loop calculation to a manageable level. We find that the next-to-leading-order corrections to the perturbative term are large and can amount to O(100%). The corrections to the corresponding Borel sum rules, however, are small since the nonperturbative condensate contributions dominate the Borel sum rules.

  2. Rotor Displacement of the Ultrasonic Motor Having an Angular Displacement Self-Correction Function

    NASA Astrophysics Data System (ADS)

    Chen, Xiaoduo; Kusakabe, Chiharu; Tomikawa, Yoshiro; Takano, Takehiro

    1993-09-01

    This paper deals with the experimental investigation for confirmation of rotor displacement of the ultrasonic stepping motor having an angular displacement self-correction function. The experiment focused on the relationship between the rotor’s vibration displacement and its staying position for the self-correction. The result proved that the rotor always stays at the position where the displacement is smallest by cutting a slit into the rotor. Moreover, it has also been found that the stable self-correction of rotor angular displacement depends upon both the rotor driving frequency and rotor clamping force.

  3. 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.

  4. 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

    NASA Astrophysics Data System (ADS)

    Mielke, Steven L.; Truhlar, Donald G.

    2015-01-01

    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.

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

    SciTech Connect

    Pederson, Mark R.; Ruzsinszky, Adrienn; Perdew, John P.; Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122

    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. 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.

  7. New Aperture Partitioning Element

    NASA Astrophysics Data System (ADS)

    Griffin, S.; Calef, B.; Williams, S.

    Postprocessing in an optical system can be aided by adding an optical element to partition the pupil into a number of segments. When imaging through the atmosphere, the recorded data are blurred by temperature-induced variations in the index of refraction along the line of sight. Using speckle imaging techniques developed in the astronomy community, this blurring can be corrected to some degree. The effectiveness of these techniques is diminished by redundant baselines in the pupil. Partitioning the pupil reduces the degree of baseline redundancy, and therefore improves the quality of images that can be obtained from the system. It is possible to implement the described approach on an optical system with a segmented primary mirror, but not very practical. This is because most optical systems do not have segmented primary mirrors, and those that do have relatively low bandwidth positioning of segments due to their large mass and inertia. It is much more practical to position an active aperture partitioning element at an aft optics pupil of the optical system. This paper describes the design, implementation and testing of a new aperture partitioning element that is completely reflective and reconfigurable. The device uses four independent, annular segments that can be positioned with a high degree of accuracy without impacting optical wavefront of each segment. This mirror has been produced and is currently deployed and working on the 3.6 m telescope.

  8. Functional Gene Correction for Cystic Fibrosis in Lung Epithelial Cells Generated from Patient iPSCs.

    PubMed

    Firth, Amy L; Menon, Tushar; Parker, Gregory S; Qualls, Susan J; Lewis, Benjamin M; Ke, Eugene; Dargitz, Carl T; Wright, Rebecca; Khanna, Ajai; Gage, Fred H; Verma, Inder M

    2015-09-01

    Lung disease is a major cause of death in the United States, with current therapeutic approaches serving only to manage symptoms. The most common chronic and life-threatening genetic disease of the lung is cystic fibrosis (CF) caused by mutations in the cystic fibrosis transmembrane regulator (CFTR). We have generated induced pluripotent stem cells (iPSCs) from CF patients carrying a homozygous deletion of F508 in the CFTR gene, which results in defective processing of CFTR to the cell membrane. This mutation was precisely corrected using CRISPR to target corrective sequences to the endogenous CFTR genomic locus, in combination with a completely excisable selection system, which significantly improved the efficiency of this correction. The corrected iPSCs were subsequently differentiated to mature airway epithelial cells where recovery of normal CFTR expression and function was demonstrated. This isogenic iPSC-based model system for CF could be adapted for the development of new therapeutic approaches. PMID:26299960

  9. 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

  10. Correcting for dispersion interaction and beyond in density functional theory through force matching

    NASA Astrophysics Data System (ADS)

    Song, Yang; Akin-Ojo, Omololu; Wang, Feng

    2010-11-01

    The force matching method is used to improve density functional theory (DFT) by designing a supplemental potential to capture the difference in atomic forces between a DFT functional and a high-quality post Hartree-Fock method. The supplemental potential has two-body terms designed to correct for dispersion and hydrogen bond interactions. The potential also has one-body terms to improve the description of the intramolecular potential energy surface. Our procedure is tested by providing corrections to the Becke-Lee-Yang-Parr exchange-correlation functional for water and is found to perform significantly better than the standard DFT-D approach, giving QCISD quality predictions for relative cluster energies, atomic forces, and molecular structures. It is found that a simple Lennard-Jones term does a good job at correcting for van der Waals interactions and possibly also providing corrections to exchange repulsion. The one-body corrections, while contributing only slightly to improving relative cluster energies, significantly reduce the errors in binding energies and atomic forces for the systems studied.

  11. 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.

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

    PubMed

    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. PMID:24832322

  13. Cavity partition and functionalization of a [2+3] organic molecular cage by inserting polar P[double bond, length as m-dash]O bonds.

    PubMed

    Feng, Genfeng; Liu, Wei; Peng, Yuxin; Zhao, Bo; Huang, Wei; Dai, Yafei

    2016-07-28

    The cavity of a [2+3] organic molecular cage was partitioned and functionalized by inserting inner-directed P[double bond, length as m-dash]O bonds, which shows CO2 capture and CH4 exclusion due to the size-matching and polarity effects. Computational results demonstrate that the successful segmentation via polar P[double bond, length as m-dash]O bonds facilitates the CO2 molecules to reside selectively inside the cavity. PMID:27356151

  14. 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. PMID:25651435

  15. 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

  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. 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.

  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. QED Correction to Asymmetry for Polarized ep Scattering from the Method of Electron Structure Functions

    SciTech Connect

    Andrei Afanasev; Igor Akushevich; Nikolai Merenkov

    2004-03-01

    The electron structure function method is applied to calculate model-independent radiative corrections to an asymmetry of electron-proton scattering. The representations for both spin-independent and spin-dependent parts of the cross-section are derived. Master formulae take into account the leading corrections in all orders and the main contribution of the second order next-to-leading ones and have accuracy at the level of one per mille. Numerical calculations illustrate our analytical results for both elastic and deep inelastic events.

  2. 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. PMID:27041908

  3. 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

  4. Correction of dispersion and the betatron functions in the CEBAF accelerator

    SciTech Connect

    Lebedev, V.A.; Bickley, M.; Schaffner, S.; Zeijts, J. van; Krafft, G.A.; Watson, C.

    1996-10-01

    During the commissioning of the CEBAF accelerator, correction of dispersion and momentum compaction, and, to a lesser extent, transverse transfer matrices were essential for robust operation. With changing machine conditions, repeated correction was found necessary. To speed the diagnostic process the authors developed a method which allows one to rapidly track the machine optics. The method is based on measuring the propagation of 30 Hz modulated betatron oscillations downstream of a point of perturbation. Compared to the usual methods of dispersion or difference orbit measurement, synchronous detection of the beam displacement, as measured by beam position monitors, offers significantly improved speed and accuracy of the measurements. The beam optics of the accelerator was altered to decrease lattice sensitivity at critical points and to simplify control of the betatron function match. The calculation of the Courant-Snyder invariant from signals of each pair of nearby beam position monitors has allowed one to perform on-line measurement and correction of the lattice properties.

  5. 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.

  6. Self-Interaction Corrected Functional Calculations of a Dipole-Bound Molecular Anion.

    PubMed

    Zhang, Yao; Weber, Peter M; Jónsson, Hannes

    2016-06-01

    A self-interaction corrected density functional is used to describe the ground state of the CH3CN(-) ion that includes a dipole bound electron with large spatial extent and low binding energy. Without the correction, some commonly used density functionals based on the generalized gradient approximation as well as hybrid functionals fail to give a bound ground state of the anion. A negative HOMO orbital energy of magnitude 0.013 eV is obtained using the self-interaction corrected PBE functional in good correspondence with the experimentally estimated binding energy of 0.019 eV. The dipole bound electron polarizes the CH3CN molecule and increases its dipole moment by 7% to 4.2 D. Because the computational effort increases slowly with system size, as the number of electrons cubed, the results presented here point to a viable approach to theoretical studies of dipole bound electrons in large and complex systems such as molecular clusters, biological systems, and solvated electrons. PMID:27166989

  7. Splice-correcting oligonucleotides restore BTK function in X-linked agammaglobulinemia model.

    PubMed

    Bestas, Burcu; Moreno, Pedro M D; Blomberg, K Emelie M; Mohammad, Dara K; Saleh, Amer F; Sutlu, Tolga; Nordin, Joel Z; Guterstam, Peter; Gustafsson, Manuela O; Kharazi, Shabnam; Piątosa, Barbara; Roberts, Thomas C; Behlke, Mark A; Wood, Matthew J A; Gait, Michael J; Lundin, Karin E; El Andaloussi, Samir; Månsson, Robert; Berglöf, Anna; Wengel, Jesper; Smith, C I Edvard

    2014-09-01

    X-linked agammaglobulinemia (XLA) is an inherited immunodeficiency that results from mutations within the gene encoding Bruton's tyrosine kinase (BTK). Many XLA-associated mutations affect splicing of BTK pre-mRNA and severely impair B cell development. Here, we assessed the potential of antisense, splice-correcting oligonucleotides (SCOs) targeting mutated BTK transcripts for treating XLA. Both the SCO structural design and chemical properties were optimized using 2'-O-methyl, locked nucleic acid, or phosphorodiamidate morpholino backbones. In order to have access to an animal model of XLA, we engineered a transgenic mouse that harbors a BAC with an authentic, mutated, splice-defective human BTK gene. BTK transgenic mice were bred onto a Btk knockout background to avoid interference of the orthologous mouse protein. Using this model, we determined that BTK-specific SCOs are able to correct aberrantly spliced BTK in B lymphocytes, including pro-B cells. Correction of BTK mRNA restored expression of functional protein, as shown both by enhanced lymphocyte survival and reestablished BTK activation upon B cell receptor stimulation. Furthermore, SCO treatment corrected splicing and restored BTK expression in primary cells from patients with XLA. Together, our data demonstrate that SCOs can restore BTK function and that BTK-targeting SCOs have potential as personalized medicine in patients with XLA. PMID:25105368

  8. Assessment of the efficiency of long-range corrected functionals for some properties of large compounds

    NASA Astrophysics Data System (ADS)

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

    2007-04-01

    Using the long-range correction (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 a series of properties that are known to be poorly reproduced by standard functionals: Bond length alternation of π-conjugated polymers, polarizabilities of delocalized chains, and electronic spectra of extended dyes. For each of these properties, we present cases in which traditional hybrid functionals do provide accurate results and cases in which they fail to reproduce the correct trends. The quality of the results is assessed with regard to experimental values and/or data arising from electron-correlated wave function approaches. It turns out that (i) both LC-DFT and CAM-B3LYP provide an accurate bond length alternation for polyacetylene and polymethineimine, although for the latter they decrease slightly too rapidly with chain length. (ii) The LC generalized gradient approximation and MP2 polarizabilities of long polyphosphazene and polymethineimine oligomers agree almost perfectly. In the same way, CAM-B3LYP corrects the major part of the B3LYP faults. (iii) LC and CAM techniques do not help in correcting the nonrealistic evolution with chain length of the absorption wavelengths of cyanine derivatives. In addition, though both schemes significantly overestimate the ground to excited state transition energy of substituted anthraquinone dyes, they provide a more consistent picture once a statistical treatment is performed than do traditional hybrid functionals.

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

    PubMed

    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. PMID:25681892

  10. 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.

  11. An ultrasonic air temperature measurement system with self-correction function for humidity

    NASA Astrophysics Data System (ADS)

    Tsai, Wen-Yuan; Chen, Hsin-Chieh; Liao, Teh-Lu

    2005-02-01

    This paper proposes an ultrasonic measurement system for air temperature with high accuracy and instant response. It can measure the average temperature of the environmental air by detecting the changes of the speed of the ultrasound in the air. The changes of speed of sound are computed from combining variations of time-of-flight (TOF) from a binary frequency shift-keyed (BFSK) ultrasonic signal and phase shift from continuous waves [11]. In addition, another proposed technique for the ultrasonic air temperature measurement is the self-correction functionality within a highly humid environment. It utilizes a relative humidity/water vapour sensor and applies the theory of how sound speed changes in a humid environment. The proposed new ultrasonic air temperature measurement has the capability of self-correction for the environment variable of humidity. Especially under the operational environment with high fluctuations of various humidity levels, the proposed system can accurately self-correct the errors on the conventional ultrasonic thermometer caused by the changing density of the vapours in the air. Including the high humidity effect, a proof-of-concept experiment demonstrates that in dry air (relative humidity, RH = 10%) without humidity correction, it is accurate to ±0.4 °C from 0 °C to 80 °C, while in highly humid air (relative humidity, RH = 90%) with self-correction functionality, it is accurate to ±0.3 °C from 0 °C to 80 °C with 0.05% resolution and temperature changes are instantly reflected within 100 ms.

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

    NASA Astrophysics Data System (ADS)

    Song, Jong-Won; Hirao, Kimihiko

    2015-12-01

    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.

  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. 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

  15. 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

  16. Empirical mode decomposition-based motion artifact correction method for functional near-infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Gu, Yue; Han, Junxia; Liang, Zhenhu; Yan, Jiaqing; Li, Zheng; Li, Xiaoli

    2016-01-01

    Functional near-infrared spectroscopy (fNIRS) is a promising technique for monitoring brain activity. However, it is sensitive to motion artifacts. Many methods have been developed for motion correction, such as spline interpolation, wavelet filtering, and kurtosis-based wavelet filtering. We propose a motion correction method based on empirical mode decomposition (EMD), which is applied to segments of data identified as having motion artifacts. The EMD method is adaptive, data-driven, and well suited for nonstationary data. To test the performance of the proposed EMD method and to compare it with other motion correction methods, we used simulated hemodynamic responses added to real resting-state fNIRS data. The EMD method reduced mean squared error in 79% of channels and increased signal-to-noise ratio in 78% of channels. Moreover, it produced the highest Pearson's correlation coefficient between the recovered signal and the original signal, significantly better than the comparison methods (p<0.01, paired t-test). These results indicate that the proposed EMD method is a first choice method for motion artifact correction in fNIRS.

  17. 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.

  18. Signatures of the Berezinskii-Kosterlitz-Thouless transition on the zeros of the canonical partition function for the 2D XY-model

    NASA Astrophysics Data System (ADS)

    Rocha, Julio; Mol, Lucas; Costa, Bismarck

    2015-03-01

    In this work we show that the canonical partition function zeros, the Fisher zeros, can be used to uniquely characterize a transition as being in the Berezinskii-Kosterlitz-Thouless (BKT) class of universality. By studying the zeros map for the 2D XY model we found that its internal border coalesces into the real positive axis in a finite region corresponding to temperatures smaller than the BKT transition temperature. This behavior is consistent with the predicted existence of a line of critical points below the transition temperature, allowing one to distinguish the BKT class of universality from other ones. This work was partially supported by CNPq and Fapemig, Brazilian Agencies.

  19. Cognitive and academic functioning of juvenile detainees: implications for correctional populations and public health.

    PubMed

    Lansing, Amy E; Washburn, Jason J; Abram, Karen M; Thomas, Ursula C; Welty, Leah J; Teplin, Linda A

    2014-01-01

    Cognitive functioning affects health. This study assessed cognitive functioning among participants in the Northwestern Juvenile Project, a stratified random sample of 1,829 newly detained juveniles (10 to 18 years old) from Cook County, Illinois. The study examined receptive vocabulary, oral reading, arithmetic computation skills, and general intellectual abilities. The sample exhibited impaired overall intellectual functioning and deficits in all areas. Males performed more poorly than females. More than three quarters of males showed below average overall intellectual functioning, and 9 in 10 had below average receptive vocabulary skills. Hispanic and African American males performed more poorly than non-Hispanic White males. The multiple systems that serve delinquent youth--correctional, health, legal, and rehabilitative--must collaborate to tailor needed services to the cognitive level of youth in the juvenile justice system. PMID:24352405

  20. Cognitive and academic functioning of juvenile detainees: Implications for correctional populations and public health

    PubMed Central

    Lansing, Amy E.; Washburn, Jason J.; Abram, Karen M.; Thomas, Ursula C.; Welty, Leah J.; Teplin, Linda A.

    2014-01-01

    Cognitive functioning affects health. This study assessed cognitive functioning among participants in the Northwestern Juvenile Project, a stratified random sample of 1,829 newly detained juveniles (10-18 years old) from Cook County, Illinois. We examined receptive vocabulary, oral reading, arithmetic computation skills, and general intellectual abilities. Our sample exhibited impaired overall intellectual functioning and deficits in all areas. Males performed more poorly than females overall. More than three-quarters of males showed below average overall intellectual functioning, and nine in ten males had below average receptive vocabulary skills. Hispanic and African American males performed more poorly than non-Hispanic white males; The multiple systems that serve delinquent youth—correctional, health, legal, and rehabilitative—must collaborate to tailor needed services to the cognitive level of youth in the juvenile justice system. PMID:24352405

  1. Glycerol replacement corrects defective skin hydration, elasticity, and barrier function in aquaporin-3-deficient mice.

    PubMed

    Hara, Mariko; Verkman, A S

    2003-06-10

    Mice deficient in the epidermal water/glycerol transporter aquaporin-3 (AQP3) have reduced stratum corneum (SC) hydration and skin elasticity, and impaired barrier recovery after SC removal. SC glycerol content is reduced 3-fold in AQP3 null mice, whereas SC structure, protein/lipid composition, and ion/osmolyte content are not changed. We show here that glycerol replacement corrects each of the defects in AQP3 null mice. SC water content, measured by skin conductance and 3H2O accumulation, was 3-fold lower in AQP3 null vs. wild-type mice, but became similar after topical or systemic administration of glycerol in quantities that normalized SC glycerol content. SC water content was not corrected by glycerol-like osmolytes such as xylitol, erythritol, and propanediol. Orally administered glycerol fully corrected the reduced skin elasticity in AQP3 null mice as measured by the kinetics of skin displacement after suction, and the delayed barrier recovery as measured by transepidermal water loss after tape-stripping. Analysis of [14C]glycerol kinetics indicated reduced blood-to-SC transport of glycerol in AQP3 null mice, resulting in slowed lipid biosynthesis. These data provide functional evidence for a physiological role of glycerol transport by an aquaglyceroporin, and indicate that glycerol is a major determinant of SC water retention, and mechanical and biosynthetic functions. Our findings establish a scientific basis for the >200-yr-old empirical practice of including glycerol in cosmetic and medicinal skin formulations. PMID:12771381

  2. Assessment of dispersion-corrected density functional approaches for extended systems

    NASA Astrophysics Data System (ADS)

    Al-Saidi, Wissam; Voora, Vamsee; Jordan, Ken

    2011-03-01

    Standard density functional (DFT) methods are known to fail in describing the long range van der Waals interactions, and currently, there is a great interest in incorporating dispersion corrections in density functionals. Recently, Tkatchenko and Scheffler introduced a new scheme where dispersion corrections are included by a summation of damped interatomic C6 / R6 terms. However, contrary to the DFT-D2 approach of Grimme, the C6 coefficients depend on the electron density through a Hirshfeld atom-in-a-molecule decomposition scheme. We have implemented the vdW-TS approach in VASP and applied it to the study of a series of prototype dispersion-dominated systems including layered materials, noble-gas solids and molecular crystals. Full optimization of all degrees of freedom is possible in our implementation because dispersion corrections are computed for the forces acting on the atoms, and also the stresses on the unitcell. Our results show that the vdW-TS method yield good structure, bulk moduli, and cohesive energies of weakly bonded systems in much better agreement with experiment than those obtained with standard DFT approaches.

  3. 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. PMID:23000705

  4. Density functional theory with modified dispersion correction for metals applied to molecular adsorption on Pt(111).

    PubMed

    Andersson, M P

    2016-07-28

    We have performed density functional theory calculations using our modified DFT-D2 dispersion correction for metals to investigate adsorption of a range of molecules on Pt(111). The agreement between our calculations and experimental adsorption energies ranging from 0 to 3 eV was excellent with a mean absolute deviation of 0.19 eV and a maximum deviation of 0.37 eV. Our results show that the DFT-D2 semiempirical dispersion correction can provide accurate results also for describing adsorption on metals, provided that relevant physical properties of the system are taken into account, such as shorter ranged dispersion because of screening by the conducting electrons and a lower polarizability of the core electrons in metals compared to isolated atoms. PMID:27357643

  5. 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

  6. 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.

  7. Shot-Noise Seeded Microbunching Instability: Second-Order Correction to the Gain Function

    SciTech Connect

    Venturini, Marco

    2008-06-30

    We determine the second-order correction to the gain function of the microbunching instability in single-pass systems of interest for the next generation of light sources. The calculation applies to the case where the instability is seeded by shot noise. We examine an analytically treatable model of beam dynamics where collective forces are active only in non-dispersive sections of the linac. We find that the second order term can augment the linear gain significantly while affecting the spectrum of the overall gain only marginally. The weight of the second-order correction relative to the linear gain is found to scale quadratically with respect to R56. The qualitative behavior predicted by the model is consistent with exact numerical solutions of the Vlasov equations for realistic lattices.

  8. Motion Correction of Whole-Body PET Data with a Joint PET-MRI Registration Functional

    PubMed Central

    2014-01-01

    Respiratory motion is known to degrade image quality in PET imaging. The necessary acquisition time of several minutes per bed position will inevitably lead to a blurring effect due to organ motion. A lot of research has been done with regards to motion correction of PET data. As full-body PET-MRI became available recently, the anatomical data provided by MRI is a promising source of motion information. Current PET-MRI-based motion correction approaches, however, do not take into account the available information provided by PET data. PET data, though, may add valuable additional information to increase motion estimation robustness and precision. In this work we propose a registration functional that is capable of performing motion detection in gated data of two modalities simultaneously. Evaluation is performed using phantom data. We demonstrate that performing a joint registration of both modalities does improve registration accuracy and PET image quality. PMID:25077815

  9. 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.

  10. 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

  11. 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.

  12. Failure of Density Functional Dispersion Correction in Metallic Systems and Its Possible Solution Using a Modified Many-Body Dispersion Correction.

    PubMed

    Kim, Won June; Kim, Minho; Lee, Eok Kyun; Lebègue, Sébastien; Kim, Hyungjun

    2016-08-18

    Previous density functional dispersion corrections to density functional theory lead to an unphysical description of metallic systems, as exemplified by alkali and alkaline earth compounds. We demonstrate that it is possible to remedy this limitation by including screening effects into the form of interacting smeared-out dipoles in the many-body expansion of the interaction. Our new approach, called the coupled fluctuating smeared dipole model, describes equally well noncovalent systems, such as molecular pairs and crystals, and metallic systems. PMID:27487413

  13. Calculation of bond dissociation energies of diatomic molecules using bond function basis sets with counterpoise corrections

    SciTech Connect

    Li, Z.; Pan, Y.K.; Tao, F.M.

    1996-01-15

    Bond function basis sets combined with the counterpoise procedure are used to calculate the molecular dissociation energies D{sub e} of 24 diatomic molecules and ions. The calculated values of D{sub e} are compared to those without bond functions and/or counterpoise corrections. The equilibrium bond lengths r{sub e}, and harmonic frequencies w{sub e} are also calculated for a few selected molecules. The calculations at the fourth-order-Moller-Plesset approximation (MP4) have consistently recovered about 95-99% of the experimental values for D{sub e}, compared to as low as 75% without use of bond functions. The calculated values of r{sub 3} are typically 0.01 {Angstrom} larger than the experimental values, and the calculated values of w{sub e} are over 95% of the experimental values. 37 refs., 2 tabs.

  14. A Cavity Corrected 3D-RISM Functional for Accurate Solvation Free Energies

    PubMed Central

    2014-01-01

    We show that an Ng bridge function modified version of the three-dimensional reference interaction site model (3D-RISM-NgB) solvation free energy method can accurately predict the hydration free energy (HFE) of a set of 504 organic molecules. To achieve this, a single unique constant parameter was adjusted to the computed HFE of single atom Lennard-Jones solutes. It is shown that 3D-RISM is relatively accurate at predicting the electrostatic component of the HFE without correction but requires a modification of the nonpolar contribution that originates in the formation of the cavity created by the solute in water. We use a free energy functional with the Ng scaling of the direct correlation function [Ng, K. C. J. Chem. Phys.1974, 61, 2680]. This produces a rapid, reliable small molecule HFE calculation for applications in drug design. PMID:24634616

  15. A Cavity Corrected 3D-RISM Functional for Accurate Solvation Free Energies.

    PubMed

    Truchon, Jean-François; Pettitt, B Montgomery; Labute, Paul

    2014-03-11

    We show that an Ng bridge function modified version of the three-dimensional reference interaction site model (3D-RISM-NgB) solvation free energy method can accurately predict the hydration free energy (HFE) of a set of 504 organic molecules. To achieve this, a single unique constant parameter was adjusted to the computed HFE of single atom Lennard-Jones solutes. It is shown that 3D-RISM is relatively accurate at predicting the electrostatic component of the HFE without correction but requires a modification of the nonpolar contribution that originates in the formation of the cavity created by the solute in water. We use a free energy functional with the Ng scaling of the direct correlation function [Ng, K. C. J. Chem. Phys. 1974, 61, 2680]. This produces a rapid, reliable small molecule HFE calculation for applications in drug design. PMID:24634616

  16. Halogen Bonding from Dispersion-Corrected Density-Functional Theory: The Role of Delocalization Error.

    PubMed

    Otero-de-la-Roza, A; Johnson, Erin R; DiLabio, Gino A

    2014-12-01

    Halogen bonds are formed when a Lewis base interacts with a halogen atom in a different molecule, which acts as an electron acceptor. Due to its charge transfer component, halogen bonding is difficult to model using many common density-functional approximations because they spuriously overstabilize halogen-bonded dimers. It has been suggested that dispersion-corrected density functionals are inadequate to describe halogen bonding. In this work, we show that the exchange-hole dipole moment (XDM) dispersion correction coupled with functionals that minimize delocalization error (for instance, BH&HLYP, but also other half-and-half functionals) accurately model halogen-bonded interactions, with average errors similar to other noncovalent dimers with less charge-transfer effects. The performance of XDM is evaluated for three previously proposed benchmarks (XB18 and XB51 by Kozuch and Martin, and the set proposed by Bauzá et al.) spanning a range of binding energies up to ∼50 kcal/mol. The good performance of BH&HLYP-XDM is comparable to M06-2X, and extends to the "extreme" cases in the Bauzá set. This set contains anionic electron donors where charge transfer occurs even at infinite separation, as well as other charge transfer dimers belonging to the pnictogen and chalcogen bonding classes. We also show that functional delocalization error results in an overly delocalized electron density and exact-exchange hole. We propose intermolecular Bader delocalization indices as an indicator of both the donor-acceptor character of an intermolecular interaction and the delocalization error coming from the underlying functional. PMID:26583227

  17. Wave function continuity and the diagonal Born-Oppenheimer correction at conical intersections.

    PubMed

    Meek, Garrett A; Levine, Benjamin G

    2016-05-14

    We demonstrate that though exact in principle, the expansion of the total molecular wave function as a sum over adiabatic Born-Oppenheimer (BO) vibronic states makes inclusion of the second-derivative nonadiabatic energy term near conical intersections practically problematic. In order to construct a well-behaved molecular wave function that has density at a conical intersection, the individual BO vibronic states in the summation must be discontinuous. When the second-derivative nonadiabatic terms are added to the Hamiltonian, singularities in the diagonal BO corrections (DBOCs) of the individual BO states arise from these discontinuities. In contrast to the well-known singularities in the first-derivative couplings at conical intersections, these singularities are non-integrable, resulting in undefined DBOC matrix elements. Though these singularities suggest that the exact molecular wave function may not have density at the conical intersection point, there is no physical basis for this constraint. Instead, the singularities are artifacts of the chosen basis of discontinuous functions. We also demonstrate that continuity of the total molecular wave function does not require continuity of the individual adiabatic nuclear wave functions. We classify nonadiabatic molecular dynamics methods according to the constraints placed on wave function continuity and analyze their formal properties. Based on our analysis, it is recommended that the DBOC be neglected when employing mixed quantum-classical methods and certain approximate quantum dynamical methods in the adiabatic representation. PMID:27179473

  18. Wave function continuity and the diagonal Born-Oppenheimer correction at conical intersections

    NASA Astrophysics Data System (ADS)

    Meek, Garrett A.; Levine, Benjamin G.

    2016-05-01

    We demonstrate that though exact in principle, the expansion of the total molecular wave function as a sum over adiabatic Born-Oppenheimer (BO) vibronic states makes inclusion of the second-derivative nonadiabatic energy term near conical intersections practically problematic. In order to construct a well-behaved molecular wave function that has density at a conical intersection, the individual BO vibronic states in the summation must be discontinuous. When the second-derivative nonadiabatic terms are added to the Hamiltonian, singularities in the diagonal BO corrections (DBOCs) of the individual BO states arise from these discontinuities. In contrast to the well-known singularities in the first-derivative couplings at conical intersections, these singularities are non-integrable, resulting in undefined DBOC matrix elements. Though these singularities suggest that the exact molecular wave function may not have density at the conical intersection point, there is no physical basis for this constraint. Instead, the singularities are artifacts of the chosen basis of discontinuous functions. We also demonstrate that continuity of the total molecular wave function does not require continuity of the individual adiabatic nuclear wave functions. We classify nonadiabatic molecular dynamics methods according to the constraints placed on wave function continuity and analyze their formal properties. Based on our analysis, it is recommended that the DBOC be neglected when employing mixed quantum-classical methods and certain approximate quantum dynamical methods in the adiabatic representation.

  19. 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.

  20. 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.

  1. [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

  2. 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

  3. 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. PMID:24309549

  4. 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.

  5. Depressed contractile function due to canine mitral regurgitation improves after correction of the volume overload.

    PubMed Central

    Nakano, K; Swindle, M M; Spinale, F; Ishihara, K; Kanazawa, S; Smith, A; Biederman, R W; Clamp, L; Hamada, Y; Zile, M R

    1991-01-01

    It is known that long-standing volume overload on the left ventricle due to mitral regurgitation eventually leads to contractile dysfunction. However, it is unknown whether or not correction of the volume overload can lead to recovery of contractility. In this study we tested the hypothesis that depressed contractile function due to volume overload in mitral regurgitation could return toward normal after mitral valve replacement. Using a canine model of mitral regurgitation which is known to produce contractile dysfunction, we examined contractile function longitudinally in seven dogs at baseline, after 3 mo of mitral regurgitation, 1 mo after mitral valve replacement, and 3 mo after mitral valve replacement. After 3 mo of mitral regurgitation (regurgitant fraction 0.62 +/- 0.04), end-diastolic volume had nearly doubled from 68 +/- 6.8 to 123 +/- 12.1 ml (P less than 0.05). All five indices of contractile function which we examined were depressed. For instance, maximum fiber elastance (EmaxF) obtained by assessment of time-varying elastance decreased from 5.95 +/- 0.71 to 2.25 +/- 0.18 (P less than 0.05). The end-systolic stiffness constant (k) was also depressed from 4.2 +/- 0.4 to 2.1 +/- 0.3. 3 mo after mitral valve replacement all indexes of contractile function had returned to or toward normal (e.g., EmaxF 3.65 +/- 0.21 and k 4.2 +/- 0.3). We conclude that previously depressed contractile function due to volume overload can improve after correction of the overload. PMID:1828252

  6. 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.

  7. Correcting the surface intrinsic error in density functional calculations using present approximations of the exchange-correlation functional

    NASA Astrophysics Data System (ADS)

    Mattsson, A. E.; Mattsson, T. R.; Jennison, D. R.

    2003-03-01

    Based on the correction scheme presented in [1] we have developed a procedure to correct for the surface self-energy error (both exchange and correlation) in density functional calculations on real systems. The method works equally well for all approximations of the exchange-correlation functional, e.g. the local density and general gradient approximations. It has been successfully applied to Al, Pt, Pd, and Mo vacancy formation energies [2,3] and the Pd(111)/α-alumina work of adhesion [4]. We present the current status of our efforts and discuss how to extend the procedure to general systems. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy under Contract DE-AC04-94AL85000. [1] A. E. Mattsson, W. Kohn, J. Chem. Phys. 115, 3441 (2001). [2] K. Carling et al, Phys. Rev. Lett. 85, 3862 (2000). [3] T. R. Mattsson, A. E. Mattsson, Phys. Rev. B (Dec. 2002). [4] A. E. Mattsson, D. R. Jennison, Surf. Sci. 58, L611 (2002).

  8. Variational polaron self-interaction-corrected total-energy functional for charge excitations in insulators

    NASA Astrophysics Data System (ADS)

    Sadigh, Babak; Erhart, Paul; Ã berg, Daniel

    2015-08-01

    We conduct a detailed investigation of the polaron self-interaction (pSI) error in standard approximations to the exchange-correlation (XC) functional within density-functional theory (DFT). The pSI leads to delocalization error in the polaron wave function and energy, as calculated from the Kohn-Sham (KS) potential in the native charge state of the polaron. This constitutes the origin of the systematic failure of DFT to describe the polaron formation in band insulators. It is shown that the delocalization error in these systems is, however, largely absent in the KS potential of the closed-shell neutral charge state. This leads to a modification of the DFT total-energy functional that corrects the pSI in the XC functional. The resulting pSIC-DFT method constitutes an accurate parameter-free ab initio methodology for calculating polaron properties in insulators at a computational cost that is orders of magnitude smaller than hybrid XC functionals. Unlike approaches that rely on parametrized localized potentials such as DFT+U , the pSIC-DFT method properly captures both site and bond-centered polaron configurations. This is demonstrated by studying formation and migration of self-trapped holes in alkali halides (bond-centered) as well as self-trapped electrons in an elpasolite compound (site-centered). The pSIC-DFT approach consistently reproduces the results obtained by hybrid XC functionals parametrized by DFT+G0W0 calculations. Finally, we generalize the pSIC approach to hybrid functionals, and show that in stark contrast to conventional hybrid calculations of polaron energies, the pSIC-hybrid method is insensitive to the parametrization of the hybrid XC functional. On this basis, we further rationalize the success of the pSIC-DFT approach.

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

    DOE PAGESBeta

    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

  10. 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

  11. 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.

  12. 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.

  13. Software with partial functions: Automating correctness proofs via nonstrict explicit domains

    SciTech Connect

    Yakhnis, A.; Yakhnis, V.; Winter, V.

    1996-07-30

    As our society becomes technologically more complex, computers are being used in greater and greater numbers of high consequence systems. Giving a machine control over the lives of humans can be disturbing, especially if the software that is run on such a machine has bugs. Formal reasoning is one of the most powerful techniques available to demonstrate the correctness of a piece of software. When reasoning about software and its development, one frequently encounters expressions that contain partial functions. As might be expected, the presence of partial functions introduces an additional dimension of difficulty to the reasoning framework. This difficulty produces an especially strong impact in the case of high consequence systems. An ability to use formal methods for constructing software is essential if we want to obtain greater confidence in such systems through formal reasoning. This is only reasonable under automation of software development and verification. However, the ubiquitous presence of partial functions prevents a uniform application to software of any tools not specifically accounting for partial functions. In this paper we will describe a framework for reasoning about software, based on the nonstrict explicit domain approach, that is applicable to a large class of software/hardware systems. In this framework the Hoare triples containing partial functions can be reasoned about automatically in a well-defined and uniform manner.

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

    NASA Astrophysics Data System (ADS)

    Castner, T. G., Jr.

    2008-05-01

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

  15. 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.

  16. Assessment of Liver Function Using 99mTc-Mebrofenin Hepatobiliary Scintigraphy in ALPPS (Associating Liver Partition and Portal Vein Ligation for Staged Hepatectomy)

    PubMed Central

    Cieslak, Kasia P.; Olthof, Pim B.; van Lienden, Krijn P.; Besselink, Marc G.; Busch, Olivier R.C.; van Gulik, Thomas M.; Bennink, Roelof J.

    2015-01-01

    ALPPS (associating liver partition and portal vein ligation for staged hepatectomy) is a new surgical technique for patients in whom conventional treatment is not feasible due to insufficient future remnant liver (FRL). During the first stage of ALPPS, accelerated hypertrophy of the FRL is induced by ligation of the portal vein and in situ split of the liver. In the second stage, the deportalized liver is removed when the FRL volume has reached ≥25% of total liver volume. However, FRL volume does not necessarily reflect FRL function. 99mTc-mebrofenin hepatobiliary scintigraphy (HBS) with SPECT-CT is a quantitative test enabling regional assessment of parenchymal uptake function using a validated cut-off value for the prediction of postoperative liver failure (2.7%/min/m2). This paper describes the changes in FRL function and FRL volume in a 79-year-old patient diagnosed with metachronous colonic liver metastases who underwent ALPPS. We have observed a substantial difference between the increase in FRL volume and FRL function suggesting that HBS with SPECT-CT enables monitoring of the FRL function and could be a useful tool in the timing of resection in the second stage of the ALPPS procedure. PMID:26675783

  17. Aberration corrected imaging of a carbon nanotube encapsulated Lindqvist Ion and correlation with Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Sloan, J.; Bichoutskaia, E.; Liu, Z.; Kuganathan, N.; Faulques, E.; Suenaga, K.; Shannon, I. J.

    2012-07-01

    80 kV aberration-corrected transmission electron microscopy (AC-TEM) of discrete [W6O19]2- polyoxometalate ions mounted within double walled carbon nanotubes (DWNTs) allow high precision structural studies to be performed. W atom column separations within the octahedral W6 tungsten template can be visualized with sufficient clarity that correlation with full-scale density functional theory (DFT) can be achieved. Calculations performed on the gas phase and DWNT-mounted [W6O19]2- anions show good agreement, in the latter case, with measured separations between pairs of W2 atom columns imaged within equatorial WO6 octahedra and single W atoms within axial WO6 octahedra. Structural data from the tilted chiral encapsulating DWNT was also determined simultaneously with the anion structural measurements, allowing the nanotube conformation to be addressed in the DFT calculations.

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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 IV, 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

  3. Configuration Interaction-Corrected Tamm-Dancoff Approximation: A Time-Dependent Density Functional Method with the Correct Dimensionality of Conical Intersections.

    PubMed

    Li, Shaohong L; Marenich, Aleksandr V; Xu, Xuefei; Truhlar, Donald G

    2014-01-16

    Linear response (LR) Kohn-Sham (KS) time-dependent density functional theory (TDDFT), or KS-LR, has been widely used to study electronically excited states of molecules and is the method of choice for large and complex systems. The Tamm-Dancoff approximation to TDDFT (TDDFT-TDA or KS-TDA) gives results similar to KS-LR and alleviates the instability problem of TDDFT near state intersections. However, KS-LR and KS-TDA share a debilitating feature; conical intersections of the reference state and a response state occur in F - 1 instead of the correct F - 2 dimensions, where F is the number of internal degrees of freedom. Here, we propose a new method, named the configuration interaction-corrected Tamm-Dancoff approximation (CIC-TDA), that eliminates this problem. It calculates the coupling between the reference state and an intersecting response state by interpreting the KS reference-state Slater determinant and linear response as if they were wave functions. Both formal analysis and test results show that CIC-TDA gives similar results to KS-TDA far from a conical intersection, but the intersection occurs with the correct dimensionality. We anticipate that this will allow more realistic application of TDDFT to photochemistry. PMID:26270707

  4. 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

  5. Accurate Ionization Potentials and Electron Affinities of Acceptor Molecules II: Non-Empirically Tuned Long-Range Corrected Hybrid Functionals.

    PubMed

    Gallandi, Lukas; Marom, Noa; Rinke, Patrick; Körzdörfer, Thomas

    2016-02-01

    The performance of non-empirically tuned long-range corrected hybrid functionals for the prediction of vertical ionization potentials (IPs) and electron affinities (EAs) is assessed for a set of 24 organic acceptor molecules. Basis set-extrapolated coupled cluster singles, doubles, and perturbative triples [CCSD(T)] calculations serve as a reference for this study. Compared to standard exchange-correlation functionals, tuned long-range corrected hybrid functionals produce highly reliable results for vertical IPs and EAs, yielding mean absolute errors on par with computationally more demanding GW calculations. In particular, it is demonstrated that long-range corrected hybrid functionals serve as ideal starting points for non-self-consistent GW calculations. PMID:26731340

  6. Functional correction by antisense therapy of a splicing mutation in the GALT gene.

    PubMed

    Coelho, Ana I; Lourenço, Sílvia; Trabuco, Matilde; Silva, Maria João; Oliveira, Anabela; Gaspar, Ana; Diogo, Luísa; Tavares de Almeida, Isabel; Vicente, João B; Rivera, Isabel

    2015-04-01

    In recent years, antisense therapy has emerged as an increasingly important therapeutic approach to tackle several genetic disorders, including inborn errors of metabolism. Intronic mutations activating cryptic splice sites are particularly amenable to antisense therapy, as the canonical splice sites remain intact, thus retaining the potential for restoring constitutive splicing. Mutational analysis of Portuguese galactosemic patients revealed the intronic variation c.820+13A>G as the second most prevalent mutation, strongly suggesting its pathogenicity. The aim of this study was to functionally characterize this intronic variation, to elucidate its pathogenic molecular mechanism(s) and, ultimately, to correct it by antisense therapy. Minigene splicing assays in two distinct cell lines and patients' transcript analyses showed that the mutation activates a cryptic donor splice site, inducing an aberrant splicing of the GALT pre-mRNA, which in turn leads to a frameshift with inclusion of a premature stop codon (p.D274Gfs*17). Functional-structural studies of the recombinant wild-type and truncated GALT showed that the latter is devoid of enzymatic activity and prone to aggregation. Finally, two locked nucleic acid oligonucleotides, designed to specifically recognize the mutation, successfully restored the constitutive splicing, thus establishing a proof of concept for the application of antisense therapy as an alternative strategy for the clearly insufficient dietary treatment in classic galactosemia. PMID:25052314

  7. 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.

  8. Correction of an input function for errors introduced with automated blood sampling

    SciTech Connect

    Schlyer, D.J.; Dewey, S.L.

    1994-05-01

    Accurate kinetic modeling of PET data requires an precise arterial plasma input function. The use of automated blood sampling machines has greatly improved the accuracy but errors can be introduced by the dispersion of the radiotracer in the sampling tubing. This dispersion results from three effects. The first is the spreading of the radiotracer in the tube due to mass transfer. The second is due to the mechanical action of the peristaltic pump and can be determined experimentally from the width of a step function. The third is the adsorption of the radiotracer on the walls of the tubing during transport through the tube. This is a more insidious effect since the amount recovered from the end of the tube can be significantly different than that introduced into the tubing. We have measured the simple mass transport using [{sup 18}F]fluoride in water which we have shown to be quantitatively recovered with no interaction with the tubing walls. We have also carried out experiments with several radiotracers including [{sup 18}F]Haloperidol, [{sup 11}C]L-deprenyl, [{sup 18}]N-methylspiroperidol ([{sup 18}F]NMS) and [{sup 11}C]buprenorphine. In all cases there was some retention of the radiotracer by untreated silicone tubing. The amount retained in the tubing ranged from 6% for L-deprenyl to 30% for NMS. The retention of the radiotracer was essentially eliminated after pretreatment with the relevant unlabeled compound. For example less am 2% of the [{sup 18}F]NMS was retained in tubing treated with unlabelled NMS. Similar results were obtained with baboon plasma although the amount retained in the untreated tubing was less in all cases. From these results it is possible to apply a mathematical correction to the measured input function to account for mechanical dispersion and to apply a chemical passivation to the tubing to reduce the dispersion due to adsorption of the radiotracer on the tubing walls.

  9. Impaired microtubule function correctable by cyclic GMP and cholinergic agonists in the Chediak-Higashi syndrome.

    PubMed Central

    Oliver, J. M.

    1976-01-01

    The Chediak-Higashi (CH) syndrome of man and several animal species is characterized by the presence of abnormal giant granules in all granule-containing cells and by defects in chemotaxis and lysosomal degranulation during phagocytosis in polymorphonuclear leukocytes (PMNs). Since similar functional abnormalities have been reported in normal PMNs following exposure to colchicine and other agents that disrupt microtubles it was proposed that microtubule function may be impaired in the CH syndrome. The mobility of concanavalin A (con A)-receptor complexes on PMN membranes was used to test microtubule integrity. Normal PMNs showed a uniform distribution of membrane-bound con A. By contrast, con A was aggregated into surface caps on both colchicine-treated normal PMNs and untreated PMNs from mice and a patient with CH syndrome. This result is consistent with impaired microtubule function in the CH cells. The spontaneous capping response of CH PMNs was inhibited by cyclic GMP and by cholinergic agonists that can elevate cyclic GMP levels in neutrophils. This raised the possibility that the microtubule defect in CH cells may be correctable by treatments that increase cyclic GMP generation. Direct evidence for both the absence of microtubule assembly in con A-treated PMNs from the CH patient and for normal microtubule assembly in CH PMNs incubated with cyclic GMP and cholinergic agonists prior to con A treatment was obtained by electron microscopy. In addition, evidence for a direct relationship between the microtubule defect and the development of giant lysosomes in CH cells was obtained. Thus, CH fibroblasts grown in vitro developed abnormal lysosomes in the majority of cells. However, the same cells cultured in the presence of cholinergic agonists developed a majority of lysosomes that were morphologically normal at the level of the light microscope. Similarly, granule morphology appeared normal in peripheral blood leukocytes from mice treated chronically in vivo with

  10. Exact finite-size corrections for the spanning-tree model under different boundary conditions

    NASA Astrophysics Data System (ADS)

    Izmailian, N. Sh.; Kenna, R.

    2015-02-01

    We express the partition functions of the spanning tree on finite square lattices under five different sets of boundary conditions in terms of a principal partition function with twisted-boundary conditions. Based on these expressions, we derive the exact asymptotic expansions of the logarithm of the partition function for each case. We have also established several groups of identities relating spanning-tree partition functions for the different boundary conditions. We also explain an apparent discrepancy between logarithmic correction terms in the free energy for a two-dimensional spanning-tree model with periodic and free-boundary conditions and conformal field theory predictions. We have obtained corner free energy for the spanning tree under free-boundary conditions in full agreement with conformal field theory predictions.

  11. 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.

  12. Subleading correction to statistical entropy for Breckenridge-Myers-Peet-Vafa black holes

    SciTech Connect

    Banerjee, Nabamita

    2009-04-15

    We study higher derivative corrections to the statistical entropy function and the statistical entropy for five-dimensional Breckenridge-Myers-Peet-Vafa black holes by doing the asymptotic expansion of the partition function. This enables us to evaluate entropy for a large range of charges, even out of the Cardy (Farey tail) limit.

  13. Estimation of boiling points using density functional theory with polarized continuum model solvent corrections.

    PubMed

    Chan, Poh Yin; Tong, Chi Ming; Durrant, Marcus C

    2011-09-01

    An empirical method for estimation of the boiling points of organic molecules based on density functional theory (DFT) calculations with polarized continuum model (PCM) solvent corrections has been developed. The boiling points are calculated as the sum of three contributions. The first term is calculated directly from the structural formula of the molecule, and is related to its effective surface area. The second is a measure of the electronic interactions between molecules, based on the DFT-PCM solvation energy, and the third is employed only for planar aromatic molecules. The method is applicable to a very diverse range of organic molecules, with normal boiling points in the range of -50 to 500 °C, and includes ten different elements (C, H, Br, Cl, F, N, O, P, S and Si). Plots of observed versus calculated boiling points gave R²=0.980 for a training set of 317 molecules, and R²=0.979 for a test set of 74 molecules. The role of intramolecular hydrogen bonding in lowering the boiling points of certain molecules is quantitatively discussed. PMID:21798775

  14. Refined lateral energy correction functions for the KASCADE-Grande experiment based on Geant4 simulations

    NASA Astrophysics Data System (ADS)

    Gherghel-Lascu, A.; Apel, W. D.; Arteaga-Velázquez, J. C.; Bekk, K.; Bertaina, M.; Blümer, J.; Bozdog, H.; Brancus, I. M.; Cantoni, E.; Chiavassa, A.; Cossavella, F.; Daumiller, K.; de Souza, V.; Di Pierro, F.; Doll, P.; Engel, R.; Engler, J.; Fuchs, B.; Fuhrmann, D.; Gils, H. J.; Glasstetter, R.; Grupen, C.; Haungs, A.; Heck, D.; Hörandel, J. R.; Huber, D.; Huege, T.; Kampert, K.-H.; Kang, D.; Klages, H. O.; Link, K.; Łuczak, P.; Mathes, H. J.; Mayer, H. J.; Milke, J.; Mitrica, B.; Morello, C.; Oehlschläger, J.; Ostapchenko, S.; Palmieri, N.; Petcu, M.; Pierog, T.; Rebel, H.; Roth, M.; Schieler, H.; Schoo, S.; Schröder, F. G.; Sima, O.; Toma, G.; Trinchero, G. C.; Ulrich, H.; Weindl, A.; Wochele, J.; Zabierowski, J.

    2015-02-01

    In previous studies of KASCADE-Grande data, a Monte Carlo simulation code based on the GEANT3 program has been developed to describe the energy deposited by EAS particles in the detector stations. In an attempt to decrease the simulation time and ensure compatibility with the geometry description in standard KASCADE-Grande analysis software, several structural elements have been neglected in the implementation of the Grande station geometry. To improve the agreement between experimental and simulated data, a more accurate simulation of the response of the KASCADE-Grande detector is necessary. A new simulation code has been developed based on the GEANT4 program, including a realistic geometry of the detector station with structural elements that have not been considered in previous studies. The new code is used to study the influence of a realistic detector geometry on the energy deposited in the Grande detector stations by particles from EAS events simulated by CORSIKA. Lateral Energy Correction Functions are determined and compared with previous results based on GEANT3.

  15. "Theory of mind and executive function in Chinese preschool children": Correction to Duh et al. (2016).

    PubMed

    2016-04-01

    Reports an error in "Theory of Mind and Executive Function in Chinese Preschool Children" by Shinchieh Duh, Jae H. Paik, Patricia H. Miller, Stephanie C. Gluck, Hui Li and Igor Himelfarb (Developmental Psychology, Advanced Online Publication, Feb 4, 2016, np). In the article, there were two errors in Table 6. The coefficient between WM and Age was incorrectly set as .46; it should have been .46. Further, the coefficient between WM and Gender should be .00 instead of .00. The correct version is provided. (The following abstract of the original article appeared in record 2016-05744-001.) Cross-cultural research on children's theory of mind (ToM) understanding has raised questions about its developmental sequence and relationship with executive function (EF). The current study examined how ToM develops (using the tasks from Wellman & Liu, 2004) in relation to 2 EF skills (conflict inhibition, working memory) in 997 Chinese preschoolers (ages 3, 4, 5) in Chengdu, China. Compared with prior research with other Chinese and non-Chinese children, some general patterns in development were replicated in this sample. However, the children showed culture-specific reversals in the developmental sequence of ToM. For example, Chengdu children performed differently on the 2 false-belief tasks that were thought to be equivalent. Furthermore, conflict inhibition as well as working memory uniquely predicted ToM performance. We discuss the issues of ToM development as they relate to test items and cross-cultural-and subcultural-differences. (PsycINFO Database Record PMID:27010231

  16. 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

  17. 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

  18. 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

  19. 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

  20. KV10.1 K(+)-channel plasma membrane discrete domain partitioning and its functional correlation in neurons.

    PubMed

    Jiménez-Garduño, Aura M; Mitkovski, Miso; Alexopoulos, Ioannis K; Sánchez, Araceli; Stühmer, Walter; Pardo, Luis A; Ortega, Alicia

    2014-03-01

    KV10.1 potassium channels are implicated in a variety of cellular processes including cell proliferation and tumour progression. Their expression in over 70% of human tumours makes them an attractive diagnostic and therapeutic target. Although their physiological role in the central nervous system is not yet fully understood, advances in their precise cell localization will contribute to the understanding of their interactions and function. We have determined the plasma membrane (PM) distribution of the KV10.1 protein in an enriched mouse brain PM fraction and its association with cholesterol- and sphingolipid-rich domains. We show that the KV10.1 channel has two different populations in a 3:2 ratio, one associated to and another excluded from Detergent Resistant Membranes (DRMs). This distribution of KV10.1 in isolated PM is cholesterol- and cytoskeleton-dependent since alteration of those factors changes the relationship to 1:4. In transfected HEK-293 cells with a mutant unable to bind Ca(2+)/CaM to KV10.1 protein, Kv10.1 distribution in DRM/non-DRM is 1:4. Mean current density was doubled in the cholesterol-depleted cells, without any noticeable effects on other parameters. These results demonstrate that recruitment of the KV10.1 channel to the DRM fractions involves its functional regulation. PMID:24269539

  1. 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. PMID:26273876

  2. Partition functions, the Bekenstein bound and temperature inversion in anti-de Sitter space and its conformal boundary

    SciTech Connect

    Gibbons, G. W.; Perry, M. J.; Pope, C. N.

    2006-10-15

    We reformulate the Bekenstein bound as the requirement of positivity of the Helmholtz free energy at the minimum value of the function L=E-S/(2{pi}R), where R is some measure of the size of the system. The minimum of L occurs at the temperature T=1/(2{pi}R). In the case of n-dimensional anti-de Sitter spacetime, the rather poorly defined size R acquires a precise definition in terms of the AdS radius l, with R=l/(n-2). We previously found that the Bekenstein bound holds for all known black holes in AdS. However, in this paper we show that the Bekenstein bound is not generally valid for free quantum fields in AdS, even if one includes the Casimir energy. Some other aspects of thermodynamics in anti-de Sitter spacetime are briefly touched upon.

  3. 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

  4. [The role of functional status and recursive partition analysis (RPA) classes for the choice of fractionation regimen in patients with high-grade gliomas].

    PubMed

    Izmaĭlov, T R; Pan'shin, G A; Datsenko, P V

    2012-01-01

    The treatment results of 396 patients with morphologically verified grade 3-4 malignant brain tumors receiving conventional irradiation regimen and irradiation by medium-sized fractions were analyzed to form institutional guidelines.The standard mode of fractionation with a single dose of 2 Gy and total focal dose (TFD) of 60 Gy is appropriate for patients with initial Karnofsky status of 60-100% and Recursive Partition Analysis (RPA) class I-III. TFD increase to 60-62 Gy in grade 4 gliomas and 54-56 Gy in grade 3 gliomas grants a significant improve in overall survival. An increase of a single irradiation fraction to 3 Gy may be used for patients with initially low functional status (Karnofsky 30-50%) and RPA classes IV-VI. In these cases it is advisable to use the TFD of 45 Gy or more (TFD of equivalent regimen with a dose greater than 54 Gy). The mentioned fractionation regimens could be recommended for the use in clinical practice to improve the results of high-grade gliomas treatment. PMID:22888653

  5. 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.

  6. 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.

  7. 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

  8. Biochemical, histological and functional correction of mucopolysaccharidosis type IIIB by intra-cerebrospinal fluid gene therapy.

    PubMed

    Ribera, Albert; Haurigot, Virginia; Garcia, Miguel; Marcó, Sara; Motas, Sandra; Villacampa, Pilar; Maggioni, Luca; León, Xavier; Molas, Maria; Sánchez, Víctor; Muñoz, Sergio; Leborgne, Christian; Moll, Xavier; Pumarola, Martí; Mingozzi, Federico; Ruberte, Jesús; Añor, Sònia; Bosch, Fatima

    2015-04-01

    Gene therapy is an attractive tool for the treatment of monogenic disorders, in particular for lysosomal storage diseases (LSD) caused by deficiencies in secretable lysosomal enzymes in which neither full restoration of normal enzymatic activity nor transduction of all affected cells are necessary. However, some LSD such as Mucopolysaccharidosis Type IIIB (MPSIIIB) are challenging because the disease's main target organ is the brain and enzymes do not efficiently cross the blood-brain barrier even if present at very high concentration in circulation. To overcome these limitations, we delivered AAV9 vectors encoding for α-N-acetylglucosaminidase (NAGLU) to the Cerebrospinal Fluid (CSF) of MPSIIIB mice with the disease already detectable at biochemical, histological and functional level. Restoration of enzymatic activity in Central Nervous System (CNS) resulted in normalization of glycosaminoglycan content and lysosomal physiology, resolved neuroinflammation and restored the pattern of gene expression in brain similar to that of healthy animals. Additionally, transduction of the liver due to passage of vectors to the circulation led to whole-body disease correction. Treated animals also showed reversal of behavioural deficits and extended lifespan. Importantly, when the levels of enzymatic activity were monitored in the CSF of dogs following administration of canine NAGLU-coding vectors to animals that were either naïve or had pre-existing immunity against AAV9, similar levels of activity were achieved, suggesting that CNS efficacy would not be compromised in patients seropositive for AAV9. Our studies provide a strong rationale for the clinical development of this novel therapeutic approach as the treatment for MPSIIIB. PMID:25524704

  9. 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.

  10. 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

    ... 30 Mineral Resources 3 2011-07-01 2011-07-01 false What functions may a State perform to ensure that reporters correct erroneous report data? 1227.500 Section 1227.500 Mineral Resources OFFICE OF SURFACE MINING RECLAMATION AND ENFORCEMENT, DEPARTMENT OF THE INTERIOR Natural Resources...

  11. The optimized effective potential and the self-interaction correction in density functional theory: Application to molecules

    NASA Astrophysics Data System (ADS)

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

    2000-05-01

    The Krieger, Li, and Iafrate approximation to the optimized effective potential including the self-interaction correction for density functional theory has been implemented in a molecular code, NWChem, that uses Gaussian functions to represent the Kohn and Sham spin-orbitals. The differences between the implementation of the self-interaction correction in codes where planewaves are used with an optimized effective potential are discussed. The importance of the localization of the spin-orbitals to maximize the exchange-correlation of the self-interaction correction is discussed. We carried out exchange-only calculations to compare the results obtained with these approximations, and those obtained with the local spin density approximation, the generalized gradient approximation and Hartree-Fock theory. Interesting results for the energy difference (GAP) between the highest occupied molecular orbital, HOMO, and the lowest unoccupied molecular orbital, LUMO, (spin-orbital energies of closed shell atoms and molecules) using the optimized effective potential and the self-interaction correction have been obtained. The effect of the diffuse character of the basis set on the HOMO and LUMO eigenvalues at the various levels is discussed. Total energies obtained with the optimized effective potential and the self-interaction correction show that the exchange energy with these approximations is overestimated and this will be an important topic for future work.

  12. 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

  13. Generalized-exchange local-spin-density-functional theory: Self-interaction correction

    NASA Astrophysics Data System (ADS)

    Manoli, S.; Whitehead, M. A.

    1988-07-01

    The local-spin-density (LSD) generalized-exchange (GX) theory is corrected for self-interaction by splitting the single-particle Fermi hole into pure-exchange and self-interaction holes. An analysis of these components shows that the non-self-interaction-corrected GX scheme overestimates the pure exchange while underestimating the self-interaction. This self-interaction-corrected scheme is called the GX-SI scheme. Using this method of correcting for self-interaction, two other approximate self-interaction-corrected (SIC) GX schemes can be derived in which (1) the GX-LSD-SI total exchange does not include the nonlocal, self-interaction potential and (2) the GX-SIX exchange is very similar to the exchange derived by Gopinathan [Phys. Rev. A 15, 2135 (1977)]. Neither of these exchanges obeys the sum rule. The GX-SI scheme contains correction terms to the LSD GX which are smaller than the corresponding ones derived in the SIC of Perdew and Zunger [Phys. Rev. B 23, 5048 (1981)]. This shows that the LSD-GX exchange is a better approximation to the true exchange of an inhomogeneous electron gas around an atom than the LSD free-electron gas exchange.

  14. 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

  15. In vitro functional correction of Hermansky-Pudlak Syndrome type-1 by lentiviral-mediated gene transfer.

    PubMed

    Ikawa, Yasuhiro; Hess, Richard; Dorward, Heidi; Cullinane, Andrew R; Huizing, Marjan; Gochuico, Bernadette R; Gahl, William A; Candotti, Fabio

    2015-01-01

    Hermansky-Pudlak syndrome (HPS) is a genetic disorder characterized by oculocutaneous albinism, bleeding tendency and susceptibility to pulmonary fibrosis. No curative therapy is available. Genetic correction directed to the lungs, bone marrow and/or gastro-intestinal tract might provide alternative forms of treatment for the diseases multi-systemic complications. We demonstrate that lentiviral-mediated gene transfer corrects the expression and function of the HPS1 gene in patient dermal melanocytes, which opens the way to development of gene therapy for HPS. PMID:25468649

  16. 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.

  17. Complex Orbitals, Multiple Local Minima, and Symmetry Breaking in Perdew-Zunger Self-Interaction Corrected Density Functional Theory Calculations.

    PubMed

    Lehtola, Susi; Head-Gordon, Martin; Jónsson, Hannes

    2016-07-12

    Implentation of seminumerical stability analysis for calculations using the Perdew-Zunger self-interaction correction is described. It is shown that real-valued solutions of the Perdew-Zunger equations for gas phase atoms are unstable with respect to imaginary orbital rotations, confirming that a proper implementation of the correction requires complex-valued orbitals. The orbital density dependence of the self-interaction corrected functional is found to lead to multiple local minima in the case of the acrylic acid, H6, and benzene molecules. In the case of benzene, symmetry breaking that results in incorrect ground state geometry is found to occur, erroneously leading to alternating bond lengths in the molecule. PMID:27232582

  18. 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.

  19. 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

    NASA Astrophysics Data System (ADS)

    Mardirossian, Narbe; Head-Gordon, Martin

    2014-05-01

    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.

  20. 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

    SciTech Connect

    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.

  1. Continuous partition lattice

    PubMed Central

    Björner, Anders

    1987-01-01

    A continuous analogue to the partition lattices is presented. This is the metric completion of the direct limit of a system of embeddings of the finite partition lattices. The construction is analogous to von Neumann's construction of a continuous geometry over a field F from the finite-dimensional projective geometries over F. PMID:16593874

  2. The Influence of Physiological Noise Correction on Test–Retest Reliability of Resting-State Functional Connectivity

    PubMed Central

    Cornejo, Maria Daniela; Molloy, Erin K.; Patriat, Rémi; Meier, Timothy B.; Kirk, Gregory R.; Nair, Veena A.; Meyerand, M. Elizabeth; Prabhakaran, Vivek

    2014-01-01

    Abstract The utility and success of resting-state functional connectivity MRI (rs-fcMRI) depend critically on the reliability of this technique and the extent to which it accurately reflects neuronal function. One challenge is that rs-fcMRI is influenced by various sources of noise, particularly cardiac- and respiratory-related signal variations. The goal of the current study was to evaluate the impact of various physiological noise correction techniques, specifically those that use independent cardiac and respiration measures, on the test–retest reliability of rs-fcMRI. A group of 25 subjects were each scanned at three time points—two within the same imaging session and another 2–3 months later. Physiological noise corrections accounted for significant variance, particularly in blood vessels, sagittal sinus, cerebrospinal fluid, and gray matter. The fraction of variance explained by each of these corrections was highly similar within subjects between sessions, but variable between subjects. Physiological corrections generally reduced intrasubject (between-session) variability, but also significantly reduced intersubject variability, and thus reduced the test–retest reliability of estimating individual differences in functional connectivity. However, based on known nonneuronal mechanisms by which cardiac pulsation and respiration can lead to MRI signal changes, and the observation that the physiological noise itself is highly stable within individuals, removal of this noise will likely increase the validity of measured connectivity differences. Furthermore, removal of these fluctuations will lead to better estimates of average or group maps of connectivity. It is therefore recommended that studies apply physiological noise corrections but also be mindful of potential correlations with measures of interest. PMID:25112809

  3. 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.

  4. 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

  5. Global modeling of the ice stripping correction in terms of the ice thickness spherical functions

    NASA Astrophysics Data System (ADS)

    Tenzer, R.; Hamayun; Vajda, P.; Novak, P.

    2009-04-01

    We model globally the ice stripping correction using techniques for a spherical harmonic analysis of the gravity field. The discrete data of ice thickness with a 2×2 arc-degree geographical resolution from the global crustal model CRUST 2.0 (http://mahi.ucsd.edu/Gabi/rem.dir/crust/crust2.html) are used to generate the Global Ice Thickness Model coefficients. The 5×5 arc-minute global elevation data from the ETOPO5 (provided by the NOAA's National Geophysical Data Centre) are used to generate the Global Elevation Model coefficients. The ice thickness and elevation spectral coefficients are utilized to compute globally the ice stripping correction with a spectral resolution complete to degree and order 90. The mean value of the ice density contrast -1757 kg/m3 (i.e., the difference between the mean ice density 913 kg/m3 and the reference crustal density 2670 kg/m3) is adopted. The expressions for computing the ice stripping corrections to the gravity field quantities are introduced in spectral domain. The results reveal that the ice stripping correction to the gravity disturbances varies globally between 2 and 300 mGal with the mean of 22 mGal and the standard deviation of 56 mGal. The complete ice stripping correction to the gravity anomalies (which comprises the direct and secondary indirect ice density contrast effects) varies from -53 to 199 mGal with the mean of -1 mGal and the standard deviation of 37 mGal. The gravitational potential generated by the ice density contrast varies from -3498 to -319 m2/s2 with the mean of -743 m2/s2 and the standard deviation of 733 m2/s2.

  6. 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.

  7. Partition signed social networks via clustering dynamics

    NASA Astrophysics Data System (ADS)

    Wu, Jianshe; Zhang, Long; Li, Yong; Jiao, Yang

    2016-02-01

    Inspired by the dynamics phenomenon occurred in social networks, the WJJLGS model is modified to imitate the clustering dynamics of signed social networks. Analyses show that the clustering dynamics of the model can be applied to partition signed social networks. Traditionally, blockmodel is applied to partition signed networks. In this paper, a detailed dynamics-based algorithm for signed social networks (DBAS) is presented. Simulations on several typical real-world and illustrative networks that have been analyzed by the blockmodel verify the correctness of the proposed algorithm. The efficiency of the algorithm is verified on large scale synthetic networks.

  8. Results of drug correction of structural and functional changes in the gingiva in experimental gastroduodenitis.

    PubMed

    Romanenko, E G

    2014-04-01

    Morphological changes in the gingiva under the effect of drugs improving microcirculation were studied in pubertal Wistar rats with experimental gastroduodenitis. Chronic gastroduodenitis was induced by intragastric administration of 50% medical bile (1 ml/100 g body weight daily) for 40 days. The best medical correction was attained with altan and citrarginine. Morphologic studies showed signs of regeneration plastic activity of the epithelium, restructuring of the gingival lamina propria, and enlargement of the vascular bed area. Calcium-D3 Nycomed disordered the regeneration processes in the rat epithelium, because of calcium ion capacity to increase oxygen demand in tissues and cause destructive processes. Hence, pathogenetic drug correction of degenerative processes in the gingiva under conditions of chronic gastroduodenitis should include drugs promoting recovery of the microcirculatory bed, altan and citrarginine. PMID:24824716

  9. A molecular dynamics study of the hydroxyl radical in solution applying self-interaction-corrected density functional methods.

    PubMed

    VandeVondele, Joost; Sprik, Michiel

    2005-04-01

    We have performed density functional theory based molecular dynamics (MD) simulations of the *OH radical in solution using self-interaction corrected (SIC) methods. We use a scheme recently proposed by M. d'Avezac, M. Calandra and F. Mauri [arXiv:cond-mat/0407750] in which a correction is only applied to the spin density within a restricted open shell formulation. In addition to two correction formulas employed within this scheme by M. d'Avezac, M. Calandra and F. Mauri, we propose and test an new empirical form which only introduces a scaled Coulomb term. This new functional leads to good agreement with reference calculations on radical cation dimers and on the hydroxyl water dimer in the gas phase. Applied in ab initio MD simulations, these three SIC methods provide a picture of the *OH solvation that differs qualitatively from the one obtained using the standard generalised gradient approximation (GGA). Hemibonded water, observed in GGA simulations and believed to be an artefact due to self-interaction error, is not present. We find that the *OH acts as a good hydrogen bond donor, but accepts less than two hydrogen bonds on average. These hydrogen bonds are part of a mobile, otherwise quasi-hydrophobic solvation cage. Our results show the potential of this computationally expedient scheme, which might extend the range of problems that can be modelled adequately with density functional theory. PMID:19787955

  10. Accurate Treatment of Large Supramolecular Complexes by Double-Hybrid Density Functionals Coupled with Nonlocal van der Waals Corrections.

    PubMed

    Calbo, Joaquín; Ortí, Enrique; Sancho-García, Juan C; Aragó, Juan

    2015-03-10

    In this work, we present a thorough assessment of the performance of some representative double-hybrid density functionals (revPBE0-DH-NL and B2PLYP-NL) as well as their parent hybrid and GGA counterparts, in combination with the most modern version of the nonlocal (NL) van der Waals correction to describe very large weakly interacting molecular systems dominated by noncovalent interactions. Prior to the assessment, an accurate and homogeneous set of reference interaction energies was computed for the supramolecular complexes constituting the L7 and S12L data sets by using the novel, precise, and efficient DLPNO-CCSD(T) method at the complete basis set limit (CBS). The correction of the basis set superposition error and the inclusion of the deformation energies (for the S12L set) have been crucial for obtaining precise DLPNO-CCSD(T)/CBS interaction energies. Among the density functionals evaluated, the double-hybrid revPBE0-DH-NL and B2PLYP-NL with the three-body dispersion correction provide remarkably accurate association energies very close to the chemical accuracy. Overall, the NL van der Waals approach combined with proper density functionals can be seen as an accurate and affordable computational tool for the modeling of large weakly bonded supramolecular systems. PMID:26579747

  11. 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. PMID:23947824

  12. Targeted Gene Correction in Osteopetrotic-Induced Pluripotent Stem Cells for the Generation of Functional Osteoclasts

    PubMed Central

    Neri, Tui; Muggeo, Sharon; Paulis, Marianna; Caldana, Maria Elena; Crisafulli, Laura; Strina, Dario; Focarelli, Maria Luisa; Faggioli, Francesca; Recordati, Camilla; Scaramuzza, Samantha; Scanziani, Eugenio; Mantero, Stefano; Buracchi, Chiara; Sobacchi, Cristina; Lombardo, Angelo; Naldini, Luigi; Vezzoni, Paolo; Villa, Anna; Ficara, Francesca

    2015-01-01

    Summary Autosomal recessive osteopetrosis is a human bone disease mainly caused by TCIRG1 gene mutations that prevent osteoclasts resorbing activity, recapitulated by the oc/oc mouse model. Bone marrow transplantation is the only available treatment, limited by the need for a matched donor. The use of induced pluripotent stem cells (iPSCs) as an unlimited source of autologous cells to generate gene corrected osteoclasts might represent a powerful alternative. We generated iPSCs from oc/oc mice, corrected the mutation using a BAC carrying the entire Tcirg1 gene locus as a template for homologous recombination, and induced hematopoietic differentiation. Similarly to physiologic fetal hematopoiesis, iPSC-derived CD41+ cells gradually gave rise to CD45+ cells, which comprised both mature myeloid cells and high proliferative potential colony-forming cells. Finally, we differentiated the gene corrected iPSC-derived myeloid cells into osteoclasts with rescued bone resorbing activity. These results are promising for a future translation into the human clinical setting. PMID:26344905

  13. AutoShim: empirically corrected scoring functions for quantitative docking with a crystal structure and IC50 training data.

    PubMed

    Martin, Eric J; Sullivan, David C

    2008-04-01

    It has been notoriously difficult to develop general all-purpose scoring functions for high-throughput docking that correlate with measured binding affinity. As a practical alternative, AutoShim uses the program Magnet to add point-pharmacophore like "shims" to the binding site of each protein target. The pharmacophore shims are weighted by partial least-squares (PLS) regression, adjusting the all-purpose scoring function to reproduce IC 50 data, much as the shims in an NMR magnet are weighted to optimize the field for a better spectrum. This dramatically improves the affinity predictions on 25% of the compounds held out at random. An iterative procedure chooses the best pose during the process of shim parametrization. This method reproducibly converges to a consistent solution, regardless of starting pose, in just 2-4 iterations, so these robust models do not overtrain. Sets of complex multifeature shims, generated by a recursive partitioning method, give the best activity predictions, but these are difficult to interpret when designing new compounds. Sets of simpler single-point pharmacophores still predict affinity reasonably well and clearly indicate the molecular interactions producing effective binding. The pharmacophore requirements are very reproducible, irrespective of the compound sets used for parametrization, lending confidence to the predictions and interpretations. The automated procedure does require a training set of experimental compounds but otherwise adds little extra time over conventional docking. PMID:18380449

  14. Gene Correction of iPSCs from a Wiskott-Aldrich Syndrome Patient Normalizes the Lymphoid Developmental and Functional Defects.

    PubMed

    Laskowski, Tamara J; Van Caeneghem, Yasmine; Pourebrahim, Rasoul; Ma, Chao; Ni, Zhenya; Garate, Zita; Crane, Ana M; Li, Xuan Shirley; Liao, Wei; Gonzalez-Garay, Manuel; Segovia, Jose Carlos; Paschon, David E; Rebar, Edward J; Holmes, Michael C; Kaufman, Dan; Vandekerckhove, Bart; Davis, Brian R

    2016-08-01

    Wiskott-Aldrich syndrome (WAS) is an X-linked primary immunodeficiency disease caused by mutations in the gene encoding the WAS protein (WASp). Here, induced pluripotent stem cells (iPSCs) were derived from a WAS patient (WAS-iPSC) and the endogenous chromosomal WAS locus was targeted with a wtWAS-2A-eGFP transgene using zinc finger nucleases (ZFNs) to generate corrected WAS-iPSC (cWAS-iPSC). WASp and GFP were first expressed in the earliest CD34(+)CD43(+)CD45(-) hematopoietic precursor cells and later in all hematopoietic lineages examined. Whereas differentiation to non-lymphoid lineages was readily obtained from WAS-iPSCs, in vitro T lymphopoiesis from WAS-iPSC was deficient with few CD4(+)CD8(+) double-positive and mature CD3(+) T cells obtained. T cell differentiation was restored for cWAS-iPSCs. Similarly, defects in natural killer cell differentiation and function were restored on targeted correction of the WAS locus. These results demonstrate that the defects exhibited by WAS-iPSC-derived lymphoid cells were fully corrected and suggests the potential therapeutic use of gene-corrected WAS-iPSCs. PMID:27396937

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

    PubMed

    Zhong, Min; Kundu, Bijoy K

    2013-10-01

    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 (18)F-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

  16. [Justifying measures to correct functional state of operators varying in personal anxiety].

    PubMed

    2012-01-01

    Workers of operating and dispatching occupations are exposed to high nervous and emotional exertion that result in increased personal anxiety, working stress and overstrain. That requires physiologically justified correction of hazardous psycho-physiologic states via various prophylactic measures (stay in schungite room, autogenous training, central electric analgesia, electric acupuncture). Attempted relaxation sessions in schungite room revealed in highly anxious individuals an increased velocity of visual signals perception, of attention concentration and shifting. Autogenous training sessions improve memory and have significant hypotensive effect in highly anxious individuals. PMID:22724349

  17. 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)

  18. Partial volume correction of the microPET blood input function using ensemble learning independent component analysis

    NASA Astrophysics Data System (ADS)

    Su, Kuan-Hao; Lee, Jih-Shian; Li, Jia-Hung; Yang, Yu-Wen; Liu, Ren-Shian; Chen, Jyh-Cheng

    2009-03-01

    Medical images usually suffer from a partial volume effect (PVE), which may degrade the accuracy of any quantitative information extracted from the images. Our aim was to recreate accurate radioactivity concentration and time-activity curves (TACs) by microPET R4 quantification using ensemble learning independent component analysis (EL-ICA). We designed a digital cardiac phantom for this simulation and in order to evaluate the ability of EL-ICA to correct the PVE, the simulated images were convoluted using a Gaussian function (FWHM = 1-4 mm). The robustness of the proposed method towards noise was investigated by adding statistical noise (SNR = 2-16). During further evaluation, another set of cardiac phantoms were generated from the reconstructed images, and Poisson noise at different levels was added to the sinogram. In real experiments, four rat microPET images and a number of arterial blood samples were obtained; these were used to estimate the metabolic rate of FDG (MRFDG). Input functions estimated using the FastICA method were used for comparison. The results showed that EL-ICA could correct PVE in both the simulated and real cases. After correcting for the PVE, the errors for MRFDG, when estimated by the EL-ICA method, were smaller than those when TACs were directly derived from the PET images and when the FastICA approach was used.

  19. 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

  20. Partitioning and parallel radiosity

    NASA Astrophysics Data System (ADS)

    Merzouk, S.; Winkler, C.; Paul, J. C.

    1996-03-01

    This paper proposes a theoretical framework, based on domain subdivision for parallel radiosity. Moreover, three various implementation approaches, taking advantage of partitioning algorithms and global shared memory architecture, are presented.

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

    PubMed Central

    van de Streek, Jacco; Neumann, Marcus A.

    2014-01-01

    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. PMID:25449625

  2. Function after correction of a clawed great toe by a modified Robert Jones transfer.

    PubMed

    Breusch, S J; Wenz, W; Döderlein, L

    2000-03-01

    We carried out a cross-sectional study in 51 patients (81 feet) with a clawed hallux in association with a cavus foot after a modified Robert Jones tendon transfer. The mean follow-up was 42 months (9 to 88). In all feet, concomitant procedures had been undertaken, such as extension osteotomy of the first metatarsal and transfer of the tendon of the peroneus longus to peroneus brevis, to correct the underlying foot deformity. All patients were evaluated clinically and radiologically. The overall rate of patient satisfaction was 86%. The deformity of the hallux was corrected in 80 feet. Catching of the big toe when walking barefoot, transfer lesions and metatarsalgia, hallux flexus, hallux limitus and asymptomatic nonunion of the interphalangeal joint were the most frequent complications. Hallux limitus was more likely when elevation of the first ray occurred (p = 0.012). Additional transfer of the tendon of peroneus longus to peroneus brevis was a significant risk factor for elevation of the first metatarsal (p < 0.0001). The deforming force of extensor hallucis longus is effectively eliminated by the Jones transfer, but the mechanics of the first metatarsophalangeal joint are altered. The muscle balance and stability of the entire first ray should be taken into consideration in the management of clawed hallux. PMID:10755436

  3. On the performance of van der Waals corrected-density functional theory in describing the atomic hydrogen physisorption on graphite

    NASA Astrophysics Data System (ADS)

    Ferullo, Ricardo M.; Domancich, Nicolás F.; Castellani, Norberto J.

    2010-11-01

    The atomic hydrogen physisorption on graphite was studied using the hydrogen-coronene model system and the van der Waals corrected-density functional theory (DFT + vdW). The results show that H preferentially occupies the hollow site. The adsorption energy at this site is calculated as 38.1 meV, in very good agreement with the available experimental measurements on a single graphite layer (39.2 ± 0.5 meV) and with reported MP2/aug-cc-pVDZ calculations (39.7 meV). The results suggest that, in DFT simulations, dispersion corrections should be considered in order to obtain accurate distances, adsorption energies and diffusion barriers in physisorption processes such as those occurring in the cold interstellar medium.

  4. QCD corrections to the Drell-Yan process for the Large Hadron Collider (LHC): Vertex functions and gluon bremsstrahlung

    SciTech Connect

    Zykunov, V. A.

    2010-07-15

    With an eye to future experiments at the Large Hadron Collider (LHC), O(aa{sub s}) QCD corrections to the Drell-Yan process are calculated for vertex functions and gluon bremsstrahlung. Use is made of fully differential cross sections, so that the result obtained in the present study can readily be applied in analyzing experimental data (in correcting data from future experiments at LHC). It is shown both analytically and numerically that the results are independent of unphysical parameters, including the parameter separating the regions of soft and hard gluons and the quark mass. A numerical analysis of radiative effects was performed by means of the FORTRAN code READY with allowance for the experimental cuts used at the Compact Muon Solenoid (CMS) detector

  5. Partial volume correction of PET-imaged tumor heterogeneity using expectation maximization with a spatially varying point spread function

    PubMed Central

    Barbee, David L; Flynn, Ryan T; Holden, James E; Nickles, Robert J; Jeraj, Robert

    2010-01-01

    Tumor heterogeneities observed in positron emission tomography (PET) imaging are frequently compromised of partial volume effects which may affect treatment prognosis, assessment, or future implementations such as biologically optimized treatment planning (dose painting). This paper presents a method for partial volume correction of PET-imaged heterogeneous tumors. A point source was scanned on a GE Discover LS at positions of increasing radii from the scanner’s center to obtain the spatially varying point spread function (PSF). PSF images were fit in three dimensions to Gaussian distributions using least squares optimization. Continuous expressions were devised for each Gaussian width as a function of radial distance, allowing for generation of the system PSF at any position in space. A spatially varying partial volume correction (SV-PVC) technique was developed using expectation maximization (EM) and a stopping criterion based on the method’s correction matrix generated for each iteration. The SV-PVC was validated using a standard tumor phantom and a tumor heterogeneity phantom, and was applied to a heterogeneous patient tumor. SV-PVC results were compared to results obtained from spatially invariant partial volume correction (SINV-PVC), which used directionally uniform three dimensional kernels. SV-PVC of the standard tumor phantom increased the maximum observed sphere activity by 55 and 40% for 10 and 13 mm diameter spheres, respectively. Tumor heterogeneity phantom results demonstrated that as net changes in the EM correction matrix decreased below 35%, further iterations improved overall quantitative accuracy by less than 1%. SV-PVC of clinically observed tumors frequently exhibited changes of ±30% in regions of heterogeneity. The SV-PVC method implemented spatially varying kernel widths and automatically determined the number of iterations for optimal restoration, parameters which are arbitrarily chosen in SINV-PVC. Comparing SV-PVC to SINV

  6. A Selective Corrective Exercise to Decrease Falling and Improve Functional Balance in Idiopathic Parkinson’s Disease

    PubMed Central

    Sedaghati, Parisa; Daneshmandi, Hassan; Karimi, Noureddin; Barati, Amir-Hossein

    2016-01-01

    Background: Posture instability and unsteady gait disorders in Parkinson’s Disease (PD) usually contribute to fall-related fractures. Fall-related trauma in PD is the most common reason for injury. Despite providing modern care for PD patients (PP) in the recent years, anti-PD drugs have no effect on falling. There is an urgent need to administer exercise interventions to reduce falls and related injuries in the rehabilitation program of PP. Objectives: To explore the effect of a selective 10-week corrective exercise with an emphasis on gait training activities (GTA) on the number of falls (NOFs), fear of falling, functional balance, timed up and go (TUG) test among PD patients. Patients and Methods: A purposeful sampling was performed on PP who had fallen or were at risk of falling in 2014. The study intervention consisted of a 10-week (3 sessions each week, each lasting 60 min) corrective exercise program. Participants were randomly allocated to control and two exercise groups; the exercise group with balance pad (EGBP) or exercise group with no balance pad (EGNBP). The analysis of variance (ANOVA) and paired t-test were used for comparison between the groups (P ≤ 0.05). Results: Administrating a selective corrective exercise in exercise group with balance pad (EGBP) showed a significant difference in number of falls (NOF), Fall Efficacy Scale-international (FES-I), Berg balance scale (BBS) (and timed up and go) TUG (P = 0.001); while administrating the same exercise in exercise group with no balance pad (EGNBP) showed no significant difference in NOF (P = 0.225) and a significant difference in FES-I (P = 0.031), BBS (P = 0.047) and TUG (P = 0.012). The control group showed no significant difference in each of the dependent variables. Conclusions: Performing a selective corrective exercise on balance pad improves falling and functional balance in idiopathic PD. PMID:27218051

  7. The role of mechanotransduction on vascular smooth muscle myocytes' [corrected] cytoskeleton and contractile function.

    PubMed

    Ye, George J C; Nesmith, Alexander P; Parker, Kevin Kit

    2014-09-01

    Smooth muscle (SM) exhibits a highly organized structural hierarchy that extends over multiple spatial scales to perform a wide range of functions at the cellular, tissue, and organ levels. Early efforts primarily focused on understanding vascular SM (VSM) function through biochemical signaling. However, accumulating evidence suggests that mechanotransduction, the process through which cells convert mechanical stimuli into biochemical cues, is requisite for regulating contractility. Cytoskeletal proteins that comprise the extracellular, intercellular, and intracellular domains are mechanosensitive and can remodel their structure and function in response to external mechanical cues. Pathological stimuli such as malignant hypertension can act through the same mechanotransductive pathways to induce maladaptive remodeling, leading to changes in cellular shape and loss of contractile function. In both health and disease, the cytoskeletal architecture integrates the mechanical stimuli and mediates structural and functional remodeling in the VSM. PMID:25125187

  8. Adaptive fuzzy logic restriction rules for error correction and safe stimulation patterns during functional electrical stimulation.

    PubMed

    Hansen, M; Haugland, M K

    2001-01-01

    Adaptive restriction rules based on fuzzy logic have been developed to eliminate errors and to increase stimulation safety in the foot-drop correction application, specifically when using adaptive logic networks to provide a stimulation control signal based on neural activity recorded from peripheral sensory nerve branches. The fuzzy rules were designed to increase flexibility and offer easier customization, compared to earlier versions of restriction rules. The rules developed quantified the duration of swing and stance phases into states of accepting or rejecting new transitions, based on the cyclic nature of gait and statistics on the current gait patterns. The rules were easy to custom design for a specific application, using linguistic terms to model the actions of the rules. The rules were tested using pre-recorded gait data processed through a gait event detector and proved to reduce detection delay and the number of errors, compared to conventional rules. PMID:11601442

  9. Bremsstrahlung function, leading Lüscher correction at weak coupling and localization

    NASA Astrophysics Data System (ADS)

    Bonini, Marisa; Griguolo, Luca; Preti, Michelangelo; Seminara, Domenico

    2016-02-01

    We discuss the near BPS expansion of the generalized cusp anomalous dimension with L units of R-charge. Integrability provides an exact solution, obtained by solving a general TBA equation in the appropriate limit: we propose here an alternative method based on supersymmetric localization. The basic idea is to relate the computation to the vacuum expectation value of certain 1/8 BPS Wilson loops with local operator insertions along the contour. These observables localize on a two-dimensional gauge theory on S 2, opening the possibility of exact calculations. As a test of our proposal, we reproduce the leading Lüscher correction at weak coupling to the generalized cusp anomalous dimension. This result is also checked against a genuine Feynman diagram approach in {N}=4 Super Yang-Mills theory.

  10. 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.

  11. On bottleneck partitioning k-ary n-cubes

    NASA Technical Reports Server (NTRS)

    Nicol, David M.; Mao, Weizhen

    1994-01-01

    Graph partitioning is a topic of extensive interest, with applications to parallel processing. In this context graph nodes typically represent computation, and edges represent communication. One seeks to distribute the workload by partitioning the graph so that every processor has approximately the same workload, and the communication cost (measured as a function of edges exposed by the partition) is minimized. Measures of partition quality vary; in this paper we consider a processor's cost to be the sum of its computation and communication costs, and consider the cost of a partition to be the bottleneck, or maximal processor cost induced by the partition. For a general graph the problem of finding an optimal partitioning is intractable. In this paper we restrict our attention to the class of k-art n-cube graphs with uniformly weighted nodes. Given mild restrictions on the node weight and number of processors, we identify partitions yielding the smallest bottleneck. We also demonstrate by example that some restrictions are necessary for the partitions we identify to be optimal. In particular, there exist cases where partitions that evenly partition nodes need not be optimal.

  12. 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.

  13. 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. PMID:26374017

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    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.

  15. Restoration of renal function does not correct impairment of uremic HDL properties.

    PubMed

    Kopecky, Chantal; Haidinger, Michael; Birner-Grünberger, Ruth; Darnhofer, Barbara; Kaltenecker, Christopher C; Marsche, Gunther; Holzer, Michael; Weichhart, Thomas; Antlanger, Marlies; Kovarik, Johannes J; Werzowa, Johannes; Hecking, Manfred; Säemann, Marcus D

    2015-03-01

    Cardiovascular disease remains the leading cause of death in renal transplant recipients, but the underlying causative mechanisms for this important problem remain elusive. Recent work has indicated that qualitative alterations of HDL affect its functional and compositional properties in ESRD. Here, we systematically analyzed HDL from stable renal transplant recipients, according to graft function, and from patients with ESRD to determine whether structural and functional properties of HDL remain dysfunctional after renal transplantation. Cholesterol acceptor capacity and antioxidative activity, representing two key cardioprotective mechanisms of HDL, were profoundly suppressed in kidney transplant recipients independent of graft function and were comparable with levels in patients with ESRD. Using a mass spectroscopy approach, we identified specific remodeling of transplant HDL with highly enriched proteins, including α-1 microglobulin/bikunin precursor, pigment epithelium-derived factor, surfactant protein B, and serum amyloid A. In conclusion, this study demonstrates that HDL from kidney recipients is uniquely altered at the molecular and functional levels, indicating a direct pathologic role of HDL that could contribute to the substantial cardiovascular risk in the transplant population. PMID:25071090

  16. Restoration of Renal Function Does Not Correct Impairment of Uremic HDL Properties

    PubMed Central

    Kopecky, Chantal; Haidinger, Michael; Birner-Grünberger, Ruth; Darnhofer, Barbara; Kaltenecker, Christopher C.; Marsche, Gunther; Holzer, Michael; Weichhart, Thomas; Antlanger, Marlies; Kovarik, Johannes J.; Werzowa, Johannes; Hecking, Manfred

    2015-01-01

    Cardiovascular disease remains the leading cause of death in renal transplant recipients, but the underlying causative mechanisms for this important problem remain elusive. Recent work has indicated that qualitative alterations of HDL affect its functional and compositional properties in ESRD. Here, we systematically analyzed HDL from stable renal transplant recipients, according to graft function, and from patients with ESRD to determine whether structural and functional properties of HDL remain dysfunctional after renal transplantation. Cholesterol acceptor capacity and antioxidative activity, representing two key cardioprotective mechanisms of HDL, were profoundly suppressed in kidney transplant recipients independent of graft function and were comparable with levels in patients with ESRD. Using a mass spectroscopy approach, we identified specific remodeling of transplant HDL with highly enriched proteins, including α-1 microglobulin/bikunin precursor, pigment epithelium-derived factor, surfactant protein B, and serum amyloid A. In conclusion, this study demonstrates that HDL from kidney recipients is uniquely altered at the molecular and functional levels, indicating a direct pathologic role of HDL that could contribute to the substantial cardiovascular risk in the transplant population. PMID:25071090

  17. TALEN-mediated functional correction of X-linked chronic granulomatous disease in patient-derived induced pluripotent stem cells.

    PubMed

    Dreyer, Anne-Kathrin; Hoffmann, Dirk; Lachmann, Nico; Ackermann, Mania; Steinemann, Doris; Timm, Barbara; Siler, Ulrich; Reichenbach, Janine; Grez, Manuel; Moritz, Thomas; Schambach, Axel; Cathomen, Toni

    2015-11-01

    X-linked chronic granulomatous disease (X-CGD) is an inherited disorder of the immune system. It is characterized by a defect in the production of reactive oxygen species (ROS) in phagocytic cells due to mutations in the NOX2 locus, which encodes gp91phox. Because the success of retroviral gene therapy for X-CGD has been hampered by insertional activation of proto-oncogenes, targeting the insertion of a gp91phox transgene into potential safe harbor sites, such as AAVS1, may represent a valid alternative. To conceptually evaluate this strategy, we generated X-CGD patient-derived induced pluripotent stem cells (iPSCs), which recapitulate the cellular disease phenotype upon granulocytic differentiation. We examined AAVS1-specific zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) for their efficacy to target the insertion of a myelo-specific gp91phox cassette to AAVS1. Probably due to their lower cytotoxicity, TALENs were more efficient than ZFNs in generating correctly targeted iPSC colonies, but all corrected iPSC clones showed no signs of mutations at the top-ten predicted off-target sites of both nucleases. Upon differentiation of the corrected X-CGD iPSCs, gp91phox mRNA levels were highly up-regulated and the derived granulocytes exhibited restored ROS production that induced neutrophil extracellular trap (NET) formation. In conclusion, we demonstrate that TALEN-mediated integration of a myelo-specific gp91phox transgene into AAVS1 of patient-derived iPSCs represents a safe and efficient way to generate autologous, functionally corrected granulocytes. PMID:26295532

  18. Adsorption studies of C6H6 on Cu (111), Ag (111), and Au (111) within dispersion corrected density functional theory

    NASA Astrophysics Data System (ADS)

    Chwee, T. S.; Sullivan, M. B.

    2012-10-01

    The adsorption energies and changes in surface work functions for benzene on unreconstructed Cu(111), Ag (111), and Au (111) at low coverages have been studied within the framework of dispersion corrected Kohn-Sham density functional theory. Corrections to account for long range dispersive effects between the adsorbate and metal substrate were incorporated via the exchange-hole dipole moment method of Becke and Johnson [J. Chem. Phys. 123, 154101 (2005), 10.1063/1.2065267]. We show that the dispersion corrected calculations yield significantly improved adsorption energies and work function shifts that are in good agreement with experimental values.

  19. 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

  20. Partitioning Breaks Communities

    NASA Astrophysics Data System (ADS)

    Reid, Fergal; McDaid, Aaron; Hurley, Neil

    Considering a clique as a conservative definition of community structure, we examine how graph partitioning algorithms interact with cliques. Many popular community-finding algorithms partition the entire graph into non-overlapping communities. We show that on a wide range of empirical networks, from different domains, significant numbers of cliques are split across the separate partitions produced by these algorithms. We then examine the largest connected component of the subgraph formed by retaining only edges in cliques, and apply partitioning strategies that explicitly minimise the number of cliques split. We further examine several modern overlapping community finding algorithms, in terms of the interaction between cliques and the communities they find, and in terms of the global overlap of the sets of communities they find. We conclude that, due to the connectedness of many networks, any community finding algorithm that produces partitions must fail to find at least some significant structures. Moreover, contrary to traditional intuition, in some empirical networks, strong ties and cliques frequently do cross community boundaries; much community structure is fundamentally overlapping and unpartitionable in nature.

  1. Correcting the Visual Bias: Assessing the Functions of Music in Film and Television.

    ERIC Educational Resources Information Center

    Berg, Charles M.

    This investigation was carried out for the purpose of encouraging speculation about and investigation into the important communicative functions of music in film and television. After examining the visual bias of media analysts, critics, and historians--a bias which tends to filter out serious exploration of music's role in film and…

  2. 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…

  3. 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.

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

    PubMed

    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. PMID:25527936

  5. ELLIPTICAL-WEIGHTED HOLICs FOR WEAK LENSING SHEAR MEASUREMENT. II. POINT-SPREAD FUNCTION CORRECTION AND APPLICATION TO A370

    SciTech Connect

    Okura, Yuki; Futamase, Toshifumi E-mail: tof@astr.tohoku.ac.jp

    2012-04-01

    We developed a new method (E-HOLICs) of estimating gravitational shear by adopting an elliptical weight function to measure background galaxy images in our previous paper. Following the previous paper, in which an isotropic point-spread function (PSF) correction is calculated, in this paper we consider an anisotropic PSF correction in order to apply E-HOLICs to real data. As an example, E-HOLICs is applied to Subaru data of the massive and compact galaxy cluster A370 and is able to detect double peaks in the central region of the cluster consistent with the analysis of strong lensing. We also study the systematic error in E-HOLICs using STEP2 simulation. In particular, we consider the dependences of the signal-to-noise ratio (S/N) of background galaxies in the shear estimation. Although E-HOLICs does improve the systematic error due to the ellipticity dependence as shown in Paper I, a systematic error due to the S/N dependence remains, namely, E-HOLICs underestimates shear when background galaxies with low S/N objects are used. We discuss a possible improvement of the S/N dependence.

  6. Alpharetroviral Vector-mediated Gene Therapy for X-CGD: Functional Correction and Lack of Aberrant Splicing

    PubMed Central

    Kaufmann, Kerstin B.; Brendel, Christian; Suerth, Julia D.; Mueller-Kuller, Uta; Chen-Wichmann, Linping; Schwäble, Joachim; Pahujani, Shweta; Kunkel, Hana; Schambach, Axel; Baum, Christopher; Grez, Manuel

    2013-01-01

    Comparative integrome analysis has revealed that the most neutral integration pattern among retroviruses is attributed to alpharetroviruses. We chose X-linked chronic granulomatous disease (X-CGD) as model to evaluate the potential of self-inactivating (SIN) alpharetroviral vectors for gene therapy of monogenic diseases. Therefore, we combined the alpharetroviral vector backbone with the elongation factor-1α short promoter, both considered to possess a low genotoxic profile, to drive transgene (gp91phox) expression. Following efficient transduction transgene expression was sustained and provided functional correction of the CGD phenotype in a cell line model at low vector copy number. Further analysis in a murine X-CGD transplantation model revealed gene-marking of bone marrow cells and oxidase positive granulocytes in peripheral blood. Transduction of human X-CGD CD34+ cells provided functional correction up to wild-type levels and long-term expression upon transplantation into a humanized mouse model. In contrast to lentiviral vectors, no aberrantly spliced transcripts containing cellular exons fused to alpharetroviral sequences were found in transduced cells, implying that the safety profile of alpharetroviral vectors may extend beyond their neutral integration profile. Taken together, this highlights the potential of this SIN alpharetroviral system as a platform for new candidate vectors for future gene therapy of hematopoietic disorders. PMID:23207695

  7. 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. PMID:20609606

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Cumulants of partitions

    NASA Astrophysics Data System (ADS)

    Weiss, Christoph; Block, Martin; Holthaus, Martin; Schmieder, Gerald

    2003-02-01

    We utilize the formal equivalence between the number-partitioning problem and a harmonically trapped ideal Bose gas within the microcanonical ensemble for characterizing the probability distribution which governs the number of addends occurring in an unrestricted partition of a natural number n. By deriving accurate asymptotic formulae for its coefficients of skewness and excess, it is shown that this distribution remains non-Gaussian even when n is made arbitrarily large. Both skewness and excess vary substantially before settling to their constant-limiting values for n > 1010.

  14. Correcting the z ˜ 8 Galaxy Luminosity Function for Gravitational Lensing Magnification Bias

    NASA Astrophysics Data System (ADS)

    Mason, Charlotte A.; Treu, Tommaso; Schmidt, Kasper B.; Collett, Thomas E.; Trenti, Michele; Marshall, Philip J.; Barone-Nugent, Robert; Bradley, Larry D.; Stiavelli, Massimo; Wyithe, Stuart

    2015-05-01

    We present a Bayesian framework to account for the magnification bias from both strong and weak gravitational lensing in estimates of high-redshift galaxy luminosity functions (LFs). We illustrate our method by estimating the z ˜ 8 UV LF using a sample of 97 Y-band dropouts (Lyman break galaxies) found in the Brightest of Reionizing Galaxies (BoRG) survey and from the literature. We find the LF is well described by a Schechter function with characteristic magnitude of {{M}\\star }=-19.85-0.35+0.30, faint-end slope of α =-1.72-0.29+0.30, and number density of {{log }10}{{{\\Psi }}\\star }(Mp{{c}-3})=-3.00-0.31+0.23. These parameters are consistent within the uncertainties with those inferred from the same sample without accounting for the magnification bias, demonstrating that the effect is small for current surveys at z ˜ 8, and cannot account for the apparent overdensity of bright galaxies compared to a Schechter function found recently by Bowler et al. and Finkelstein et al. We estimate that the probability of finding a strongly lensed z ˜ 8 source in our sample is in the range ˜3-15% depending on limiting magnitude. We identify one strongly lensed candidate and three cases of intermediate lensing in BoRG (estimated magnification μ > 1.4) in addition to the previously known candidate group-scale strong lens. Using a range of theoretical LFs we conclude that magnification bias will dominate wide field surveys—such as those planned for the Euclid and WFIRST missions—especially at z > 10. Magnification bias will need to be accounted for in order to derive accurate estimates of high-redshift LFs in these surveys and to distinguish between galaxy formation models.

  15. [The correction of functional disorders of the bile-secreting system by using laser radiation].

    PubMed

    Vorob'ev, L P; Salova, L M; Chubarov, G V; Meshkov, V M

    1992-01-01

    He-Ne laser irradiation of biologically active points and infrared laser irradiation of the liver were employed to improve gallbladder and sphincter functions, bile production and biochemistry, respectively, in a total of 57 patients with biliary dyskinesia presenting as hypokinetic dyskinesia of the gallbladder, hyperkinetic dyskinesia of the sphincter of Oddi or the combination of the two affections. Simultaneous use of the two kinds of laser irradiation appreciably shortens treatment duration, abolishes biliferous dysfunction, reestablishes physiological balance of bile components in case of its initial lithogenic potential. PMID:1455793

  16. A novel corrective approach to achieve satisfactory function of a 'sunk' colostomy.

    PubMed

    Siddique, K; Prud'Homme, G; Samuel, N; Avil-Griffiths, K; Offori, T

    2016-05-01

    Introduction Creation of gastrointestinal stomas is a common colorectal procedure associated with early or late complications, some of which demand advanced technical skills and expertise for optimal management. Case History A 63-year-old male underwent a defunctioning loop colostomy for locally advanced rectal cancer with liver metastasis. Three months later, he had developed a skinfold over his stoma that resulted in a horizontal skin crease traversing through the stoma, causing the stoma to 'sink' leading to obliteration of the stomal opening. This scenario led to ineffective attachment of a stoma appliance, resulting in painful peristomal ulcers. After excision of the anterior abdominal wall, assessment of colostomy opening was carried out, followed by closure of the subcutaneous tissues and drain fixation. An elevated colostomy with an adequate functional opening was seen after wound closure. The patient made an uneventful recovery and was discharged home. After 3 weeks, he had a fully opened, normally functioning colostomy and peristomal ulcers were almost healed. Conclusions This case highlights the challenges of stoma management, its related risks, avoidance of delay in chemotherapy, a patient wish for early return to work, and the novel approach we adopted to deal with these issues. PMID:27087345

  17. An AP endonuclease functions in active DNA demethylation and gene imprinting in Arabidopsis [corrected].

    PubMed

    Li, Yan; Córdoba-Cañero, Dolores; Qian, Weiqiang; Zhu, Xiaohong; Tang, Kai; Zhang, Huiming; Ariza, Rafael R; Roldán-Arjona, Teresa; Zhu, Jian-Kang

    2015-01-01

    Active DNA demethylation in plants occurs through base excision repair, beginning with removal of methylated cytosine by the ROS1/DME subfamily of 5-methylcytosine DNA glycosylases. Active DNA demethylation in animals requires the DNA glycosylase TDG or MBD4, which functions after oxidation or deamination of 5-methylcytosine, respectively. However, little is known about the steps following DNA glycosylase action in the active DNA demethylation pathways in plants and animals. We show here that the Arabidopsis APE1L protein has apurinic/apyrimidinic endonuclease activities and functions downstream of ROS1 and DME. APE1L and ROS1 interact in vitro and co-localize in vivo. Whole genome bisulfite sequencing of ape1l mutant plants revealed widespread alterations in DNA methylation. We show that the ape1l/zdp double mutant displays embryonic lethality. Notably, the ape1l+/-zdp-/- mutant shows a maternal-effect lethality phenotype. APE1L and the DNA phosphatase ZDP are required for FWA and MEA gene imprinting in the endosperm and are important for seed development. Thus, APE1L is a new component of the active DNA demethylation pathway and, together with ZDP, regulates gene imprinting in Arabidopsis. PMID:25569774

  18. [Oxidative homeostasis and functional parameters of rats at high altitudes with alpha-lipoic acid correction].

    PubMed

    Vishnevskiĭ, A A; Dzhantaeva, G A; Zhaparalieva, Ch O

    2011-01-01

    Oxidative and functional effects of alpha-lipoic acid (a-LA) were studied in the course of 45-day adaptation to high altitudes (3200 m in the Central Tien Shan, June - August). Comparison of a-LA with mildronate stated similarity of their antioxidant and membrane effects on the third (stable) phase of adaptation (day 45), as both substances demonstrated a distinct lyso-PL-limiting effect and did not change dramatically concentration of diene conjugates (primary products of lipid peroxidation) in brain tissue. a-LA surpassed mildronate in the rate of the compensating effect in respect of behavior disorders and anxiety in rats. Besides, the substances contributed equally to physical performance increment by the end of adaptation. The positive effect of a-LA on the functional characteristics was hand in hand with minimization of the consequences of oxidative stress. These experimental data imply that a-LA can be effective in controlling the long process of adaptation to high altitude conditions. PMID:21916251

  19. 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

  20. Wavelet-based functional linear mixed models: an application to measurement error–corrected distributed lag models

    PubMed Central

    Malloy, Elizabeth J.; Morris, Jeffrey S.; Adar, Sara D.; Suh, Helen; Gold, Diane R.; Coull, Brent A.

    2010-01-01

    Frequently, exposure data are measured over time on a grid of discrete values that collectively define a functional observation. In many applications, researchers are interested in using these measurements as covariates to predict a scalar response in a regression setting, with interest focusing on the most biologically relevant time window of exposure. One example is in panel studies of the health effects of particulate matter (PM), where particle levels are measured over time. In such studies, there are many more values of the functional data than observations in the data set so that regularization of the corresponding functional regression coefficient is necessary for estimation. Additional issues in this setting are the possibility of exposure measurement error and the need to incorporate additional potential confounders, such as meteorological or co-pollutant measures, that themselves may have effects that vary over time. To accommodate all these features, we develop wavelet-based linear mixed distributed lag models that incorporate repeated measures of functional data as covariates into a linear mixed model. A Bayesian approach to model fitting uses wavelet shrinkage to regularize functional coefficients. We show that, as long as the exposure error induces fine-scale variability in the functional exposure profile and the distributed lag function representing the exposure effect varies smoothly in time, the model corrects for the exposure measurement error without further adjustment. Both these conditions are likely to hold in the environmental applications we consider. We examine properties of the method using simulations and apply the method to data from a study examining the association between PM, measured as hourly averages for 1–7 days, and markers of acute systemic inflammation. We use the method to fully control for the effects of confounding by other time-varying predictors, such as temperature and co-pollutants. PMID:20156988

  1. 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

  2. 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

  3. Electronic and magnetic properties of T i4O7 predicted by self-interaction-corrected density functional theory

    NASA Astrophysics Data System (ADS)

    Zhong, X.; Rungger, I.; Zapol, P.; Heinonen, O.

    2015-03-01

    Understanding electronic properties of substoichiometric phases of titanium oxide such as Magnéli phase T i4O7 is crucial in designing and modeling resistive switching devices. Here we present our study on Magnéli phase T i4O7 together with rutile Ti O2 and T i2O3 using density functional theory methods with atomic-orbital-based self-interaction correction (ASIC). We predict a new antiferromagnetic (AF) ground state in the low temperature (LT) phase, and we explain energy difference with a competing AF state using a Heisenberg model. The predicted energy ordering of these states in the LT phase is calculated to be robust in a wide range of modeled isotropic strain. We have also investigated the dependence of the electronic structures of the Ti-O phases on stoichiometry. The splitting of titanium t2 g orbitals is enhanced with increasing oxygen deficiency as Ti-O is reduced. The electronic properties of all these phases can be reasonably well described by applying ASIC with a "standard" value for transition metal oxides of the empirical parameter α of 0.5 representing the magnitude of the applied self-interaction correction.

  4. 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.

  5. Band-gap corrected density functional theory calculations for InAs/GaSb type II superlattices

    SciTech Connect

    Wang, Jianwei; Zhang, Yong

    2014-12-07

    We performed pseudopotential based density functional theory (DFT) calculations for GaSb/InAs type II superlattices (T2SLs), with bandgap errors from the local density approximation mitigated by applying an empirical method to correct the bulk bandgaps. Specifically, this work (1) compared the calculated bandgaps with experimental data and non-self-consistent atomistic methods; (2) calculated the T2SL band structures with varying structural parameters; (3) investigated the interfacial effects associated with the no-common-atom heterostructure; and (4) studied the strain effect due to lattice mismatch between the two components. This work demonstrates the feasibility of applying the DFT method to more exotic heterostructures and defect problems related to this material system.

  6. 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.

  7. Hydrogen storage on metal oxide model clusters using density-functional methods and reliable van der Waals corrections.

    PubMed

    Gebhardt, Julian; Viñes, Francesc; Bleiziffer, Patrick; Hieringer, Wolfgang; Görling, Andreas

    2014-03-21

    We investigate the capability of low-coordinated sites on small model clusters to act as active centers for hydrogen storage. A set of small magic clusters with the formula (XY)6 (X = Mg, Ba, Be, Zn, Cd, Na, Li, B and Y = O, Se, S, F, I, N) and a "drumlike" hexagonal shape showing a low coordination number of three was screened. Oxide clusters turned out to be the most promising candidates for hydrogen storage. For these ionic compounds we explored the suitability of different van der Waals (vdW) corrections to density-functional calculations by comparing the respective H2 physisorption profile to highly accurate CCSD(T) (Coupled Cluster Singles Doubles with perturbative Triples) calculations. The Grimme D3 vdW correction in combination with the Perdew-Burke-Ernzerhof exchange-correlation functional was found to be the best approach compared to CCSD(T) hydrogen physisorption profiles and is, therefore, suited to study these and other light metal oxide systems. H2 adsorption on sites of oxide model clusters is found to meet the adsorption energy criteria for H2 storage, with bond strengths ranging from 0.15 to 0.21 eV. Energy profiles and estimates of kinetic constants for the H2 splitting reaction reveal that H2 is likely to be adsorbed molecularly on sites of (MgO)6, (BaO)6, and (BeO)6 clusters, suggesting a rapid H2 uptake/release at operating temperatures and moderate pressures. The small mass of beryllium and magnesium makes such systems appealing for meeting the gravimetric criterion for H2 storage. PMID:24499810

  8. DNA Partitioning in Confining Nanofluidic Slits

    NASA Astrophysics Data System (ADS)

    Greenier, Madeline; Levy, Stephen

    We measure the partitioning of double stranded DNA molecules in moderately and strongly confining nanofluidic slit-like structures. Using fluorescent microscopy, the free energy penalty of confinement is inferred by comparing the concentration of DNA molecules in adjoining slits of different depths. These depths range in size from several persistence lengths to the DNA molecule's radius of gyration. The partition coefficient is determined as a function of the slit depth, DNA contour length, and DNA topology. We compare our results to theory and Monte Carlo simulations that predict the loss of free energy for ideal and semiflexible excluded volume polymers confined between parallel plates.

  9. [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

  10. 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. PMID:23039692

  11. Compton backscattered and primary X-rays from solar flares: angle dependent Green's function correction for photospheric albedo

    NASA Astrophysics Data System (ADS)

    Kontar, E. P.; MacKinnon, A. L.; Schwartz, R. A.; Brown, J. C.

    2006-02-01

    The observed hard X-ray (HXR) flux spectrum I(ɛ) from solar flares is a combination of primary bremsstrahlung photons I_P(ɛ) with a spectrally modified component from photospheric Compton backscatter of downward primary emission. The latter can be significant, distorting or hiding the true features of the primary spectrum which are key diagnostics for acceleration and propagation of high energy electrons and of their energy budget. For the first time in solar physics, we use a Green's function approach to the backscatter spectral deconvolution problem, constructing a Green's matrix including photoelectric absorption. This approach allows spectrum-independent extraction of the primary spectrum for several HXR flares observed by the Ramaty High Energy Solar Spectroscopic Imager (RHESSI). We show that the observed and primary spectra differ very substantially for flares with hard spectra close to the disk centre. We show in particular that the energy dependent photon spectral index γ (ɛ)=-d log I/d log ɛ is very different for I_P(ɛ) and for I(ɛ) and that inferred mean source electron spectra F(E) differ greatly. Even for a forward fitting of a parametric F(E) to the data, a clear low-energy cutoff required to fit I(ɛ) essentially disappears when the fit is to I_P(ɛ) - i.e. when albedo correction is included. The self-consistent correction for backscattered photons is thus shown to be crucial in determining the energy spectra of flare accelerated electrons, and hence their total number and energy.

  12. An Efficient Simulation Budget Allocation Method Incorporating Regression for Partitioned Domains*

    PubMed Central

    Brantley, Mark W.; Lee, Loo Hay; Chen, Chun-Hung; Xu, Jie

    2014-01-01

    Simulation can be a very powerful tool to help decision making in many applications but exploring multiple courses of actions can be time consuming. Numerous ranking & selection (R&S) procedures have been developed to enhance the simulation efficiency of finding the best design. To further improve efficiency, one approach is to incorporate information from across the domain into a regression equation. However, the use of a regression metamodel also inherits some typical assumptions from most regression approaches, such as the assumption of an underlying quadratic function and the simulation noise is homogeneous across the domain of interest. To extend the limitation while retaining the efficiency benefit, we propose to partition the domain of interest such that in each partition the mean of the underlying function is approximately quadratic. Our new method provides approximately optimal rules for between and within partitions that determine the number of samples allocated to each design location. The goal is to maximize the probability of correctly selecting the best design. Numerical experiments demonstrate that our new approach can dramatically enhance efficiency over existing efficient R&S methods. PMID:24936099

  13. 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

  14. Hyperprolactinemia inhibits natural killer (NK) cell function in vivo and its bromocriptine treatment not only corrects it but makes it more efficient.

    PubMed

    Vidaller, A; Guadarrama, F; Llorente, L; Méndez, J B; Larrea, F; Villa, A R; Alarcón-Segovia, D

    1992-05-01

    We studied NK cell function in eight patients with pathological hyperprolactinemia by measuring 51Cr release by K562 cells exposed to their mononuclear cells and found it decreased compared to normal controls (P less than 0.01). Bromocriptine (BrC) treatment corrected NK function but also made it more efficient at 12:1 than at 25:1 or 50:1 effector:target ratios (ANOVA; P = 0.01). The study of NK cell function in agarose revealed that its decrease in hyperprolactinemia is due to their low active binding to target cells, active killing, and recycling capacity. BrC tended to correct them but also increased recycling capacity to levels higher than those of controls (P less than 0.05). Sequential studies in three hyperprolactinemic patients before and after BrC showed correction of NK function within 1 week but its increased efficiency at the 12:1 effector:target ratio required 8 weeks. We conclude that hyperprolactinemia decreases NK cell function. BrC corrects this by decreasing prolactin levels but also makes NK function more efficient by increasing the capacity of NK cells to recycle after killing. PMID:1400902

  15. Successes and failures of Hubbard-corrected density functional theory: The case of Mg doped LiCoO2

    NASA Astrophysics Data System (ADS)

    Santana, Juan A.; Kim, Jeongnim; Kent, P. R. C.; Reboredo, Fernando A.

    2014-10-01

    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.

  16. Successes and failures of Hubbard-corrected density functional theory: the case of Mg doped LiCoO2.

    PubMed

    Santana, Juan A; Kim, Jeongnim; Kent, P R C; 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. PMID:25362331

  17. Successes and failures of Hubbard-corrected density functional theory. The case of Mg doped LiCoO2

    DOE PAGESBeta

    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

  18. 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

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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...

  4. 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

  5. Crystal/liquid partitioning in augite - Effects of cooling rate

    NASA Technical Reports Server (NTRS)

    Gamble, R. P.; Taylor, L. A.

    1980-01-01

    The partitioning of major and minor elements between augite and melt was determined as a function of cooling rate for two high-titanium basalt compositions. The results of this study of lunar rock systems 10017 and 75055 were compared with the results of other kinetic studies of augite-liquid partitioning in other rock systems. It was found that the partitioning of major elements (i.e., Ca, Fe, Mg) is essentially rate independent and is insensitive to bulk rock composition and to the nature and order of appearance of coexisting phases for cooling rates of less than 100 C/hr. The partitioning behavior of minor elements (i.e., Al, Cr, Ti) for the same range of cooling rates is complex, being dependent on cooling rate and bulk rock composition. Consideration of these factors is important when augite chemistry and/or partitioning behavior are used in modeling certain magmatic processes or in estimating the thermal history of basaltic rocks.

  6. Chemical amplification based on fluid partitioning

    DOEpatents

    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.

  7. 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.

  8. Spectroscopic constants of diatomic molecules computed correcting Hartree-Fock or general-valence-bond potential-energy curves with correlation-energy functionals

    NASA Astrophysics Data System (ADS)

    Pérez-Jordá, José M.; San-Fabián, Emilio; Moscardó, Federico

    1992-04-01

    The Kohn-Sham energy with exact exchange [using the exact Hartree-Fock (HF) exchange but an approximate correlation-energy functional] may be computed very accurately by adding the correlation obtained from the HF density to the total HF energy. Three density functionals are used: local spin density (LSD), LSD with self-interaction correction, and LSD with generalized gradient correction. This scheme has been extended (Lie-Clementi, Colle-Salvetti, and Moscardo-San-Fabian) to be used with general-valence-bond (GVB) energies and wave functions, so that the extra correlation included in the GVB energy is not counted again. The effect of all these approximate correlations on HF or GVB spectroscopic constants (Re,ωe, and De) is studied. Approximate relations showing how correlation affects them are derived, and may be summarized as follows: (1) the effect on Re and ωe depends only on the correlation derivative at Re, and (2) the effect on De depends mainly on the correlation difference between quasidissociated and equilibrium geometries. A consequence is that all the correlation corrections tested here give larger ωe and De and shorter Re than the uncorrected HF or GVB values. This trend is correct for De for both HF and GVB. For Re and ωe, it is correct in most cases for GVB, but it often fails for the HF cases. A comparison is made with Kohn-Sham calculations with both exchange and correlation approximated. As a final conclusion, it is found that, within the present scheme, a qualitatively correct HF or GVB potential-energy curve, together with a correlation-energy approximation with correct dissociation behavior, is crucial for obtaining good estimates of spectroscopic constants.

  9. 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

  10. 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.

  11. Energy hyperspace for stacking interaction in AU/AU dinucleotide step: Dispersion-corrected density functional theory study.

    PubMed

    Mukherjee, Sanchita; Kailasam, Senthilkumar; Bansal, Manju; Bhattacharyya, Dhananjay

    2014-01-01

    Double helical structures of DNA and RNA are mostly determined by base pair stacking interactions, which give them the base sequence-directed features, such as small roll values for the purine-pyrimidine steps. Earlier attempts to characterize stacking interactions were mostly restricted to calculations on fiber diffraction geometries or optimized structure using ab initio calculations lacking variation in geometry to comment on rather unusual large roll values observed in AU/AU base pair step in crystal structures of RNA double helices. We have generated stacking energy hyperspace by modeling geometries with variations along the important degrees of freedom, roll, and slide, which were chosen via statistical analysis as maximally sequence dependent. Corresponding energy contours were constructed by several quantum chemical methods including dispersion corrections. This analysis established the most suitable methods for stacked base pair systems despite the limitation imparted by number of atom in a base pair step to employ very high level of theory. All the methods predict negative roll value and near-zero slide to be most favorable for the purine-pyrimidine steps, in agreement with Calladine's steric clash based rule. Successive base pairs in RNA are always linked by sugar-phosphate backbone with C3'-endo sugars and this demands C1'-C1' distance of about 5.4 Å along the chains. Consideration of an energy penalty term for deviation of C1'-C1' distance from the mean value, to the recent DFT-D functionals, specifically ωB97X-D appears to predict reliable energy contour for AU/AU step. Such distance-based penalty improves energy contours for the other purine-pyrimidine sequences also. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 107-120, 2014. PMID:23722519

  12. Analytical model for macromolecular partitioning during yeast cell division

    PubMed Central

    2014-01-01

    Background Asymmetric cell division, whereby a parent cell generates two sibling cells with unequal content and thereby distinct fates, is central to cell differentiation, organism development and ageing. Unequal partitioning of the macromolecular content of the parent cell — which includes proteins, DNA, RNA, large proteinaceous assemblies and organelles — can be achieved by both passive (e.g. diffusion, localized retention sites) and active (e.g. motor-driven transport) processes operating in the presence of external polarity cues, internal asymmetries, spontaneous symmetry breaking, or stochastic effects. However, the quantitative contribution of different processes to the partitioning of macromolecular content is difficult to evaluate. Results Here we developed an analytical model that allows rapid quantitative assessment of partitioning as a function of various parameters in the budding yeast Saccharomyces cerevisiae. This model exposes quantitative degeneracies among the physical parameters that govern macromolecular partitioning, and reveals regions of the solution space where diffusion is sufficient to drive asymmetric partitioning and regions where asymmetric partitioning can only be achieved through additional processes such as motor-driven transport. Application of the model to different macromolecular assemblies suggests that partitioning of protein aggregates and episomes, but not prions, is diffusion-limited in yeast, consistent with previous reports. Conclusions In contrast to computationally intensive stochastic simulations of particular scenarios, our analytical model provides an efficient and comprehensive overview of partitioning as a function of global and macromolecule-specific parameters. Identification of quantitative degeneracies among these parameters highlights the importance of their careful measurement for a given macromolecular species in order to understand the dominant processes responsible for its observed partitioning. PMID

  13. Properties of noncovalent tetraphenylporphine···C60 dyads as studied by different long-range and dispersion-corrected DFT functionals.

    PubMed

    Amelines-Sarria, Oscar; Basiuk, Vladimir A; Duarte-Alaniz, Víctor; Rivera, Margarita

    2015-11-01

    The noncovalent dyad of tetraphenylporphine and C60 fullerene (H2TPP···C60) and the tetraphenylporphine dimer (H2TPP···H2TPP) were studied by density functional theory (DFT), using functionals that incorporate empirical dispersion correction (DFT-D), functionals that use a long-range correction (LC) scheme, a hybrid functional (B3LYP) and a highly parametrized empirical exchange-correlation functional (M05-2X). The results were compared to X-ray structures and interaction energies reported in previous experimental and theoretical studies. It was found that B3LYP and CAM-B3LYP functionals fail to reproduce the X-ray structures and binding energies of the TPP···C60 system. DFT-D functionals overestimated the π···π energy interactions for both systems, however, the optimized structures agree well with those observed experimentally. The LC-BLYP functional predicts geometries similar to X-ray structures; nevertheless, due to the lack of correction in the dispersion energy, the predicted energies for both model systems are low. On the other hand, the M05-2X functional exhibited the best performance. Both the structures and binding energies calculated with M05-2X are consistent with experimental and theoretical evidence reported by other authors, as well as with our experimental results obtained by means of atomic force microscopy on H2TPP thin films grown on the HOPG/C60 substrate by physical vapor deposition. PMID:26422808

  14. Density-functional approaches to non-bonding interactions: a comparison of dispersion corrections (DFT-D), exchange-hole dipole moment (XDM) theory, and specialized functionals

    SciTech Connect

    Burns, Lori A; Sherrill, David; Vazquez-Mayagoitia, Alvaro; Sumpter, Bobby G

    2011-01-01

    A systematic study of techniques for treating non-covalent interactions within the computationally efficient density functional theory (DFT) framework is presented through comparison to benchmark-quality evaluations of binding strength com- piled for molecular complexes of diverse size and nature. In particular, the effi- cacy of functionals deliberately crafted to encompass long-range forces, a posteri- ori DFT+dispersion corrections (DFT-D2 and DFT-D3), and exchange-hole dipole moment (XDM) theory is assessed against a large collection (469 energy points) of reference interaction energies at the CCSD(T) level of theory extrapolated to the estimated complete basis set limit. The established S22 and JSCH test sets of minimum-energy structures, as well as collections of dispersion-bound (NBC10) and hydrogen-bonded (HBC6) dissociation curves and a pairwise decomposition of a protein-ligand reaction site (HSG), comprise the chemical systems for this work. From evaluations of accuracy, consistency, and efficiency for PBE-D, BP86-D, B97-D, PBE0-D, B3LYP-D, B970-D, M05-2X, M06-2X, B97X-D, B2PLYP-D, XYG3, and B3LYP-XDM methodologies, it is concluded that distinct, often contrasting, groups of these elicit the best performance within the accessible double- or robust triple- basis set regimes and among hydrogen-bonded or dispersion-dominated complexes. For overall results, M05-2X, B97-D3, and B970-D2 yield superior values in conjunc- tion with aug-cc-pVDZ, for a mean absolute deviation of 0.41 0.49 kcal/mol, and B3LYP-D3, B97-D3, B97X-D, and B2PLYP-D3 dominate with aug-cc-pVTZ, af- fording, together with XYG3/6-311+G(3df,2p), a mean absolute deviation of 0.33 0.38 kcal/mol.

  15. 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.

  16. Human Cardiac Function Simulator for the Optimal Design of a Novel Annuloplasty Ring with a Sub-valvular Element for Correction of Ischemic Mitral Regurgitation.

    PubMed

    Baillargeon, Brian; Costa, Ivan; Leach, Joseph R; Lee, Lik Chuan; Genet, Martin; Toutain, Arnaud; Wenk, Jonathan F; Rausch, Manuel K; Rebelo, Nuno; Acevedo-Bolton, Gabriel; Kuhl, Ellen; Navia, Jose L; Guccione, Julius M

    2015-06-01

    Ischemic mitral regurgitation is associated with substantial risk of death. We sought to: (1) detail significant recent improvements to the Dassault Systèmes human cardiac function simulator (HCFS); (2) use the HCFS to simulate normal cardiac function as well as pathologic function in the setting of posterior left ventricular (LV) papillary muscle infarction; and (3) debut our novel device for correction of ischemic mitral regurgitation. We synthesized two recent studies of human myocardial mechanics. The first study presented the robust and integrative finite element HCFS. Its primary limitation was its poor diastolic performance with an LV ejection fraction below 20% caused by overly stiff ex vivo porcine tissue parameters. The second study derived improved diastolic myocardial material parameters using in vivo MRI data from five normal human subjects. We combined these models to simulate ischemic mitral regurgitation by computationally infarcting an LV region including the posterior papillary muscle. Contact between our novel device and the mitral valve apparatus was simulated using Dassault Systèmes SIMULIA software. Incorporating improved cardiac geometry and diastolic myocardial material properties in the HCFS resulted in a realistic LV ejection fraction of 55%. Simulating infarction of posterior papillary muscle caused regurgitant mitral valve mechanics. Implementation of our novel device corrected valve dysfunction. Improvements in the current study to the HCFS permit increasingly accurate study of myocardial mechanics. The first application of this simulator to abnormal human cardiac function suggests that our novel annuloplasty ring with a sub-valvular element will correct ischemic mitral regurgitation. PMID:25984248

  17. 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

  18. 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

  19. 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.}

  20. Probabilistic framework for network partition

    NASA Astrophysics Data System (ADS)

    Li, Tiejun; Liu, Jian; E, Weinan

    2009-08-01

    Given a large and complex network, we would like to find the partition of this network into a small number of clusters. This question has been addressed in many different ways. In a previous paper, we proposed a deterministic framework for an optimal partition of a network as well as the associated algorithms. In this paper, we extend this framework to a probabilistic setting, in which each node has a certain probability of belonging to a certain cluster. Two classes of numerical algorithms for such a probabilistic network partition are presented and tested. Application to three representative examples is discussed.

  1. 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

  2. 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

  3. 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

  4. The Digital Correction Unit: A data correction/compaction chip

    SciTech Connect

    MacKenzie, S.; Nielsen, B.; Paffrath, L.; Russell, J.; Sherden, D.

    1986-10-01

    The Digital Correction Unit (DCU) is a semi-custom CMOS integrated circuit which corrects and compacts data for the SLD experiment. It performs a piece-wise linear correction to data, and implements two separate compaction algorithms. This paper describes the basic functionality of the DCU and its correction and compaction algorithms.

  5. 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. PMID:25129167

  6. Rigidity-Preserving Team Partitions in Multiagent Networks.

    PubMed

    Carboni, Daniela; Williams, Ryan K; Gasparri, Andrea; Ulivi, Giovanni; Sukhatme, Gaurav S

    2015-12-01

    Motivated by the strong influence network rigidity has on collaborative systems, in this paper, we consider the problem of partitioning a multiagent network into two sub-teams, a bipartition, such that the resulting sub-teams are topologically rigid. In this direction, we determine the existence conditions for rigidity-preserving bipartitions, and provide an iterative algorithm that identifies such partitions in polynomial time. In particular, the relationship between rigid graph partitions and the previously identified Z-link edge structure is given, yielding a feasible direction for graph search. Adapting a supergraph search mechanism, we then detail a methodology for discerning graphs cuts that represent valid rigid bipartitions. Next, we extend our methods to a decentralized context by exploiting leader election and an improved graph search to evaluate feasible cuts using only local agent-to-agent communication. Finally, full algorithm details and pseudocode are provided, together with simulation results that verify correctness and demonstrate complexity. PMID:25561600

  7. Graph Partitioning and Sequencing Software

    Energy Science and Technology Software Center (ESTSC)

    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

  8. Rational function representation of flap noise spectra including correction for reflection effects. [acoustic properties of engine exhaust jets deflected for externally blown flaps

    NASA Technical Reports Server (NTRS)

    Miles, J. H.

    1974-01-01

    A rational function is presented for the acoustic spectra generated by deflection of engine exhaust jets for under-the-wing and over-the-wing versions of externally blown flaps. The functional representation is intended to provide a means for compact storage of data and for data analysis. The expressions are based on Fourier transform functions for the Strouhal normalized pressure spectral density, and on a correction for reflection effects based on the N-independent-source model of P. Thomas extended by use of a reflected ray transfer function. Curve fit comparisons are presented for blown flap data taken from turbofan engine tests and from large scale cold-flow model tests. Application of the rational function to scrubbing noise theory is also indicated.

  9. ESFRAD. FORTRAN code for calculation of QED corrections to polarized ep-scattering by the electron structure function method

    SciTech Connect

    A. Afanasev, I. Akushevich, A. Ilyichev, N. Merenkov

    2003-09-01

    The main features of the electron structure method for calculations of the higher order QED radiative effects to polarized deep-inelastic ep-scattering are presented. A new FORTRAN code ESFRAD based on this method was developed. A detailed quantitative comparison between the results of ESFRAD and other methods implemented in the codes POLRAD and RADGEN for calculation of the higher order radiative corrections is performed.

  10. The impact of physiologic noise correction applied to functional MRI of pain at 1.5 & 3.0 Tesla

    PubMed Central

    Vogt, Keith M.; Ibinson, James W.; Schmalbrock, Petra; Small, Robert H.

    2011-01-01

    This study quantified the impact of the well-known physiologic noise correction algorithm RETROICOR applied to a pain FMRI experiment at two field strengths: 1.5 and 3.0 Tesla (T). In the 1.5 T acquisition, there was an 8.2% decrease in timecourse variance (σ) and a 227% improvement in average model fit (increase in mean R2 a). In the 3.0 T acquisition, significantly greater improvements were seen: a 10.4% decrease in σ and 240% increase in mean R2 a. End-tidal carbon dioxide (ETCO2) data was also collected during scanning and used to account for low-frequency changes in cerebral blood flow; however, the impact of this correction was trivial compared to applying RETROICOR. Comparison between two implementations of RETROICOR demonstrated that oversampled physiologic data can be applied either by down-sampling or modification of the timing in the RETROICOR algorithm with equivalent results. Further, there was no significant effect from manually aligning the physiologic data with corresponding image slices from an interleaved acquisition, indicating that RETROICOR accounts for timing differences between physiologic changes and MR signal changes. These findings suggest that RETROICOR correction, as it is commonly implemented, should be included as part of the data analysis for pain FMRI studies performed at 1.5 and 3.0 T. PMID:21571474

  11. 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

  12. 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.

  13. 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.

  14. The importance of self-interaction and nonlocal exchange corrections to the density functional theory of intracavity electrons in Na-doped sodalites

    NASA Astrophysics Data System (ADS)

    Blake, Nick P.; Metiu, Horia

    1999-04-01

    Electrons that are confined to zeolite cavities are modeled using a simplified pseudopotential scheme to represent the interaction of the electrons with both the sodalite framework and the Na+ ions. By comparing theory with recent experimental studies of G centers in Na-doped NaBr-SOD it is demonstrated that restricted forms of density functional theory, where two electrons are forced to pair in the same Kohn-Sham orbital, fail to correctly predict the true nature of the singlet, (spin unpolarized), G center. Electron confinement leads to generalized gradient corrections to the exchange of 0.74 eV and self-interaction corrections (SIC) of 0.7 eV over calculations performed in the local spin density approximation (LSDA). Only the self-interaction corrected generalized gradient approximation and the unrestricted Hartree-Fock approximation are in accord with experiment for the relative stability of the triplet (spin polarized) state. The unrestricted Hartree-Fock method is used to show that G-center absorptions will be blueshifted with respect to absorptions due to the isolated F centers. Constructing a Hubbard Hamiltonian we show that the exchange coupling ranges in values from 2.3 meV(UHF) to 3.6 meV(SIC-LSDA) corresponding to Neel temperatures that range from 27 to 41 K in agreement with experiment.

  15. Partitioning networks into communities by message passing.

    PubMed

    Lai, Darong; Nardini, Christine; Lu, Hongtao

    2011-01-01

    Community structures are found to exist ubiquitously in a number of systems conveniently represented as complex networks. Partitioning networks into communities is thus important and crucial to both capture and simplify these systems' complexity. The prevalent and standard approach to meet this goal is related to the maximization of a quality function, modularity, which measures the goodness of a partition of a network into communities. However, it has recently been found that modularity maximization suffers from a resolution limit, which prevents its effectiveness and range of applications. Even when neglecting the resolution limit, methods designed for detecting communities in undirected networks cannot always be easily extended, and even less directly applied, to directed networks (for which specifically designed community detection methods are very limited). Furthermore, real-world networks are frequently found to possess hierarchical structure and the problem of revealing such type of structure is far from being addressed. In this paper, we propose a scheme that partitions networks into communities by electing community leaders via message passing between nodes. Using random walk on networks, this scheme derives an effective similarity measure between nodes, which is closely related to community memberships of nodes. Importantly, this approach can be applied to a very broad range of networks types. In fact, the successful validation of the proposed scheme on real and synthetic networks shows that this approach can effectively (i) address the problem of resolution limit and (ii) find communities in both directed and undirected networks within a unified framework, including revealing multiple levels of robust community partitions. PMID:21405752

  16. Self-Oscillated Ultrasonic Stepping Motor with Function of Angular Displacement Self-Correction: Nonaxisymmetric ((2,1))-Mode Thin Disk Motor

    NASA Astrophysics Data System (ADS)

    Chen, Xiaoduo; Aoyagi, Manabu; Kusakabe, Chiharu; Tomikawa, Yoshiro

    1994-05-01

    This paper deals with experimental investigation of a self-oscillated open-loop driving motor using a slitted rotor and a nonaxisymmetric ((2,1)) vibration mode thin annular disk which has four projection teeth on its inner circumference. This motor is suitable for application to watches because it can be constructed in a thin configuration and the slitted rotor enables the self-correction of angular displacement. In the experiment, two types of self-oscillation circuits were investigated for suitable driving. The results were that the self-oscillated driving motor could be achieved by using an operational amplifier and some inverter IC elements. That is, the self-correction function of the angular displacement of a stepping motor was confirmed in the case of the nonaxisymmetric-mode disk motor.

  17. 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.

  18. Looking for simple correction functions between the mean radiant temperature from the "standard black globe" and the "six-directional" techniques in Taiwan

    NASA Astrophysics Data System (ADS)

    Kántor, Noémi; Kovács, Attila; Lin, Tzu-Ping

    2015-07-01

    Mean radiant temperature ( T mrt) values were calculated and compared to each other in Taiwan based on the six-directional and globe techniques. In the case of the six-directional technique (measurements with pyranometers and pyrgeometers), two different T mrt values were calculated: one representing the radiation load on a standing man [ T mrt(st)] and the other which refers to a spherical reference shape [ T mrt(sp)]. Moreover, T mrt( T g ) was obtained through the globe thermometer technique applying the standard black globe. Comparing T mrt values based on the six-directional technique but with different reference shapes revealed that the difference was always in the +/-5 °C domain. Of the cases, 75 % fell into the +/-5 °C Delta Tmrt range when we compared different techniques with similar reference shapes [ T mrt(sp) and T mrt( T g )] and only 69 % when we compared the different techniques with different reference shapes [ T mrt(st) and T mrt( T g )]. Based on easily accessible factors, simple correction functions were determined to make the T mrt( T g ) values of already existing outdoor thermal comfort databases comparable with other databases which involve sixdirectional T mrt. The corrections were conducted directly between the T mrt( T g ) and T mrt(sp) values and also indirectly, i.e., by using the values of T g to reduce the differences between T mrt(sp) and T mrt( T g ). Both correction methods resulted in considerable improvement and reduced the differences between the T mrt(sp) and the T mrt( T g ) values. However, validations with an independent database from Hungary revealed that it is not suggested to apply the correction functions under totally different background climate conditions.

  19. Qubits in phase space: Wigner-function approach to quantum-error correction and the mean-king problem

    SciTech Connect

    Paz, Juan Pablo; Roncaglia, Augusto Jose; Saraceno, Marcos

    2005-07-15

    We analyze and further develop a method to represent the quantum state of a system of n qubits in a phase-space grid of NxN points (where N=2{sup n}). The method, which was recently proposed by Wootters and co-workers (Gibbons et al., Phys. Rev. A 70, 062101 (2004).), is based on the use of the elements of the finite field GF(2{sup n}) to label the phase-space axes. We present a self-contained overview of the method, we give insights into some of its features, and we apply it to investigate problems which are of interest for quantum-information theory: We analyze the phase-space representation of stabilizer states and quantum error-correction codes and present a phase-space solution to the so-called mean king problem.

  20. 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

  1. 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.

  2. New Instrumentation for Phase Partitioning

    NASA Technical Reports Server (NTRS)

    Harris, J. M.

    1985-01-01

    Cells and molecules can be purified by partitioning between the two immiscible liquid phases formed by aqueous solutions of poly/ethylene glycol and dextran. Such purification can be more selective, higher yielding, and less destructive to sensitive biological materials than other available techniques. Earth's gravitational field is a hindering factor as it causes sedimentation of particles to be purified and shear-induced particle randomization. The present proposal is directed toward developing new instrumentation for performing phase partitioning both on Earth and in microgravity.

  3. 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.

  4. 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

  5. Machine-learning approach for one- and two-body corrections to density functional theory: Applications to molecular and condensed water

    NASA Astrophysics Data System (ADS)

    Bartók, Albert P.; Gillan, Michael J.; Manby, Frederick R.; Csányi, Gábor

    2013-08-01

    We show how machine learning techniques based on Bayesian inference can be used to enhance the computer simulation of molecular materials, focusing here on water. We train our machine-learning algorithm using accurate, correlated quantum chemistry, and predict energies and forces in molecular aggregates ranging from clusters to solid and liquid phases. The widely used electronic-structure methods based on density functional theory (DFT) by themselves give poor accuracy for molecular materials like water, and we show how our techniques can be used to generate systematically improvable one- and two-body corrections to DFT with modest extra resources. The resulting corrected DFT scheme is considerably more accurate than uncorrected DFT for the relative energies of small water clusters and different ice structures and significantly improves the description of the structure and dynamics of liquid water. However, our results for ice structures and the liquid indicate that beyond-two-body DFT errors cannot be ignored, and we suggest how our machine-learning methods can be further developed to correct these errors.

  6. Hybrid two-dimensional navigator correction: a new technique to suppress respiratory-induced physiological noise in multi-shot echo-planar functional MRI

    PubMed Central

    Barry, Robert L.; Klassen, L. Martyn; Williams, Joy M.; Menon, Ravi S.

    2008-01-01

    A troublesome source of physiological noise in functional magnetic resonance imaging (fMRI) is due to the spatio-temporal modulation of the magnetic field in the brain caused by normal subject respiration. fMRI data acquired using echo-planar imaging is very sensitive to these respiratory-induced frequency offsets, which cause significant geometric distortions in images. Because these effects increase with main magnetic field, they can nullify the gains in statistical power expected by the use of higher magnetic fields. As a study of existing navigator correction techniques for echo-planar fMRI has shown that further improvements can be made in the suppression of respiratory-induced physiological noise, a new hybrid two-dimensional (2D) navigator is proposed. Using a priori knowledge of the slow spatial variations of these induced frequency offsets, 2D field maps are constructed for each shot using spatial frequencies between ±0.5 cm−1 in k-space. For multi-shot fMRI experiments, we estimate that the improvement of hybrid 2D navigator correction over the best performance of one-dimensional navigator echo correction translates into a 15% increase in the volume of activation, 6% and 10% increases in the maximum and average t-statistics, respectively, for regions with high t-statistics, and 71% and 56% increases in the maximum and average t-statistics, respectively, in regions with low t-statistics due to contamination by residual physiological noise. PMID:18024159

  7. Crystal and electronic structure of BiTeI, AuTeI, and PdTeI compounds: A dispersion-corrected density-functional study

    NASA Astrophysics Data System (ADS)

    Güler-Kılıç, Sümeyra; Kılıç, ćetin

    2015-06-01

    Semilocal and dispersion-corrected density-functional calculations have been performed to study the crystal structure, equation of state, and electronic structure of metal tellurohalides with chemical formula MeTeI where Me=Bi, Au, or Pd. A comparative investigation of the results of these calculations is conducted which reveals the role of van der Waals attraction. It is shown that the prediction of crystal structure of metal tellurohalides is systematically improved thanks to the inclusion of van der Waals dispersion. It is found for BiTeI and AuTeI that the energy versus volume curve is anomalously flat in the vicinity of equilibrium volume and the calculated equation of state has an excessively steep slope in the low-pressure region; these are also fixed in the dispersion-corrected calculations. Analysis based on the computation of the volume and axial compressibilities shows that predicting the anisotropy of BiTeI via the semilocal calculations yields an unrealistic result, whereas the results of dispersion-corrected calculations agree with the experimental compressibility data. Our calculations render that BiTeI (AuTeI) is a narrow band gap semiconductor with Rashba-type spin splitting at the band edges (with an indirect band gap) while PdTeI is a metal with relatively low density of states at the Fermi level. The band gaps of BiTeI and AuTeI obtained via semilocal (dispersion-corrected) calculations are found to be greater (smaller) than the respective experimental values, which is against (in line with) the expected trend. Similarly, the Rashba parameters of BiTeI are bracketed by the respective values obtained via semilocal and dispersion-corrected calculations, e.g., a larger value for the Rashba parameter αR is obtained in association with the reduction of the band gap caused by modification of the crystal structure owing to van der Waals attraction. Excellent agreement with the experimental Rashba parameters is obtained via interpolation of the

  8. 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.

  9. 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

  10. Spin crossover transition of Fe(phen)2(NCS)2: periodic dispersion-corrected density-functional study.

    PubMed

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

    2012-04-28

    Periodic dispersion corrected DFT calculations have been performed to study the spin-crossover transition of Fe(phen)(2)(NCS)(2) in the molecular and in the crystalline state. We show that London dispersion interactions play a crucial role in the cohesion of the crystals. Based on calculations of vibrational eigenstates of the isolated molecule and of the crystalline phase in both the low- and high-spin states, the transition entropies and enthalpies have been calculated. We demonstrate that, due to the stabilization of the low-spin state by intermolecular dispersion forces, the transition enthalpy at the transition temperature is larger for the crystalline phase in comparison with an isolated molecule. The effective coordination number of the nitrogen atoms of the ligands around the iron atom has been identified as the order parameter driving the quasi-reversible low-spin to high-spin transition in the crystal. Finally, using constrained geometry relaxations at fixed values of the coordination number, we computed the energy barrier of the LS to HS transition and found it to be in a reasonable agreement with the experimental value. PMID:22415338

  11. 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

  12. Modeling and analysis of sampling artifacts in measurements of gas-particle partitioning of semivolatile organic contaminants using filter-sorbent samplers

    NASA Astrophysics Data System (ADS)

    Wang, Xinke; Bi, Chenyang; Xu, Ying

    2015-09-01

    Measurements of gas/particle partition coefficients for semivolatile organic compounds (SVOCs) using filter-sorbent samplers can be biased if a fraction of gas-phase mass is measured erroneously as particle-phase due to sorption of SVOC gases to the filter, or, if a fraction of particle-phase mass is measured erroneously as gas-phase due to penetration of particles into the sorbent. A fundamental mechanistic model to characterize the air sampling process with filter-sorbent samplers for SVOCs was developed and partially validated. The potential sampling artifacts associated with measurements of gas-particle partitioning were examined for 19 SVOCs. Positive sampling bias (i.e., overestimation of gas/particle partition coefficients) was observed for almost all the SVOCs. For certain compounds, the measured partition coefficient was several orders of magnitude greater than the presumed value. It was found that the sampling artifacts can be ignored when the value of log [Kf /(Kp ṡCp , a) ] is less than 7. By normalizing the model, general factors that influence the sampling artifacts were investigated. Correlations were obtained between the dimensionless time required for the gas-phase SVOCs within the filter to reach steady state (Ts,s∗) and the chemical Vp values, which can be used to estimate appropriate sampling time. The potential errors between measured and actual gas/particle partition coefficients of SVOCs as a function of sampling velocity and time were calculated and plotted for a range of SVOCs (vapor pressures: 10-8 ∼ 10-3 Pa). These plots were useful in identifying bias from the sampling in previously-completed field measurements. Penetration of particles into the sorbent may result in significant underestimation of the partition coefficient for particles in the size range between 10 nm and 2 μm. For most of the selected compounds, backup filters can be used to correct artifacts effectively. However, for some compounds with very low vapor pressure

  13. Monomial Crystals and Partition Crystals

    NASA Astrophysics Data System (ADS)

    Tingley, Peter

    2010-04-01

    Recently Fayers introduced a large family of combinatorial realizations of the fundamental crystal B(Λ0) for ^sln, where the vertices are indexed by certain partitions. He showed that special cases of this construction agree with the Misra-Miwa realization and with Berg's ladder crystal. Here we show that another special case is naturally isomorphic to a realization using Nakajima's monomial crystal.

  14. Set covering, partition and packing

    SciTech Connect

    Hulme, B.L.; Baca, L.S.

    1984-03-01

    Set covering problems are known to be solvable by Boolean algebraic methods. This report shows that set partition and set packing problems can be solved by the same algebraic methods because these problems can be converted into covering problems. Many applications are possible including security patrol assignment which is used as an example.

  15. 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...

  16. A nucleotide-analogue-induced gain of function corrects the error-prone nature of human DNA polymerase iota.

    PubMed

    Ketkar, Amit; Zafar, Maroof K; Banerjee, Surajit; Marquez, Victor E; Egli, Martin; Eoff, Robert L

    2012-06-27

    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 ι) is the most error-prone. In the current study, we elucidate the molecular basis for improving the fidelity of hpol ι through use of the fixed-conformation nucleotide North-methanocarba-2'-deoxyadenosine triphosphate (N-MC-dATP). Three crystal structures were solved of hpol ι in complex with DNA containing a template 2'-deoxythymidine (dT) paired with an incoming dNTP or modified nucleotide triphosphate. The ternary complex of hpol ι 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 ι. 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 ι by preventing the Hoogsteen base-pairing mode normally observed for hpol ι-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. PMID:22632140

  17. 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.

  18. 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.

  19. 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.

  20. Increasing the applicability of density functional theory. V. X-ray absorption spectra with ionization potential corrected exchange and correlation potentials.

    PubMed

    Verma, Prakash; Bartlett, Rodney J

    2016-07-21

    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. PMID:27448875

  1. 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. PMID:26744089

  2. 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.

  3. Massive Idiosyncratic Exon Skipping Corrects the Nonsense Mutation in Dystrophic Mouse Muscle and Produces Functional Revertant Fibers by Clonal Expansion

    PubMed Central

    Lu, Q.L.; Morris, G.E.; Wilton, S.D.; Ly, T.; Artem'yeva, O.V.; Strong, P.; Partridge, T.A.

    2000-01-01

    Conventionally, nonsense mutations within a gene preclude synthesis of a full-length functional protein. Obviation of such a blockage is seen in the mdx mouse, where despite a nonsense mutation in exon 23 of the dystrophin gene, occasional so-called revertant muscle fibers are seen to contain near-normal levels of its protein product. Here, we show that reversion of dystrophin expression in mdx mice muscle involves unprecedented massive loss of up to 30 exons. We detected several alternatively processed transcripts that could account for some of the revertant dystrophins and could not detect genomic deletion from the region commonly skipped in revertant dystrophin. This, together with exon skipping in two noncontiguous regions, favors aberrant splicing as the mechanism for the restoration of dystrophin, but is hard to reconcile with the clonal idiosyncrasy of revertant dystrophins. Revertant dystrophins retain functional domains and mediate plasmalemmal assembly of the dystrophin-associated glycoprotein complex. Physiological function of revertant fibers is demonstrated by the clonal growth of revertant clusters with age, suggesting that revertant dystrophin could be used as a guide to the construction of dystrophin expression vectors for individual gene therapy. The dystrophin gene in the mdx mouse provides a favored system for study of exon skipping associated with nonsense mutations. PMID:10704448

  4. 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.

  5. 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.

  6. 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

  7. Insights into the catalytic mechanism of coral allene oxide synthase: a dispersion corrected density functional theory study.

    PubMed

    Bushnell, Eric A C; Gherib, Rami; Gauld, James W

    2013-06-01

    In this present work the mechanism by which cAOS catalyzes the formation of allene oxide from its hydroperoxy substrate was computationally investigated by using a DFT-chemical cluster approach. In particular, the effects of dispersion interactions and DFT functional choice (M06, B3LYP, B3LYP*, and BP86), as well as the roles of multistate reactivity and the tyrosyl proximal ligand, were examined. It is observed that the computed relative free energies of stationary points along the overall pathway are sensitive to the choice of DFT functional, while the mechanism obtained is generally not. Large reductions in relative free energies for stationary points along the pathway (compared to the initial reactant complex) of on average 46.3 and 97.3 kJ mol(-1) for the doublet and quartet states, respectively, are observed upon going from the M06 to BP86 functional. From results obtained by using the B3LYP* method, well-tested previously on heme-containing systems, the mechanism of cAOS appears to occur with considerably higher Gibbs free energies than that for the analogous pathway in pAOS, possibly due to the presence of a ligating tyrosyl residue in cAOS. Furthermore, at the IEFPCM-B3LYP*/6-311+G(2df,p)//B3LYP/BS1 level of theory the inclusion of dispersion effects leads to the suggestion that the overall mechanism of cAOS could occur without the need for spin inversion. PMID:23676102

  8. Correction of the occlusal and functional sequelae of mandibular condyle fractures using orthodontic mini-implant molar intrusion.

    PubMed

    Cousley, Richard R J; Gibbons, Andrew J

    2014-09-01

    We report on the non-surgical management of an adult female whose bilateral mandibular condylar fractures had resulted in a clockwise (posterior) mandibular rotation, limitation of mandibular movements and increased occlusal loading on the molar teeth. She refused maxillary surgery and was treated with a minimally-invasive approach, involving orthodontic fixed appliances and mini-implant intrusion of the maxillary molar teeth. This provided both occlusal and functional improvements, including a significant increase in the inter-incisal distance, which were stable after one year of retention. PMID:24521751

  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. 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).

  11. [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

  12. 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.

  13. 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.

  14. Dispersion-correcting potentials can significantly improve the bond dissociation enthalpies and noncovalent binding energies predicted by density-functional theory

    SciTech Connect

    DiLabio, Gino A.; Koleini, Mohammad

    2014-05-14

    Dispersion-correcting potentials (DCPs) are atom-centered Gaussian functions that are applied in a manner that is similar to effective core potentials. Previous work on DCPs has focussed on their use as a simple means of improving the ability of conventional density-functional theory methods to predict the binding energies of noncovalently bonded molecular dimers. We show in this work that DCPs developed for use with the LC-ωPBE functional along with 6-31+G(2d,2p) basis sets are capable of simultaneously improving predicted noncovalent binding energies of van der Waals dimer complexes and covalent bond dissociation enthalpies in molecules. Specifically, the DCPs developed herein for the C, H, N, and O atoms provide binding energies for a set of 66 noncovalently bonded molecular dimers (the “S66” set) with a mean absolute error (MAE) of 0.21 kcal/mol, which represents an improvement of more than a factor of 10 over unadorned LC-ωPBE/6-31+G(2d,2p) and almost a factor of two improvement over LC-ωPBE/6-31+G(2d,2p) used in conjunction with the “D3” pairwise dispersion energy corrections. In addition, the DCPs reduce the MAE of calculated X-H and X-Y (X,Y = C, H, N, O) bond dissociation enthalpies for a set of 40 species from 3.2 kcal/mol obtained with unadorned LC-ωPBE/6-31+G(2d,2p) to 1.6 kcal/mol. Our findings demonstrate that broad improvements to the performance of DFT methods may be achievable through the use of DCPs.

  15. Asymptotic correction of the exchange-correlation kernel of time-dependent density functional theory for long-range charge-transfer excitations

    NASA Astrophysics Data System (ADS)

    Gritsenko, Oleg; Baerends, Evert Jan

    2004-07-01

    Time-dependent density functional theory (TDDFT) calculations of charge-transfer excitation energies ωCT are significantly in error when the adiabatic local density approximation (ALDA) is employed for the exchange-correlation kernel fxc. We relate the error to the physical meaning of the orbital energy of the Kohn-Sham lowest unoccupied molecular orbital (LUMO). The LUMO orbital energy in Kohn-Sham DFT—in contrast to the Hartree-Fock model—approximates an excited electron, which is correct for excitations in compact molecules. In CT transitions the energy of the LUMO of the acceptor molecule should instead describe an added electron, i.e., approximate the electron affinity. To obtain a contribution that compensates for the difference, a specific divergence of fxc is required in rigorous TDDFT, and a suitable asymptotically correct form of the kernel fxcasymp is proposed. The importance of the asymptotic correction of fxc is demonstrated with the calculation of ωCT(R) for the prototype diatomic system HeBe at various separations R(He-Be). The TDDFT-ALDA curve ωCT(R) roughly resembles the benchmark ab initio curve ωCTCISD(R) of a configuration interaction calculation with single and double excitations in the region R=1-1.5 Å, where a sizable He-Be interaction exists, but exhibits the wrong behavior ωCT(R)≪ωCTCISD(R) at large R. The TDDFT curve obtained with fxcasymp however approaches ωCTCISD(R) closely in the region R=3-10 Å. Then, the adequate rigorous TDDFT approach should interpolate between the LDA/GGA ALDA xc kernel for excitations in compact systems and fxcasymp for weakly interacting fragments and suitable interpolation expressions are considered.

  16. Mechanism and kinetics of peptide partitioning into membranes

    SciTech Connect

    Ulmschneider, Martin; Killian, J Antoinette; Doux, Jacques P. F.; Smith, Jeremy C; Ulmschneider, Jakob

    2010-02-01

    Partitioning properties of transmembrane (TM) polypeptide segments directly determine membrane protein folding, stability, and function, and their understanding is vital for rational design of membrane active peptides. However, direct determination of water-to-bilayer transfer of TM peptides has proved difficult. Experimentally, sufficiently hydrophobic peptides tend to aggregate, while atomistic computer simulations at physiological temperatures cannot yet reach the long time scales required to capture partitioning. Elevating temperatures to accelerate the dynamics has been avoided, as this was thought to lead to rapid denaturing. However, we show here that model TM peptides (WALP) are exceptionally thermostable. Circular dichroism experiments reveal that the peptides remain inserted into the lipid bilayer and are fully helical, even at 90 C. At these temperatures, sampling is 50 500 times faster, sufficient to directly simulate spontaneous partitioning at atomic resolution. A folded insertion pathway is observed, consistent with three-stage partitioning theory. Elevated temperature simulation ensembles further allow the direct calculation of the insertion kinetics, which is found to be first-order for all systems. Insertion barriers are Hin = 15 kcal/mol for a general hydrophobic peptide and 23 kcal/mol for the tryptophan-flanked WALP peptides. The corresponding insertion times at room temperature range from 8.5 s to 163 ms. High-temperature simulations of experimentally validated thermostable systems suggest a new avenue for systematic exploration of peptide partitioning properties.

  17. 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.

  18. 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. PMID:25655486

  19. 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

  20. Aplication of Kohn-Sham Theory for Orbital Dependent (Self-Interaction-Corrected) Exchange-Correlation Energy Functionals to First Row Homonuclear Diatomic Molecules

    NASA Astrophysics Data System (ADS)

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

    1996-03-01

    We have attempted to employ the LSD approximation with orbital self-interaction-correction (LSDSIC) for the exchange-correlation energy functional in the calculation of the ground state properties of first row homonuclear diatomic molecules. As a higher symmetry is involved in these systems, a different LSDSIC approach has to be taken in order to obtain an appropriate self-interaction correction.( M. R. Pederson, R. A. Heaton, and C. C. Lin, J. Chem. Phys. \\underline82), 2688 (1985) Two methods of employing LSDSIC are considered: Localizing all the "paired" orbitals from an LSD calculation at the experimental bond length, and then calculating LSDSIC total energy and dissociation energy; (2)Employing SIC only to electrons in the outer-shell with the inner-shell electrons treated in the LSD, and then obtaining the Kohn-Sham molecular orbitals by fully numerical solution in the KLI approximation. We find that the total energies are much improved with method (1), but this does not always lead to improved dissociation energies; Method (2) results in better highest occupied orbital energies, and better dissociation energies for most molecules, but the bond length is less accurately given and the vibration frequency is significantly in error.

  1. 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

  2. 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.

  3. Broad Functional Correction of Molecular Impairments by Systemic Delivery of scAAVrh74-hSGSH Gene Delivery in MPS IIIA Mice

    PubMed Central

    Duncan, F Jason; Naughton, Bartholomew J; Zaraspe, Kimberly; Murrey, Darren A; Meadows, Aaron S; Clark, Kelly Reed; Newsom, David E; White, Peter; Fu, Haiyan; McCarty, Douglas M

    2015-01-01

    Mucopolysaccharidosis (MPS) IIIA is a neuropathic lysosomal storage disease caused by deficiency in N-sulfoglucosamine sulfohydrolase (SGSH). Genome-wide gene expression microarrays in MPS IIIA mice detected broad molecular abnormalities (greater than or equal to twofold, false discovery rate ≤10) in numerous transcripts (314) in the brain and blood (397). Importantly, 22 dysregulated blood transcripts are known to be enriched in the brain and linked to broad neuronal functions. To target the root cause, we used a self-complementary AAVrh74 vector to deliver the human SGSH gene into 4–6 weeks old MPS IIIA mice by an intravenous injection. The treatment resulted in global central nervous system (CNS) and widespread somatic restoration of SGSH activity, clearance of CNS and somatic glycosaminoglycan storage, improved behavior performance, and significantly extended survival. The scAAVrh74-hSGSH treatment also led to the correction of the majority of the transcriptional abnormalities in the brain (95.9%) and blood (97.7%), of which 182 and 290 transcripts were normalized in the brain and blood, respectively. These results demonstrate that a single systemic scAAVrh74-hSGSH delivery mediated efficient restoration of SGSH activity and resulted in a near complete correction of MPS IIIA molecular pathology. This study also demonstrates that blood transcriptional profiles reflect the biopathological status of MPS IIIA, and also respond well to effective treatments. PMID:25592334

  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. 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.

  6. A generalized information function applied to the genetic code.

    PubMed

    Alvager, T; Graham, G; Hilleke, R; Hutchison, D; Westgard, J

    1990-01-01

    The problem of the partitioning of the degeneracy of the codons in the genetic code is considered in the framework of a generalized information function IG = c sigma kpk(ln pk + G(Ek] where k represents the number of codons in a specific degeneracy class and G(Ek) is an arbitrary real valued function. For G(Ek) = 0 the Shannon information function is recovered. For a particular choice of G(Ek) that takes the dominance of even degeneracies into account, it is found by direct numerical calculations that the correct degeneracy partitioning appears as optimal values of the Ig function. This results is also supported by optimization calculations in which the generalized information function is regarded as a continuous function in the degeneracy variables. PMID:2073543

  7. Background intensity correction for terabyte-sized time-lapse images.

    PubMed

    Chalfoun, J; Majurski, M; Bhadriraju, K; Lund, S; Bajcsy, P; Brady, M

    2015-03-01

    Several computational challenges associated with large-scale background image correction of terabyte-sized fluorescent images are discussed and analysed in this paper. Dark current, flat-field and background correction models are applied over a mosaic of hundreds of spatially overlapping fields of view (FOVs) taken over the course of several days, during which the background diminishes as cell colonies grow. The motivation of our work comes from the need to quantify the dynamics of OCT-4 gene expression via a fluorescent reporter in human stem cell colonies. Our approach to background correction is formulated as an optimization problem over two image partitioning schemes and four analytical correction models. The optimization objective function is evaluated in terms of (1) the minimum root mean square (RMS) error remaining after image correction, (2) the maximum signal-to-noise ratio (SNR) reached after downsampling and (3) the minimum execution time. Based on the analyses with measured dark current noise and flat-field images, the most optimal GFP background correction is obtained by using a data partition based on forming a set of submosaic images with a polynomial surface background model. The resulting image after correction is characterized by an RMS of about 8, and an SNR value of a 4 × 4 downsampling above 5 by Rose criterion. The new technique generates an image with half RMS value and double SNR value when compared to an approach that assumes constant background throughout the mosaic. We show that the background noise in terabyte-sized fluorescent image mosaics can be corrected computationally with the optimized triplet (data partition, model, SNR driven downsampling) such that the total RMS value from background noise does not exceed the magnitude of the measured dark current noise. In this case, the dark current noise serves as a benchmark for the lowest noise level that an imaging system can achieve. In comparison to previous work, the past fluorescent

  8. Relativistic density-functional theory with the optimized effective potential and self-interaction correction: Application to atomic structure calculations (Z=2-106)

    NASA Astrophysics Data System (ADS)

    Tong, Xiao-Min; Chu, Shih-I.

    1998-02-01

    We present a self-interaction-free relativistic density-functional theory (DFT). The theory is based on the extension of our recent nonrelativistic DFT treatment with optimized effective potential (OEP) and self-interaction correction (SIC) [Phys. Rev. A 55, 3406 (1997)] to the relativistic domain. Such a relativistic OEP-SIC procedure yields an orbital-independent single-particle local potential with proper long-range Coulombic (-1/r) behavior. The method is applied to the ground-state energy calculations for atoms with Z=2-106. A comparison with the corresponding nonrelativistic OEP-SIC calculations and other relativistic calculations is made. It is shown that the ionization potentials (obtained from the highest occupied orbital energies) and individual orbital binding energies determined by the present relativistic OEP-SIC method agree well with the experimental data across the Periodic Table.

  9. A density functional theory study of Na(H2O)n: an example of the impact of self-interaction corrections

    NASA Astrophysics Data System (ADS)

    Dinh, Phuong Mai; Gao, Cong Zhang; Klüpfel, Peter; Reinhard, Paul-Gerhard; Suraud, Eric; Vincendon, Marc; Wang, Jing; Zhang, Feng Shou

    2014-08-01

    We present a detailed analysis of ground state and optical response properties of small metal water complexes. Such complexes represent prototypical systems for analysing chromophore effects in relation to irradiation in a biological environment. The mixing of a metal atom with organic ones leads to the coexistence of covalent and metallic bondings which requires an elaborate treatment of the self interaction correction (SIC) within density functional theory (DFT). This is a particularly key issue in the context of time dependent DFT which represents the natural tool of investigation of irradiation scenarios in such systems. We show that these complexes require a highly elaborate treatment of the SIC which can be attributed to the mixing of bonding types.

  10. 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.

  11. The performance of functional methods for correcting non-Gaussian measurement error within Poisson regression: corrected excess risk of lung cancer mortality in relation to radon exposure among French uranium miners.

    PubMed

    Allodji, Rodrigue S; Thiébaut, Anne C M; Leuraud, Klervi; Rage, Estelle; Henry, Stéphane; Laurier, Dominique; Bénichou, Jacques

    2012-12-30

    A broad variety of methods for measurement error (ME) correction have been developed, but these methods have rarely been applied possibly because their ability to correct ME is poorly understood. We carried out a simulation study to assess the performance of three error-correction methods: two variants of regression calibration (the substitution method and the estimation calibration method) and the simulation extrapolation (SIMEX) method. Features of the simulated cohorts were borrowed from the French Uranium Miners' Cohort in which exposure to radon had been documented from 1946 to 1999. In the absence of ME correction, we observed a severe attenuation of the true effect of radon exposure, with a negative relative bias of the order of 60% on the excess relative risk of lung cancer death. In the main scenario considered, that is, when ME characteristics previously determined as most plausible from the French Uranium Miners' Cohort were used both to generate exposure data and to correct for ME at the analysis stage, all three error-correction methods showed a noticeable but partial reduction of the attenuation bias, with a slight advantage for the SIMEX method. However, the performance of the three correction methods highly depended on the accurate determination of the characteristics of ME. In particular, we encountered severe overestimation in some scenarios with the SIMEX method, and we observed lack of correction with the three methods in some other scenarios. For illustration, we also applied and compared the proposed methods on the real data set from the French Uranium Miners' Cohort study. PMID:22996087

  12. 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.

  13. Aplication of Kohn-Sham Theory for Orbital Dependent (Self-Interaction-Corrected) Exchange-Correlation Energy Functionals to First Row Heteropolar Diatomic Molecules

    NASA Astrophysics Data System (ADS)

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

    1996-03-01

    We have employed the local-spin-density approximation with orbital self-interaction-correction (LSDSIC) for the exchange-correlation energy functional in the calculation of the ground state properties of first row heteropolar diatomic molecules. The Kohn-Sham molecular orbitals are obtained by fully numerical solution of a Schrodinger equation including the Optimized Effective Potential in the KLIfootnote J. B. Krieger, Y. Li and G. J Iafrate in "Density Functional Theory" eds. E. K. U. Gross and R. M. Dreizler, NATO ASI SERIES, Plenum, New York (1995) approximation. We find that in the exchange-only case, our results closely approximate those of non-local Hartree-Fock calculations. Results for the bond length, total energy, dissociation energy, single particle energy eigenvalue, ɛ _m, for the highest lying occupied state, and vibration frequency obtained by employing the LSDSIC for exchange and correlation will be presented. These results will be compared to experimental values as well as to the results obtained by employing the LSD exchange-correlation energy functional. We find that the total energy, dissociation energy and ɛ m are given with greater accuracy than the corresponding LSD results. However, the bond length is less accurately given and the vibration frequency is significantly in error.

  14. Target Mass Corrections Revisited

    SciTech Connect

    W. Melnitchouk; F. Steffens

    2006-03-07

    We propose a new implementation of target mass corrections to nucleon structure functions which, unlike existing treatments, has the correct kinematic threshold behavior at finite Q{sup 2} in the x {yields} 1 limit. We illustrate the differences between the new approach and existing prescriptions by considering specific examples for the F{sub 2} and F{sub L} structure functions, and discuss the broader implications of our results, which call into question the notion of universal parton distribution at finite Q{sup 2}.

  15. 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.

  16. Energy Partition and Variability of Earthquakes

    NASA Astrophysics Data System (ADS)

    Kanamori, H.

    2003-12-01

    During an earthquake the potential energy (strain energy + gravitational energy + rotational energy) is released, and the released potential energy (Δ W) is partitioned into radiated energy (ER), fracture energy (EG), and thermal energy (E H). How Δ W is partitioned into these energies controls the behavior of an earthquake. The merit of the slip-weakening concept is that only ER and EG control the dynamics, and EH can be treated separately to discuss the thermal characteristics of an earthquake. In general, if EG/E_R is small, the event is ``brittle", if EG /ER is large, the event is ``quasi static" or, in more common terms, ``slow earthquakes" or ``creep". If EH is very large, the event may well be called a thermal runaway rather than an earthquake. The difference in energy partition has important implications for the rupture initiation, evolution and excitation of long-period ground motions from very large earthquakes. We review the current state of knowledge on this problem in light of seismological observations and the basic physics of fracture. With seismological methods, we can measure only ER and the lower-bound of Δ W, Δ W0, and estimation of other energies involves many assumptions. ER: Although ER can be directly measured from the radiated waves, its determination is difficult because a large fraction of energy radiated at the source is attenuated during propagation. With the commonly used teleseismic and regional methods, only for events with MW>7 and MW>4, respectively, we can directly measure more than 10% of the total radiated energy. The rest must be estimated after correction for attenuation. Thus, large uncertainties are involved, especially for small earthquakes. Δ W0: To estimate Δ W0, estimation of the source dimension is required. Again, only for large earthquakes, the source dimension can be estimated reliably. With the source dimension, the static stress drop, Δ σ S, and Δ W0, can be estimated. EG: Seismologically, EG is the energy

  17. Barometric and Earth Tide Correction

    Energy Science and Technology Software Center (ESTSC)

    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.

  18. 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.

  19. Wave spectra partitioning and long term statistical distribution

    NASA Astrophysics Data System (ADS)

    Portilla-Yandún, Jesús; Cavaleri, Luigi; Van Vledder, Gerbrant Ph.

    2015-12-01

    A new method is presented for a physically based statistical description of wind wave climatology. The method applies spectral partitioning to identify individual wave systems (partitions) in time series of 2D-wave spectra, followed by computing the probability of occurrence of their (peak) position in frequency-direction space. This distribution can be considered as a spectral density function to which another round of partitioning is applied to obtain spectral domains, each representing a typical wave system or population in a statistical sense. This two-step partitioning procedure allows identifying aggregate wave systems without the need to discuss specific characteristics as wind sea and swell systems. We suggest that each of these aggregate wave systems (populations) is linked to a specific generation pattern opening the way to dedicated analyses. Each population (of partitions) can be subjected to further analyses to add dimension carrying information based on integrated wave parameters of each partition, such as significant wave height, wave age, mean wave period and direction, among others. The new method is illustrated by analysing model spectra from a numerical wave prediction model and measured spectra from a directional wave buoy located in the Southern North Sea. It is shown that these two sources of information yield consistent results. Examples are given of computing the statistical distribution of significant wave height, spectral energy distribution and the spatial variation of wind wave characteristics along a north-south transect in the North Sea. Wind or wave age information can be included as an extra attribute of the members of a population to label them as wind sea or swell systems. Finally, suggestions are given for further applications of this new method.

  20. 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. PMID:18434328