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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

    2016-05-01

    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.

  18. 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.

  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 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

  1. 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.

  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. 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

  5. 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.

  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 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.

  16. 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.

  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. 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.

  2. 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.

  3. 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…

  4. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  2. 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.

  3. 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.

  4. 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.

  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. 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.

  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. 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).

  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. 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.

  7. 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

  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. 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

  16. 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.

  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. 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.

  10. 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.

  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. 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).

  2. 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

  3. 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.

  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. 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

  17. 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.

  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. 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

  12. 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

  13. 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

  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. 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.

  2. 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.

  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. 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.

  6. 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.

  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 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

  3. 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

  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. 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.

  8. 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

  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. 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

  5. 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

  6. 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.

  7. 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

  8. 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.

  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