The EPRL intertwiners and corrected partition function
NASA Astrophysics Data System (ADS)
Kamiński, Wojciech; Kisielowski, Marcin; Lewandowski, Jerzy
2010-08-01
Do the SU(2) intertwiners parametrize the space of the Engle, Pereira, Rovelli, Livine (EPRL) solutions to the simplicity constraint? What is the complete form of the partition function written in terms of this parametrization? We prove that the EPRL map is injective in the general n-valent vertex case for the Barbero-Immirzi parameter less than 1. We find, however, that the EPRL map is not isometric. In the consequence, a partition function can be defined either using the EPRL intertwiners Hilbert product or the SU(2) intertwiners Hilbert product. We use the EPRL one and derive a new, complete formula for the partition function. Next, we view it in terms of the SU(2) intertwiners. The result, however, goes beyond the SU(2) spin-foam models' framework and the original EPRL proposal.
Partition Density Functional Theory
NASA Astrophysics Data System (ADS)
Wasserman, Adam
2012-02-01
Partition Density Functional Theory (PDFT) is a formally exact method for obtaining molecular properties from self-consistent calculations on isolated fragments [1,2]. For a given choice of fragmentation, PDFT outputs the (in principle exact) molecular energy and density, as well as fragment densities that sum to the correct molecular density. I describe our progress understanding the behavior of the fragment energies as a function of fragment occupations, derivative discontinuities, practical implementation, and applications of PDFT to small molecules. I also discuss implications for ground-state Density Functional Theory, such as the promise of PDFT to circumvent the delocalization error of approximate density functionals. [4pt] [1] M.H. Cohen and A. Wasserman, J. Phys. Chem. A, 111, 2229(2007).[0pt] [2] P. Elliott, K. Burke, M.H. Cohen, and A. Wasserman, Phys. Rev. A 82, 024501 (2010).
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.
Gluing Nekrasov Partition Functions
NASA Astrophysics Data System (ADS)
Qiu, Jian; Tizzano, Luigi; Winding, Jacob; Zabzine, Maxim
2015-07-01
In this paper we summarise the localisation calculation of 5D super Yang-Mills on simply connected toric Sasaki-Einstein (SE) manifolds. We show how various aspects of the computation, including the equivariant index, the asymptotic behaviour and the factorisation property are governed by the combinatorial data of the toric geometry. We prove that the perturbative partition function on a simply connected SE manifold corresponding to an n-gon toric diagram factorises to n copies of perturbative part (zero instanton sector) of the Nekrasov partition function. This leads us to conjecture a prescription for the computation of the complete partition function, by gluing n copies of the full Nekrasov partition functions. This work is a generalisation of some earlier computation carried out on Y p, q manifolds, whose moment map cone has a quadrangle base and our result is valid for manifolds whose moment map cones have pentagon base, hexagon base, etc. The algorithm we used for dealing with general cones may also be of independent interest.
The stringy instanton partition function
NASA Astrophysics Data System (ADS)
Bonelli, Giulio; Sciarappa, Antonio; Tanzini, Alessandro; Vasko, Petr
2014-01-01
We perform an exact computation of the gauged linear sigma model associated to a D1-D5 brane system on a resolved A 1 singularity. This is accomplished via supersymmetric localization on the blown-up two-sphere. We show that in the blow-down limit the partition function reduces to the Nekrasov partition function evaluating the equivariant volume of the instanton moduli space. For finite radius we obtain a tower of world-sheet instanton corrections, that we identify with the equivariant Gromov-Witten invariants of the ADHM moduli space. We show that these corrections can be encoded in a deformation of the Seiberg-Witten prepotential. From the mathematical viewpoint, the D1-D5 system under study displays a twofold nature: the D1-branes viewpoint captures the equivariant quantum cohomology of the ADHM instanton moduli space in the Givental formalism, and the D5-branes viewpoint is related to higher rank equivariant Donaldson-Thomas invariants of.
Intersecting surface defects and instanton partition functions
Pan, Yiwen; Peelaers, Wolfger
2017-07-14
We analyze intersecting surface defects inserted in interacting four-dimensional N = 2 supersymmetric quantum field theories. We employ the realization of a class of such systems as the infrared xed points of renormalization group flows from larger theories, triggered by perturbed Seiberg-Witten monopole-like con gurations, to compute their partition functions. These results are cast into the form of a partition function of 4d/2d/0d coupled systems. In conclusion, our computations provide concrete expressions for the instanton partition function in the presence of intersecting defects and we study the corresponding ADHM model.
Intersecting surface defects and instanton partition functions
NASA Astrophysics Data System (ADS)
Pan, Yiwen; Peelaers, Wolfger
2017-07-01
We analyze intersecting surface defects inserted in interacting four-dimensional N=2 supersymmetric quantum field theories. We employ the realization of a class of such systems as the infrared fixed points of renormalization group flows from larger theories, triggered by perturbed Seiberg-Witten monopole-like configurations, to compute their partition functions. These results are cast into the form of a partition function of 4d/2d/0d coupled systems. Our computations provide concrete expressions for the instanton partition function in the presence of intersecting defects and we study the corresponding ADHM model.
Virasoro constraint for Nekrasov instanton partition function
NASA Astrophysics Data System (ADS)
Kanno, Shoichi; Matsuo, Yutaka; Zhang, Hong
2012-10-01
We show that Nekrasov instanton partition function for SU( N ) gauge theories satisfies recursion relations in the form of U(1)+Virasoro constraints when β = 1. The constraints give a direct support for AGT conjecture for general quiver gauge theories.
Factorization of the bosonic partition function
NASA Astrophysics Data System (ADS)
Alsharafat, Ayed; Chair, Noureddine
2017-04-01
The factorization formula in the non-interacting quantum field theories that relates the fermionic partition function to the bosonic partition function considered recently by Chair (2013) [3] is obtained for the harmonic oscillator using the path integral formulation. By using the latter, the fermionic partition function turns out to be the ratio of two determinants of the same operator (∂τ + ω), whose eigenmodes being both periodic on the imaginary time intervals [ 0 , 2 β ], [ 0 , β ]. The natural generalization of the factorization formula when β →2m β is derived, such a factorization implies that the bosonic oscillator at temperature β can be seen as a non-interacting mixture of a bosonic oscillator at temperature 2m β and m-fermionic oscillators at different temperatures 2 m - k β, k = 1 , 2 , … , m. As a consequence, a general relationship between the bosonic and fermionic thermal zeta functions is deduced.
Chiral partition functions of quantum Hall droplets
Cappelli, Andrea Viola, Giovanni; Zemba, Guillermo R.
2010-02-15
Chiral partition functions of conformal field theory describe the edge excitations of isolated Hall droplets. They are characterized by an index specifying the quasiparticle sector and transform among themselves by a finite-dimensional representation of the modular group. The partition functions are derived and used to describe electron transitions leading to Coulomb blockade conductance peaks. We find the peak patterns for Abelian hierarchical states and non-Abelian Read-Rezayi states, and compare them. Experimental observation of these features can check the qualitative properties of the conformal field theory description, such as the decomposition of the Hilbert space into sectors, involving charged and neutral parts, and the fusion rules.
Bounds for the Eventual Positivity of Difference Functions of Partitions
NASA Astrophysics Data System (ADS)
Woodford, Roger
2007-01-01
In this paper we specialize work done by Bateman and Erdos concerning difference functions of partition functions. In particular, we are concerned with partitions into fixed powers of the primes. We show that any difference function of these partition functions is eventually increasing, and derive explicit bounds for when it will attain strictly positive values. From these bounds an asymptotic result is derived.
Genuine N -partite entanglement without N -partite correlation functions
NASA Astrophysics Data System (ADS)
Tran, Minh Cong; Zuppardo, Margherita; de Rosier, Anna; Knips, Lukas; Laskowski, Wiesław; Paterek, Tomasz; Weinfurter, Harald
2017-06-01
A genuinely N -partite entangled state may display vanishing N -partite correlations measured for arbitrary local observables. In such states the genuine entanglement is noticeable solely in correlations between subsets of particles. A straightforward way to obtain such states for odd N is to design an "antistate" in which all correlations between an odd number of observers are exactly opposite. Evenly mixing a state with its antistate then produces a mixed state with no N -partite correlations, with many of them genuinely multiparty entangled. Intriguingly, all known examples of "entanglement without correlations" involve an odd number of particles. Here we further develop the idea of antistates, thereby shedding light on the different properties of even and odd particle systems. We conjecture that there is no antistate to any pure even-N -party entangled state making the simple construction scheme unfeasible. However, as we prove by construction, higher-rank examples of entanglement without correlations for arbitrary even N indeed exist. These classes of states exhibit genuine entanglement and even violate an N -partite Bell inequality, clearly demonstrating the nonclassical features of these states as well as showing their applicability for quantum information processing.
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.
On the Potts Model Partition Function in an External Field
NASA Astrophysics Data System (ADS)
McDonald, Leslie M.; Moffatt, Iain
2012-03-01
We study the partition function of the Potts model in an external (magnetic) field, and its connections with the zero-field Potts model partition function. Using a deletion-contraction formulation for the partition function Z for this model, we show that it can be expanded in terms of the zero-field partition function. We also show that Z can be written as a sum over the spanning trees, and the spanning forests, of a graph G. Our results extend to Z the well-known spanning tree expansion for the zero-field partition function that arises though its connections with the Tutte polynomial.
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.
Huang, WenJuan; Blinov, Nikolay; Kovalenko, Andriy
2015-04-30
The octanol-water partition coefficient is an important physical-chemical characteristic widely used to describe hydrophobic/hydrophilic properties of chemical compounds. The partition coefficient is related to the transfer free energy of a compound from water to octanol. Here, we introduce a new protocol for prediction of the partition coefficient based on the statistical-mechanical, 3D-RISM-KH molecular theory of solvation. It was shown recently that with the compound-solvent correlation functions obtained from the 3D-RISM-KH molecular theory of solvation, the free energy functional supplemented with the correction linearly related to the partial molar volume obtained from the Kirkwood-Buff/3D-RISM theory, also called the "universal correction" (UC), provides accurate prediction of the hydration free energy of small compounds, compared to explicit solvent molecular dynamics [ Palmer , D. S. ; J. Phys.: Condens. Matter 2010 , 22 , 492101 ]. Here we report that with the UC reparametrized accordingly this theory also provides an excellent agreement with the experimental data for the solvation free energy in nonpolar solvent (1-octanol) and so accurately predicts the octanol-water partition coefficient. The performance of the Kovalenko-Hirata (KH) and Gaussian fluctuation (GF) functionals of the solvation free energy, with and without UC, is tested on a large library of small compounds with diverse functional groups. The best agreement with the experimental data for octanol-water partition coefficients is obtained with the KH-UC solvation free energy functional.
Partition functions, duality and the tube metric
NASA Astrophysics Data System (ADS)
Dolan, L.; Langham, M.
1998-08-01
The partition function of type IIA and B strings on R6 × K3 , in the T 4/ Z2 orbifold limit, is explicitly computed as a modular invariant sum over spin structures required by perturbative unitarity in order to extend the analysis to include type II strings on R6 × W4 , where W4 is associated with the tube metric conformal field theory, given by the degrees of freedom transverse to the Neveu-Schwarz fivebrane solution. This generates partition functions and perturbative spectra of string theories in six space-time dimensions, associated with the modular invariants of the level- k affine SU(2) Kac-Moody algebra. These theories provide a conformal field theory (i.e. perturbative) probe of non-perturbative (fivebrane) vacua. We contrast them with theories whose N = (4, 4) sigma-model action contains nH = k + 2 hypermultiplets as well as vector supermultiplets, and where k is the level just mentioned. In Appendix B we also give a D = 6, N = (1, 1) 'free fermion' string model which has. a different moduli space of vacua from the 81-parameter space relevant to the above examples.
A Partition Function Approximation Using Elementary Symmetric Functions
Anandakrishnan, Ramu
2012-01-01
In statistical mechanics, the canonical partition function can be used to compute equilibrium properties of a physical system. Calculating however, is in general computationally intractable, since the computation scales exponentially with the number of particles in the system. A commonly used method for approximating equilibrium properties, is the Monte Carlo (MC) method. For some problems the MC method converges slowly, requiring a very large number of MC steps. For such problems the computational cost of the Monte Carlo method can be prohibitive. Presented here is a deterministic algorithm – the direct interaction algorithm (DIA) – for approximating the canonical partition function in operations. The DIA approximates the partition function as a combinatorial sum of products known as elementary symmetric functions (ESFs), which can be computed in operations. The DIA was used to compute equilibrium properties for the isotropic 2D Ising model, and the accuracy of the DIA was compared to that of the basic Metropolis Monte Carlo method. Our results show that the DIA may be a practical alternative for some problems where the Monte Carlo method converge slowly, and computational speed is a critical constraint, such as for very large systems or web-based applications. PMID:23251504
Level density of a Fermi gas and integer partitions: A Gumbel-like finite-size correction
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.
Exact partition functions for gauge theories on Rλ3
NASA Astrophysics Data System (ADS)
Wallet, Jean-Christophe
2016-11-01
The noncommutative space Rλ3, a deformation of R3, supports a 3-parameter family of gauge theory models with gauge-invariant harmonic term, stable vacuum and which are perturbatively finite to all orders. Properties of this family are discussed. The partition function factorizes as an infinite product of reduced partition functions, each one corresponding to the reduced gauge theory on one of the fuzzy spheres entering the decomposition of Rλ3. For a particular sub-family of gauge theories, each reduced partition function is exactly expressible as a ratio of determinants. A relation with integrable 2-D Toda lattice hierarchy is indicated.
Modular invariant partition function of critical dense polymers
NASA Astrophysics Data System (ADS)
Morin-Duchesne, Alexi; Pearce, Paul A.; Rasmussen, Jørgen
2013-09-01
A lattice model of critical dense polymers is solved exactly for arbitrary system size on the torus. More generally, an infinite family of lattice loop models is studied on the torus and related to the corresponding Fortuin-Kasteleyn random cluster models. Starting with a cylinder, the commuting periodic single-row transfer matrices are built from the periodic Temperley-Lieb algebra extended by the shift operators Ω±1. In this enlarged algebra, the non-contractible loop fugacity is α and the contractible loop fugacity is β. The torus is formed by gluing the top and bottom of the cylinder. This gives rise to a variety of non-contractible loops winding around the torus. Because of their nonlocal nature, the standard matrix trace does not produce the proper geometric torus. Instead, we introduce a modified matrix trace for this purpose. This is achieved by using a representation of the enlarged periodic Temperley-Lieb algebra with a parameter v that keeps track of the winding of defects on the cylinder. The transfer matrix representatives and their eigenvalues thus depend on v. The modified trace is constructed as a linear functional on planar connectivity diagrams in terms of matrix traces Trd (with a fixed number of defects d) and Chebyshev polynomials of the first kind. For critical dense polymers, where β=0, the transfer matrix eigenvalues are obtained by solving a functional equation in the form of an inversion identity. The solution depends on d and is subject to selection rules which we prove. Simplifications occur if all non-contractible loop fugacities are set to α=2 in which case the traces are evaluated at v=1. In the continuum scaling limit, the corresponding conformal torus partition function obtained from finite-size corrections agrees with the known modular invariant partition function of symplectic fermions.
Spectrum of CHL dyons from genus-two partition function
NASA Astrophysics Data System (ADS)
Dabholkar, Atish; Gaiotto, Davide
2007-12-01
We compute the genus-two chiral partition function of the left-moving heterotic string for a Bbb Z2 CHL orbifold. The required twisted determinants can be evaluated explicitly in terms of the untwisted determinants and theta functions using orbifold techniques. The dependence on Prym periods cancels neatly once summation over odd charges is properly taken into account. The resulting partition function is a Siegel modular form of level two and precisely equals recently proposed dyon partition function for this model. This result provides an independent weak coupling derivation of the dyon partition function using the M-theory lift of string webs representing the dyons. We discuss generalization of this technique to general Bbb ZN orbifolds.
Reduced partition function ratios of iron and oxygen in goethite
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.
2015-02-15
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 (beta-factors). The calculated iron phonon density of states (pDOS), force constant and beta-factor are compared with reevaluated experimental beta-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 Mossbauer-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 Mossbauer 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 beta-factors, which suggests almost no fractionation between the two minerals at equilibrium.
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.
How Incorrect Is the Classical Partition Function for the Ideal Gas?
ERIC Educational Resources Information Center
Kroemer, Herbert
1980-01-01
Discussed is the classical partition function for the ideal gas and how it differs from the exact value for bosons or fermions in the classical regime. The differences in the two values are negligible hence the classical treatment leads in the end to correct answers for all observables. (Author/DS)
How Incorrect Is the Classical Partition Function for the Ideal Gas?
ERIC Educational Resources Information Center
Kroemer, Herbert
1980-01-01
Discussed is the classical partition function for the ideal gas and how it differs from the exact value for bosons or fermions in the classical regime. The differences in the two values are negligible hence the classical treatment leads in the end to correct answers for all observables. (Author/DS)
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)
Distances in spaces of physical models: partition functions versus spectra
NASA Astrophysics Data System (ADS)
Cornelissen, Gunther; Kontogeorgis, Aristides
2017-01-01
We study the relation between convergence of partition functions (seen as general Dirichlet series) and convergence of spectra and their multiplicities. We describe applications to convergence in physical models, e.g., related to topology change and averaging in cosmology.
Dominant partition method. [based on a wave function formalism
NASA Technical Reports Server (NTRS)
Dixon, R. M.; Redish, E. F.
1979-01-01
By use of the L'Huillier, Redish, and Tandy (LRT) wave function formalism, a partially connected method, the dominant partition method (DPM) is developed for obtaining few body reductions of the many body problem in the LRT and Bencze, Redish, and Sloan (BRS) formalisms. The DPM maps the many body problem to a fewer body one by using the criterion that the truncated formalism must be such that consistency with the full Schroedinger equation is preserved. The DPM is based on a class of new forms for the irreducible cluster potential, which is introduced in the LRT formalism. Connectivity is maintained with respect to all partitions containing a given partition, which is referred to as the dominant partition. Degrees of freedom corresponding to the breakup of one or more of the clusters of the dominant partition are treated in a disconnected manner. This approach for simplifying the complicated BRS equations is appropriate for physical problems where a few body reaction mechanism prevails.
Graviton 1-loop partition function for 3-dimensional massive gravity
NASA Astrophysics Data System (ADS)
Gaberdiel, Matthias R.; Grumiller, Daniel; Vassilevich, Dmitri
2010-11-01
Thegraviton1-loop partition function in Euclidean topologically massivegravity (TMG) is calculated using heat kernel techniques. The partition function does not factorize holomorphically, and at the chiral point it has the structure expected from a logarithmic conformal field theory. This gives strong evidence for the proposal that the dual conformal field theory to TMG at the chiral point is indeed logarithmic. We also generalize our results to new massive gravity.
ATOMIC PARTITION FUNCTION FOR STELLAR ATMOSPHERES AND PLASMA DIAGNOSTICS
Cardona, O.; Martinez-Arroyo, M.; Lopez-Castillo, M. A. E-mail: mmtz@inaoep.m
2010-03-01
A new approximate partition function is derived as a function of temperature and total number density of particles in the given system, and three adjustable parameters. The derivation assumes that we can simulate the calculations of the partition function for hydrogen by means of averages of the energies and sums of the statistical weights. We present the procedure and mathematical process to obtain an approximate analytic function and its derivatives that depend on those parameters. The comparisons with other calculations reported in the literature show good agreement. The free parameters of this function are calculated and given in a table for all the ions of the first 20 atomic species.
Optimized replica gas estimation of absolute integrals and partition functions
NASA Astrophysics Data System (ADS)
Minh, David D. L.
2010-09-01
In contrast with most Monte Carlo integration algorithms, which are used to estimate ratios, the replica gas identities recently introduced by Adib enable the estimation of absolute integrals and partition functions using multiple copies of a system and normalized transition functions. Here, an optimized form is presented. After generalizing a replica gas identity with an arbitrary weighting function, we obtain a functional form that has the minimal asymptotic variance for samples from two replicas and is provably good for a larger number. This equation is demonstrated to improve the convergence of partition function estimates in a two-dimensional Ising model.
Optimized replica gas estimation of absolute integrals and partition functions.
Minh, D.
2010-01-01
In contrast with most Monte Carlo integration algorithms, which are used to estimate ratios, the replica gas identities recently introduced by Adib enable the estimation of absolute integrals and partition functions using multiple copies of a system and normalized transition functions. Here, an optimized form is presented. After generalizing a replica gas identity with an arbitrary weighting function, we obtain a functional form that has the minimal asymptotic variance for samples from two replicas and is provably good for a larger number. This equation is demonstrated to improve the convergence of partition function estimates in a two-dimensional Ising model.
A brief history of partitions of numbers, partition functions and their modern applications
NASA Astrophysics Data System (ADS)
Debnath, Lokenath
2016-04-01
Quantum Mechanical Single Molecule Partition Function from PathIntegral Monte Carlo Simulations
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.
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.
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.
Further Stable methods for the calculation of partition functions
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.
Partition functions and concentrations in plasmas out of thermal equilibrium
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.
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.
Many-body formalism for fermions: The partition function
NASA Astrophysics Data System (ADS)
Watson, D. K.
2017-09-01
The partition function, a fundamental tenet in statistical thermodynamics, contains in principle all thermodynamic information about a system. It encapsulates both microscopic information through the quantum energy levels and statistical information from the partitioning of the particles among the available energy levels. For identical particles, this statistical accounting is complicated by the symmetry requirements of the allowed quantum states. In particular, for Fermi systems, the enforcement of the Pauli principle is typically a numerically demanding task, responsible for much of the cost of the calculations. The interplay of these three elements—the structure of the many-body spectrum, the statistical partitioning of the N particles among the available levels, and the enforcement of the Pauli principle—drives the behavior of mesoscopic and macroscopic Fermi systems. In this paper, we develop an approach for the determination of the partition function, a numerically difficult task, for systems of strongly interacting identical fermions and apply it to a model system of harmonically confined, harmonically interacting fermions. This approach uses a recently introduced many-body method that is an extension of the symmetry-invariant perturbation method (SPT) originally developed for bosons. It uses group theory and graphical techniques to avoid the heavy computational demands of conventional many-body methods which typically scale exponentially with the number of particles. The SPT application of the Pauli principle is trivial to implement since it is done "on paper" by imposing restrictions on the normal-mode quantum numbers at first order in the perturbation. The method is applied through first order and represents an extension of the SPT method to excited states. Our method of determining the partition function and various thermodynamic quantities is accurate and efficient and has the potential to yield interesting insight into the role played by the Pauli
NASA Astrophysics Data System (ADS)
Kannan, N.; White, S. M.; Worrall, F.; Whelan, M. J.
2007-02-01
SummaryThe performance of the SWAT-2000 model was evaluated using stream flow at the outlet of the 142 ha Colworth catchment (Bedfordshire, UK). This catchment has been monitored since October 1999. The soil type consists of clay loam soil over stony calcareous clay and a rotation of wheat, oil seed rape, grass, beans and peas is grown. Much of the catchment is tile drained. Acceptable performance in hydrological modelling, along with correct simulation of the processes driving the water balance were essential first requirements for predicting contaminant transport. Initial results from SWAT-2000 identified some necessary modifications in the model source code for correct simulation of processes driving water balance. After modification of the code, hydrological simulation, crop growth and evapotranspiration (ET) patterns were realistic when compared with empirical data. Acceptable model performance (based on a number of error measures) was obtained in final model runs, with reasonable runoff partitioning into overland flow, tile drainage and base flow.
q-Virasoro Modular Double and 3d Partition Functions
NASA Astrophysics Data System (ADS)
Nedelin, Anton; Nieri, Fabrizio; Zabzine, Maxim
2017-08-01
We study partition functions of 3d {\\mathcal{N}=2} {U(N)} gauge theories on compact manifolds which are S 1 fibrations over S 2. We show that the partition functions are free field correlators of vertex operators and screening charges of the q-Virasoro modular double, which we define. The inclusion of supersymmetric Wilson loops in arbitrary representations allows us to show that the generating functions of Wilson loop vacuum expectation values satisfy two {SL(2,\\mathbb{Z})}-related commuting sets of q-Virasoro constraints. We generalize our construction to 3d {\\mathcal{N}=2} unitary quiver gauge theories and as an example we give the free boson realization of the ABJ(M) model.
Time-dependent Partition Density-functional Theory
NASA Astrophysics Data System (ADS)
Mosquera, Martin; Wasserman, Adam
2012-02-01
We present an extension of time-dependent density functional theory that allows to partition the time-dependent external potential in terms of localized molecular fragment potentials. As a consequence, localized time-dependent densities arise for each molecular fragment. To enforce the condition that the sum of fragments must add up to the exact total density, a new quantity termed ``time-dependent partition potential'' is introduced. The Runge-Gross theorem is employed to show that there is a quasi one-to-one correspondence between the partition potential and the electronic density. The corresponding quantum-mechanical actions are derived by using the van Leeuwen's action and are used to derive a decomposition of the partition potential which allows for practical approximations. Linear response formulas are deduced to obtain the transition energies, and an approximation is suggested to obtain localized excitations in large molecular systems. Finally, numerical illustration of our theory is shown for one-dimensional fermions under the influence of a laser field.
Potts model partition functions on two families of fractal lattices
NASA Astrophysics Data System (ADS)
Gong, Helin; Jin, Xian'an
2014-11-01
The partition function of q-state Potts model, or equivalently the Tutte polynomial, is computationally intractable for regular lattices. The purpose of this paper is to compute partition functions of q-state Potts model on two families of fractal lattices. Based on their self-similar structures and by applying the subgraph-decomposition method, we divide their Tutte polynomials into two summands, and for each summand we obtain a recursive formula involving the other summand. As a result, the number of spanning trees and their asymptotic growth constants, and a lower bound of the number of connected spanning subgraphs or acyclic root-connected orientations for each of such two lattices are obtained.
Identities between dimer partition functions on different surfaces
NASA Astrophysics Data System (ADS)
Cimasoni, David; Pham, Anh Minh
2016-10-01
Given a weighted graph G embedded in a non-orientable surface Σ , one can consider the corresponding weighted graph \\widetilde{G} embedded in the so-called orientation cover \\widetildeΣ of Σ . We prove identities relating twisted partition functions of the dimer model on these two graphs. When Σ is the Möbius strip or the Klein bottle, then \\widetildeΣ is the cylinder or the torus, respectively, and under some natural assumptions, these identities imply relations between the genuine dimer partition functions Z(G) and Z(\\widetilde{G}) . For example, we show that if G is a locally but not globally bipartite graph embedded in the Möbius strip, then Z(\\widetilde{G}) is equal to the square of Z(G). This extends results for the square lattice previously obtained by various authors.
High-temperature asymptotics of supersymmetric partition functions
Ardehali, Arash Arabi
2016-07-05
We study the supersymmetric partition function of 4d supersymmetric gauge theories with a U(1) R-symmetry on Euclidean 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. The partition function can be computed exactly using the supersymmetric localization of the gauge theory path-integral. It takes the form of an elliptic hypergeometric integral, which may be viewed as a matrix-integral over the moduli space of the holonomies of the gauge fields around S_{β}^{1}. At high temperatures (β → 0, corresponding to the hyperbolic limit of the elliptic hypergeometric integral) we obtain from the matrix-integral a quantum effective potential for the holonomies. The effective potential is proportional to the temperature. Therefore the high-temperature limit further localizes the matrix-integral to the locus of the minima of the potential. If the effective potential is positive semi-definite, the leading high-temperature asymptotics of the partition function is given by the formula of Di Pietro and Komargodski, and the subleading asymptotics is connected to the Coulomb branch dynamics on R^{3} × S^{1}. In theories where the effective potential is not positive semi-definite, the Di Pietro-Komargodski formula needs to be modified. In particular, this modification occurs in the SU(2) theory of Intriligator-Seiberg-Shenker, and the SO(N) theory of Brodie-Cho-Intriligator, both believed to exhibit “misleading” anomaly matchings, and both believed to yield interacting superconformal field theories with c < a. Lastly, two new simple tests for dualities between 4d supersymmetric gauge theories emerge as byproducts of our analysis.
High-temperature asymptotics of supersymmetric partition functions
Ardehali, Arash Arabi
2016-07-05
We study the supersymmetric partition function of 4d supersymmetric gauge theories with a U(1) R-symmetry on Euclidean S3 × Sβ1, with S3 the unit-radius squashed three-sphere, and β the circumference of the circle. For superconformal theories, this partition function coincides (up to a Casimir energy factor) with the 4d superconformal index. The partition function can be computed exactly using the supersymmetric localization of the gauge theory path-integral. It takes the form of an elliptic hypergeometric integral, which may be viewed as a matrix-integral over the moduli space of the holonomies of the gauge fields around Sβ1. At high temperatures (βmore » → 0, corresponding to the hyperbolic limit of the elliptic hypergeometric integral) we obtain from the matrix-integral a quantum effective potential for the holonomies. The effective potential is proportional to the temperature. Therefore the high-temperature limit further localizes the matrix-integral to the locus of the minima of the potential. If the effective potential is positive semi-definite, the leading high-temperature asymptotics of the partition function is given by the formula of Di Pietro and Komargodski, and the subleading asymptotics is connected to the Coulomb branch dynamics on R3 × S1. In theories where the effective potential is not positive semi-definite, the Di Pietro-Komargodski formula needs to be modified. In particular, this modification occurs in the SU(2) theory of Intriligator-Seiberg-Shenker, and the SO(N) theory of Brodie-Cho-Intriligator, both believed to exhibit “misleading” anomaly matchings, and both believed to yield interacting superconformal field theories with c < a. Lastly, two new simple tests for dualities between 4d supersymmetric gauge theories emerge as byproducts of our analysis.« less
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.
Commuting quantum circuits and complexity of Ising partition functions
NASA Astrophysics Data System (ADS)
Fujii, Keisuke; Morimae, Tomoyuki
2017-03-01
Instantaneous quantum polynomial-time (IQP) computation is a class of quantum computation consisting only of commuting two-qubit gates and is not universal. Nevertheless, it has been shown that if there is a classical algorithm that can simulate IQP efficiently, the polynomial hierarchy collapses to the third level, which is highly implausible. However, the origin of the classical intractability is still less understood. Here we establish a relationship between IQP and computational complexity of calculating the imaginary-valued partition functions of Ising models. We apply the established relationship in two opposite directions. One direction is to find subclasses of IQP that are classically efficiently simulatable by using exact solvability of certain types of Ising models. Another direction is applying quantum computational complexity of IQP to investigate (im)possibility of efficient classical approximations of Ising partition functions with imaginary coupling constants. Specifically, we show that a multiplicative approximation of Ising partition functions is #P-hard for almost all imaginary coupling constants even on planar lattices of a bounded degree.
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.
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.
NASA Astrophysics Data System (ADS)
Popovas, A.; Jørgensen, U. G.
2016-11-01
Context. Hydrogen is the most abundant molecule in the Universe. Its thermodynamic quantities dominate the physical conditions in molecular clouds, protoplanetary disks, etc. It is also of high interest in plasma physics. Therefore thermodynamic data for molecular hydrogen have to be as accurate as possible in a wide temperature range. Aims: We here rigorously show the shortcomings of various simplifications that are used to calculate the total internal partition function. These shortcomings can lead to errors of up to 40 percent or more in the estimated partition function. These errors carry on to calculations of thermodynamic quantities. Therefore a more complicated approach has to be taken. Methods: Seven possible simplifications of various complexity are described, together with advantages and disadvantages of direct summation of experimental values. These were compared to what we consider the most accurate and most complete treatment (case 8). Dunham coefficients were determined from experimental and theoretical energy levels of a number of electronically excited states of H2. Both equilibrium and normal hydrogen was taken into consideration. Results: Various shortcomings in existing calculations are demonstrated, and the reasons for them are explained. New partition functions for equilibrium, normal, and ortho and para hydrogen are calculated and thermodynamic quantities are reported for the temperature range 1-20 000 K. Our results are compared to previous estimates in the literature. The calculations are not limited to the ground electronic state, but include all bound and quasi-bound levels of excited electronic states. Dunham coefficients of these states of H2 are also reported. Conclusions: For most of the relevant astrophysical cases it is strongly advised to avoid using simplifications, such as a harmonic oscillator and rigid rotor or ad hoc summation limits of the eigenstates to estimate accurate partition functions and to be particularly careful when
Partition function zeros and finite size scaling for polymer adsorption
Taylor, Mark P.; Luettmer-Strathmann, Jutta
2014-11-28
The zeros of the canonical partition functions for a flexible polymer chain tethered to an attractive flat surface are computed for chains up to length N = 1536. We use a bond-fluctuation model for the polymer and obtain the density of states for the tethered chain by Wang-Landau sampling. The partition function zeros in the complex e{sup β}-plane are symmetric about the real axis and densest in a boundary region that has the shape of a nearly closed circle, centered at the origin, terminated by two flaring tails. This structure defines a root-free zone about the positive real axis and follows Yang-Lee theory. As the chain length increases, the base of each tail moves toward the real axis, converging on the phase-transition point in the thermodynamic limit. We apply finite-size scaling theory of partition-function zeros and show that the crossover exponent defined through the leading zero is identical to the standard polymer adsorption crossover exponent ϕ. Scaling analysis of the leading zeros locates the polymer adsorption transition in the thermodynamic (N → ∞) limit at reduced temperature T{sub c}{sup *}=1.027(3) [β{sub c}=1/T{sub c}{sup *}=0.974(3)] with crossover exponent ϕ = 0.515(25). Critical exponents for the order parameter and specific heat are determined to be β{sup ~}=0.97(5) and α = 0.03(4), respectively. A universal scaling function for the average number of surface contacts is also constructed.
Semiclassical partition function for the double-well potential
NASA Astrophysics Data System (ADS)
Kroff, D.; Bessa, A.; de Carvalho, C. A. A.; Fraga, E. S.; Jorás, S. E.
2014-07-01
We compute the partition function and specific heat for a quantum-mechanical particle under the influence of a quartic double-well potential nonperturbatively, using the semiclassical method. Near the region of bounded motion in the inverted potential, the usual quadratic approximation fails due to the existence of multiple classical solutions and caustics. Using the tools of catastrophe theory, we identify the relevant classical solutions, showing that at most two have to be considered. This corresponds to the first step towards the study of spontaneous symmetry breaking and thermal phase transitions in the nonperturbative framework of the boundary effective theory.
Random matrices and the convergence of partition function zeros in finite density QCD
Halasz, M. A.; Osborn, J. C.; Stephanov, M. A.; Verbaarschot, J. J. M.
2000-04-01
We apply the Glasgow method for lattice QCD at finite chemical potential to a schematic random matrix model. In this method the zeros of the partition function are obtained by averaging the coefficients of its expansion in powers of the chemical potential. In this paper we investigate the phase structure by means of Glasgow averaging and demonstrate that the method converges to the correct analytically known result. We conclude that the statistics needed for complete convergence grows exponentially with the size of the system--in our case, the dimension of the Dirac matrix. The use of an unquenched ensemble at {mu}=0 does not give an improvement over a quenched ensemble. We elucidate the phenomenon of a faster convergence of certain zeros of the partition function. The imprecision affecting the coefficients of the polynomial in the chemical potential can be interpeted as the appearance of a spurious phase. This phase dominates in the regions where the exact partition function is exponentially small, introducing additional phase boundaries, and hiding part of the true ones. The zeros along the surviving parts of the true boundaries remain unaffected. (c) 2000 The American Physical Society.
Large N techniques for Nekrasov partition functions and AGT conjecture
NASA Astrophysics Data System (ADS)
Bourgine, Jean-Emile
2013-05-01
The AGT conjecture relates {N} = 2 4d SUSY gauge theories to 2d CFTs. Matrix model techniques can be used to investigate both sides of this relation. The large N limit refers here to the size of Young tableaux in the expression of the gauge theory partition function. It corresponds to the vanishing of Ω-background equivariant deformation parameters, and should not be confused with the t'Hooft expansion at large number of colors. In this paper, a saddle point approach is employed to study the Nekrasov-Shatashvili limit of the gauge theory, leading to define β-deformed, or quantized, Seiberg-Witten curve and differential form. Then this formalism is compared to the large N limit of the Dijkgraaf-Vafa β-ensemble. A transformation law relating the wave functions appearing at both sides of the conjecture is proposed. It implies a transformation of the Seiberg-Witten 1-form in agreement with the definition specified earlier. As a side result, a remarkable property of {N} = 2 theories emerged: the instanton contribution to the partition function can be determined from the perturbative term analysis.
Chamber identity programs drive early functional partitioning of the heart.
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
2015-08-26
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.
Partition function zeros and phase transitions of a polymer chain
NASA Astrophysics Data System (ADS)
Phyo Aung, Pyie; Taylor, Mark
2011-10-01
The zeros of the canonical partition functions for flexible square-well polymer chains have been computed for chains up to length 256 for a range of square-well diameters. We have previously shown that such chain molecules can undergo a coil-globule and globule-crystal transition as well as a direct coil-crystal transition [1]. Here we show that each of these transitions has a well-defined signature in the complex-plane map of the partition function zeros. The freezing transitions are characterized by nearly circular rings of uniformly spaced roots, indicative of a discontinuous transition. The collapse transition is signaled by the coalescence of roots onto an elliptical horse-shoe segment pinching down towards the positive real axis. For sufficiently small square-well diameter the elliptical collapse ring merges with the circular freezing ring yielding the direct coil-crystal transition. The root density of all rings increases with increasing chain length and the leading roots move towards the positive real axis, implying a divergence of the specific heat in the thermodynamic limit (as originally proposed by Yang and Lee). [4pt] [1] M.P. Taylor, W. Paul, and K. Binder, J. Chem. Phys. 131, 114907 (2009).
Computing black hole partition functions from quasinormal modes
Arnold, Peter; Szepietowski, Phillip; Vaman, Diana
2016-07-07
We propose a method of computing one-loop determinants in black hole space-times (with emphasis on asymptotically anti-de Sitter black holes) that may be used for numerics when completely-analytic results are unattainable. The method utilizes the expression for one-loop determinants in terms of quasinormal frequencies determined by Denef, Hartnoll and Sachdev in [1]. A numerical evaluation must face the fact that the sum over the quasinormal modes, indexed by momentum and overtone numbers, is divergent. A necessary ingredient is then a regularization scheme to handle the divergent contributions of individual fixed-momentum sectors to the partition function. To this end, we formulatemore » an effective two-dimensional problem in which a natural refinement of standard heat kernel techniques can be used to account for contributions to the partition function at fixed momentum. We test our method in a concrete case by reproducing the scalar one-loop determinant in the BTZ black hole background. Furthermore, we then discuss the application of such techniques to more complicated spacetimes.« less
Computing black hole partition functions from quasinormal modes
Arnold, Peter; Szepietowski, Phillip; Vaman, Diana
2016-07-07
We propose a method of computing one-loop determinants in black hole space-times (with emphasis on asymptotically anti-de Sitter black holes) that may be used for numerics when completely-analytic results are unattainable. The method utilizes the expression for one-loop determinants in terms of quasinormal frequencies determined by Denef, Hartnoll and Sachdev in [1]. A numerical evaluation must face the fact that the sum over the quasinormal modes, indexed by momentum and overtone numbers, is divergent. A necessary ingredient is then a regularization scheme to handle the divergent contributions of individual fixed-momentum sectors to the partition function. To this end, we 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. Furthermore, we then discuss the application of such techniques to more complicated spacetimes.
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.
Partitioned density functional approach for a Lennard-Jones fluid.
Zhou, Shiqi
2003-12-01
The existing classical density functional approach for nonuniform Lennard-Jones fluid, which is based on dividing the Lennard-Jones interaction potential into a short-range, repulsive part, and a smoothly varying, long-range, attractive tail, was improved by dividing the bulk second-order direct correlation function into strongly density-depending short-range part and weakly density-depending long-range part. The latter is treated by functional perturbation expansion truncated at the lowest order whose accuracy depends on how weakly the long-range part depends on the bulk density. The former is treated by the truncated functional perturbation expansion which is rewritten in the form of the simple weighted density approximation and incorporates the omitted higher-order terms by applying Lagrangian theorem of differential calculus to the reformulated form. The two approximations are put into the density profile equation of the density functional theory formalism to predict the density distribution for Lennard-Jones fluid in contact with a hard wall or between two hard walls within the whole density range for reduced temperature T(*)=1.35 and a density point for reduced temperature T(*)=1. The present partitioned density functional theory performs much better than several previous density functional perturbation theory approaches and a recently proposed bridge density functional approximation.
Structural and functional partitioning of bread wheat chromosome 3B.
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.
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.
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.
What is the correct value for the brain: blood partition coefficient for water
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.
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.
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.
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.
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
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.
Dualities and Curved Space Partition Functions of Supersymmetric Theories
NASA Astrophysics Data System (ADS)
Agarwal, Prarit
In this dissertation we discuss some conjectured dualities in supersymmetric field theories and provide non-trivial checks for these conjectures. A quick review of supersymmetry and related topics is provided in chapter 1. In chapter 2, we develop a method to identify the so called BPS states in the Hilbert space of a supersymmetric field theory (that preserves at least two real supercharges) on a generic curved space. As an application we obtain the superconformal index (SCI) of 4d theories. The large N SCI of quiver gauge theories has been previously noticed to factorize over the set of extremal BPS mesonic operators. In chapter 3, we reformulate this factorization in terms of the zigzag paths in the dimer model associated to the quiver and extend the factorization theorem of the index to include theories obtained from D-branes probing orbifold singularities. In chapter 4, we consider the dualities in two classes of 3 dimensional theories. The first class consist of dualities of certain necklace type Chern-Simons (CS) quiver gauge theories. A non trivial check of these dualities is provided by matching their squashed sphere partition functions. The second class consists of theories whose duals are described by a collection of free fields. In such cases, due to mixing between the superconformal R-symmetry and accidental symmetries, the matching of electric and magnetic partition functions is not straightforward. We provide a prescription to rectify this mismatch. In chapter 5, we consider some the N = 1 4d theories with orthogonal and symplectic gauge groups, arising from N = 1 preserving reduction of 6d theories on a Riemann surface. This construction allows us to dual descriptions of 4d theories. Some of the dual frames have no known Lagrangian description. We check the dualities by computing the anomaly coefficients and the superconformal indices. We also give a prescription to write the index of the theory obtained by reduction of 6d theories on a three
Developmental and functional considerations of masseter muscle partitioning.
Widmer, C G; English, A W; Morris-Wiman, J
2007-04-01
The masseter muscle participates in a wide variety of activities including mastication, swallowing and speech. The functional demands for accurate mandibular positioning and generation of forces during incising or a power stroke require a diverse set of forces that are determined by the innate muscle form. The complex internal tendon architecture subdivides the masseter into multiple partitions that can be further subdivided into neuromuscular compartments representing small motor unit territories. Individual masseter compartments have unique biomechanical properties that, when activated individually or in groups, can generate a wide range of sagittal and off-sagittal torques about the temporomandibular joint. The myosin heavy chain (MyHC) fibre-type distribution in the adult masseter is sexually dimorphic and is influenced by hormones such as testosterone. These testosterone-dependent changes cause a phenotype switch from slower to faster fibre-types in the male. The development of the complex organization of the masseter muscle, the MyHC fibre-type message and protein expression, and the formation of endplates appear to be pre-programmed and not under control of the muscle nerve. However, secondary myotube generation and endplate maturation are nerve dependent. The delayed development of the masseter muscle compared with the facial, tongue and jaw-opening muscles may be related to the delayed functional requirements for chewing. In summary, masseter muscle form is pre-programmed prior to birth while muscle fibre contractile characteristics are refined postnatally in response to functional requirements. The motor control mechanisms that are required to coordinate the activation of discrete functional elements of this muscle remain to be determined.
Adiabatic corrections to density functional theory energies and wave functions.
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.
NASA Astrophysics Data System (ADS)
Luchko, Tyler; Blinov, Nikolay; Limon, Garrett C.; Joyce, Kevin P.; Kovalenko, Andriy
2016-11-01
Implicit solvent methods for classical molecular modeling are frequently used to provide fast, physics-based hydration free energies of macromolecules. Less commonly considered is the transferability of these methods to other solvents. The Statistical Assessment of Modeling of Proteins and Ligands 5 (SAMPL5) distribution coefficient dataset and the accompanying explicit solvent partition coefficient reference calculations provide a direct test of solvent model transferability. Here we use the 3D reference interaction site model (3D-RISM) statistical-mechanical solvation theory, with a well tested water model and a new united atom cyclohexane model, to calculate partition coefficients for the SAMPL5 dataset. The cyclohexane model performed well in training and testing (R=0.98 for amino acid neutral side chain analogues) but only if a parameterized solvation free energy correction was used. In contrast, the same protocol, using single solute conformations, performed poorly on the SAMPL5 dataset, obtaining R=0.73 compared to the reference partition coefficients, likely due to the much larger solute sizes. Including solute conformational sampling through molecular dynamics coupled with 3D-RISM (MD/3D-RISM) improved agreement with the reference calculation to R=0.93. Since our initial calculations only considered partition coefficients and not distribution coefficients, solute sampling provided little benefit comparing against experiment, where ionized and tautomer states are more important. Applying a simple pK_{ {a}} correction improved agreement with experiment from R=0.54 to R=0.66, despite a small number of outliers. Better agreement is possible by accounting for tautomers and improving the ionization correction.
Luchko, Tyler; Blinov, Nikolay; Limon, Garrett C; Joyce, Kevin P; Kovalenko, Andriy
2016-11-01
Implicit solvent methods for classical molecular modeling are frequently used to provide fast, physics-based hydration free energies of macromolecules. Less commonly considered is the transferability of these methods to other solvents. The Statistical Assessment of Modeling of Proteins and Ligands 5 (SAMPL5) distribution coefficient dataset and the accompanying explicit solvent partition coefficient reference calculations provide a direct test of solvent model transferability. Here we use the 3D reference interaction site model (3D-RISM) statistical-mechanical solvation theory, with a well tested water model and a new united atom cyclohexane model, to calculate partition coefficients for the SAMPL5 dataset. The cyclohexane model performed well in training and testing ([Formula: see text] for amino acid neutral side chain analogues) but only if a parameterized solvation free energy correction was used. In contrast, the same protocol, using single solute conformations, performed poorly on the SAMPL5 dataset, obtaining [Formula: see text] compared to the reference partition coefficients, likely due to the much larger solute sizes. Including solute conformational sampling through molecular dynamics coupled with 3D-RISM (MD/3D-RISM) improved agreement with the reference calculation to [Formula: see text]. Since our initial calculations only considered partition coefficients and not distribution coefficients, solute sampling provided little benefit comparing against experiment, where ionized and tautomer states are more important. Applying a simple [Formula: see text] correction improved agreement with experiment from [Formula: see text] to [Formula: see text], despite a small number of outliers. Better agreement is possible by accounting for tautomers and improving the ionization correction.
Research of partition function on optical properties and temperature diagnosis of air plasma
NASA Astrophysics Data System (ADS)
Qiu, Dechuan; Gao, Guoqiang; Wei, Wenfu; Hu, Haixing; Li, Chunmao; Wu, Guangning
2017-08-01
The relationship between partition function, particle density, refractive index, and temperature for atmospheric plasma is calculated based on thermodynamics and chemical equilibrium. Taking into account the contribution of hydrogen-like levels to the atomic partition function, a compact method to calculate the atomic partition function is first used with the Eindhoven model to deduce the plasma's refractive index. Results calculated by the new approach and two other traditional simplified methods are compared and analyzed. For a better understanding on the temperature measurement accuracy deduced by different partition function disposal approaches, moiré deflectometry is employed as the experimental scheme to acquire the refractive index-position curve. Finally, applicability of different partition function disposal approaches are discussed, and results indicate that the optical properties deduced in this paper are well suited for the refractive index-based plasma diagnosis.
2D CFT partition functions at late times
NASA Astrophysics Data System (ADS)
Dyer, Ethan; Gur-Ari, Guy
2017-08-01
We consider the late time behavior of the analytically continued partition function Z( β + it) Z( β - it) in holographic 2 d CFTs. This is a probe of information loss in such theories and in their holographic duals. We show that each Virasoro character decays in time, and so information is not restored at the level of individual characters. We identify a universal decaying contribution at late times, and conjecture that it describes the behavior of generic chaotic 2 d CFTs out to times that are exponentially large in the central charge. It was recently suggested that at sufficiently late times one expects a crossover to random matrix behavior. We estimate an upper bound on the crossover time, which suggests that the decay is followed by a parametrically long period of late time growth. Finally, we discuss gravitationally-motivated integrable theories and show how information is restored at late times by a series of characters. This hints at a possible bulk mechanism, where information is restored by an infinite sum over non-perturbative saddles.
Semiclassical limits of quantum partition functions on infinite graphs
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)
Current density partitioning in time-dependent current density functional theory
Mosquera, Martín A.; Wasserman, Adam
2014-05-14
We adapt time-dependent current density functional theory to allow for a fragment-based solution of the many-electron problem of molecules in the presence of time-dependent electric and magnetic fields. Regarding a molecule as a set of non-interacting subsystems that individually evolve under the influence of an auxiliary external electromagnetic vector-scalar potential pair, the partition 4-potential, we show that there are one-to-one mappings between this auxiliary potential, a sharply-defined set of fragment current densities, and the total current density of the system. The partition electromagnetic (EM) 4-potential is expressed in terms of the real EM 4-potential of the system and a gluing EM 4-potential that accounts for exchange-correlation effects and mutual interaction forces between fragments that are required to yield the correct electron dynamics. We prove the zero-force theorem for the fragmented system, establish a variational formulation in terms of action functionals, and provide a simple illustration for a charged particle in a ring.
Wang, Y X; Zhao, H; Harding, T M; Gomes de Mesquita, D S; Woldringh, C L; Klionsky, D J; Munn, A L; Weisman, L S
1996-01-01
In Saccharomyces cerevisiae the vacuoles are partitioned from mother cells to daughter cells in a cell-cycle-coordinated process. The molecular basis of this event remains obscure. To date, few yeast mutants had been identified that are defective in vacuole partitioning (vac), and most such mutants are also defective in vacuole protein sorting (vps) from the Golgi to the vacuole. Both the vps mutants and previously identified non-vps vac mutants display an altered vacuolar morphology. Here, we report a new method to monitor vacuole inheritance and the isolation of six new non-vps vac mutants. They define five complementation groups (VAC8-VAC12). Unlike mutants identified previously, three of the complementation groups exhibit normal vacuolar morphology. Zygote studies revealed that these vac mutants are also defective in intervacuole communication. Although at least four pathways of protein delivery to the vacuole are known, only the Vps pathway seems to significantly overlap with vacuole partitioning. Mutants defective in both vacuole partitioning and endocytosis or vacuole partitioning and autophagy were not observed. However, one of the new vac mutants was additionally defective in direct protein transport from the cytoplasm to the vacuole. Images PMID:8885233
The crystal structures of the eukaryotic chaperonin CCT reveal its functional partitioning.
Kalisman, Nir; Schröder, Gunnar F; Levitt, Michael
2013-04-02
In eukaryotes, CCT is essential for the correct and efficient folding of many cytosolic proteins, most notably actin and tubulin. Structural studies of CCT have been hindered by the failure of standard crystallographic analysis to resolve its eight different subunit types at low resolutions. Here, we exhaustively assess the R value fit of all possible CCT models to available crystallographic data of the closed and open forms with resolutions of 3.8 Å and 5.5 Å, respectively. This unbiased analysis finds the native subunit arrangements with overwhelming significance. The resulting structures provide independent crystallographic proof of the subunit arrangement of CCT and map major asymmetrical features of the particle onto specific subunits. The actin and tubulin substrates both bind around subunit CCT6, which shows other structural anomalies. CCT is thus clearly partitioned, both functionally and evolutionary, into a substrate-binding side that is opposite to the ATP-hydrolyzing side.
Partition function of free conformal fields in 3-plet representation
NASA Astrophysics Data System (ADS)
Beccaria, Matteo; Tseytlin, Arkady A.
2017-05-01
Simplest examples of AdS/CFT duality correspond to free CFTs in d dimensions with fields in vector or adjoint representation of an internal symmetry group dual in the large N limit to a theory of massless or massless plus massive higher spins in AdS d+1. One may also study generalizations when conformal fields belong to higher dimensional representations, i.e. carry more than two internal symmetry indices. Here we consider the case of the 3-fundamental ("3-plet") representation. One motivation is a conjectured connection to multiple M5-brane theory: heuristic arguments suggest that it may be related to an (interacting) CFT of 6d (2,0) tensor multiplets in 3-plet representation of large N symmetry group that has an AdS7 dual. We compute the singlet partition function Z on S 1 × S d-1 for a free field in 3-plet representation of U( N) and analyse its novel large N behaviour. The large N limit of the low temperature expansion of Z which is convergent in the vector and adjoint cases here is only asymptotic, reflecting the much faster growth of the number of singlet operators with dimension, indicating a phase transition at very low temperature. Indeed, while the critical temperatures in the vector ( T c ˜ N γ , γ > 0) and adjoint ( T c ˜ 1) cases are finite, we find that in the 3-plet case T c ˜ (log N)-1, i.e. it approaches zero at large N. We discuss some details of large N solution for the eigenvalue distribution. Similar conclusions apply to higher p-plet representations of U( N) or O( N) and also to the free p-tensor theories invariant under [U( N)] p or [ O( N)] p with p ≥ 3.
Conformal partition functions of critical percolation from D 3 thermodynamic Bethe Ansatz equations
NASA Astrophysics Data System (ADS)
Morin-Duchesne, Alexi; Klümper, Andreas; Pearce, Paul A.
2017-08-01
Using the planar Temperley-Lieb algebra, critical bond percolation on the square lattice can be reformulated as a loop model. In this form, it is incorporated as {{ L}}{{ M}}(2, 3) in the Yang-Baxter integrable family of logarithmic minimal models {{ L}}{{ M}}( p, p\\prime) . We consider this model of percolation in the presence of boundaries and with periodic boundary conditions. Inspired by Kuniba, Sakai and Suzuki, we rewrite the recently obtained infinite Y-system of functional equations. In this way, we obtain nonlinear integral equations in the form of a closed finite set of TBA equations described by a D 3 Dynkin diagram. Following the methods of Klümper and Pearce, we solve the TBA equations for the conformal finite-size corrections. For the ground states of the standard modules on the strip, these agree with the known central charge c = 0 and conformal weights Δ1, s for \\renewcommand≥≥slant} s\\in {{ Z}≥slant 1} with Δr, s=\\big((3r-2s){\\hspace{0pt}}^2-1\\big)/24 . For the periodic case, the finite-size corrections agree with the conformal weights Δ0, s , Δ1, s with \\renewcommand{≥{≥slant} s\\in\\frac{1}{2}{{ Z}≥slant 0} . These are obtained analytically using Rogers dilogarithm identities. We incorporate all finite excitations by formulating empirical selection rules for the patterns of zeros of all the eigenvalues of the standard modules. We thus obtain the conformal partition functions on the cylinder and the modular invariant partition function (MIPF) on the torus. By applying q-binomial and q-Narayana identities, it is shown that our refined finitized characters on the strip agree with those of Pearce, Rasmussen and Zuber. For percolation on the torus, the MIPF is a non-diagonal sesquilinear form in affine u(1) characters given by the u(1) partition function Z2, 3(q)=Z2, 3{Circ}(q) . The u(1) operator content is {{ N}}Δ, \\barΔ=1 for Δ=\\barΔ=-\\frac{1}{24}, \\frac{35}{24} and {{ N}}Δ, \\barΔ=2 for
Quantum correction to the pair distribution function.
Levashov, V A; Billinge, S J L; Thorpe, M F
2007-08-01
We report a numerical technique that allows the quantum effects of zero-point motion to be incorporated into Pair Distribution Functions calculated classically for molecules using Monte Carlo or Molecular Dynamics simulations. We establish the basis for this approximation using a diatomic molecule described by a Morse potential. The correction should significantly improve the agreement between modeled and experimental data, and facilitate conclusions about inter- and intra-molecular motion and flexibility. We describe a similar approach to obtain the energy and the specific heat.
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.
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.
NASA Astrophysics Data System (ADS)
Bučko, Tomáš; Lebègue, Sébastien; Ángyán, János G.; Hafner, Jürgen
2014-07-01
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.
Nagesh, Jayashree; Frisch, Michael J; Brumer, Paul; Izmaylov, Artur F
2016-12-28
We extend the localized operator partitioning method (LOPM) [J. Nagesh, A. F. Izmaylov, and P. Brumer, J. Chem. Phys. 142, 084114 (2015)] to the time-dependent density functional theory framework to partition molecular electronic energies of excited states in a rigorous manner. A molecular fragment is defined as a collection of atoms using Becke's atomic partitioning. A numerically efficient scheme for evaluating the fragment excitation energy is derived employing a resolution of the identity to preserve standard one- and two-electron integrals in the final expressions. The utility of this partitioning approach is demonstrated by examining several excited states of two bichromophoric compounds: 9-((1- naphthyl)- methyl)- anthracene and 4-((2- naphthyl)- methyl)- benzaldehyde. The LOPM is found to provide nontrivial insights into the nature of electronic energy localization that is not accessible using a simple density difference analysis.
Transfer functions for solid-solution partitioning of cadmium for Australian soils.
de Vries, W; McLaughlin, M J; Groenenberg, J E
2011-12-01
To assess transport and ecotoxicological risks of metals, such as cadmium (Cd) in soils, models are needed for partitioning and speciation. We derived regression-based "partition-relations" based on adsorption and desorption experiments for main Australian soil types. First, batch adsorption experiments were carried out over a realistic range of dissolved Cd concentrations in agricultural soils in Australia. Results showed linear sorption relationships, implying the adequacy of using Kd values to describe partitioning. Desorption measurements were then carried out to assess in-situ Kd values and relate these to soil properties The best transfer functions for solid-solution partitioning were found for Kd values relating total dissolved Cd concentration to total soil Cd concentrations, accounting for the variation in pH, SOM contents and DOC concentrations. Model predictions compared well with measurements of an independent data set, but there was a tendency to underestimate dissolved Cd concentrations of highly polluted soils.
NASA Astrophysics Data System (ADS)
Nagesh, Jayashree; Frisch, Michael J.; Brumer, Paul; Izmaylov, Artur F.
2016-12-01
We extend the localized operator partitioning method (LOPM) [J. Nagesh, A. F. Izmaylov, and P. Brumer, J. Chem. Phys. 142, 084114 (2015)] to the time-dependent density functional theory framework to partition molecular electronic energies of excited states in a rigorous manner. A molecular fragment is defined as a collection of atoms using Becke's atomic partitioning. A numerically efficient scheme for evaluating the fragment excitation energy is derived employing a resolution of the identity to preserve standard one- and two-electron integrals in the final expressions. The utility of this partitioning approach is demonstrated by examining several excited states of two bichromophoric compounds: 9-((1- naphthyl)- methyl)- anthracene and 4-((2- naphthyl)- methyl)- benzaldehyde. The LOPM is found to provide nontrivial insights into the nature of electronic energy localization that is not accessible using a simple density difference analysis.
Partition and generating function zeros in adsorbing self-avoiding walks
NASA Astrophysics Data System (ADS)
Janse van Rensburg, E. J.
2017-03-01
The Lee–Yang theory of adsorbing self-avoiding walks is presented. It is shown that Lee–Yang zeros of the generating function of this model asymptotically accumulate uniformly on a circle in the complex plane, and that Fisher zeros of the partition function distribute in the complex plane such that a positive fraction are located in annular regions centred at the origin. These results are examined in a numerical study of adsorbing self-avoiding walks in the square and cubic lattices. The numerical data are consistent with the rigorous results; for example, Lee–Yang zeros are found to accumulate on a circle in the complex plane and a positive fraction of partition function zeros appear to accumulate on a critical circle. The radial and angular distributions of partition function zeros are also examined and it is found to be consistent with the rigorous results.
3D-partition functions on the sphere: exact evaluation and mirror symmetry
NASA Astrophysics Data System (ADS)
Benvenuti, Sergio; Pasquetti, Sara
2012-05-01
We study {N} = {4} quiver theories on the three-sphere. We compute partition functions using the localisation method by Kapustin et al. solving exactly the matrix integrals at finite N, as functions of mass and Fayet-Iliopoulos parameters. We find a simple explicit formula for the partition function of the quiver tail T(SU( N)). This formula opens the way for the analysis of star-shaped quivers and their mirrors (that are the Gaiotto-type theories arising from M5 branes on punctured Riemann surfaces). We provide non-perturbative checks of mirror symmetry for infinite classes of theories and find the partition functions of the T N theory, the building block of generalised quiver theories.
Efficient algorithm for computing exact partition functions of lattice polymer models
NASA Astrophysics Data System (ADS)
Hsieh, Yu-Hsin; Chen, Chi-Ning; Hu, Chin-Kun
2016-12-01
Polymers are important macromolecules in many physical, chemical, biological and industrial problems. Studies on simple lattice polymer models are very helpful for understanding behaviors of polymers. We develop an efficient algorithm for computing exact partition functions of lattice polymer models, and we use this algorithm and personal computers to obtain exact partition functions of the interacting self-avoiding walks with N monomers on the simple cubic lattice up to N = 28 and on the square lattice up to N = 40. Our algorithm can be extended to study other lattice polymer models, such as the HP model for protein folding and the charged HP model for protein aggregation. It also provides references for checking accuracy of numerical partition functions obtained by simulations.
NASA Astrophysics Data System (ADS)
Kamarchik, Eugene; Jasper, Ahren W.
2013-05-01
An algorithm is presented for calculating fully anharmonic vibrational state counts, state densities, and partition functions for molecules using Monte Carlo integration of classical phase space. The algorithm includes numerical evaluations of the elements of the Jacobian and is general enough to allow for sampling in arbitrary curvilinear or rectilinear coordinate systems. Invariance to the choice of coordinate system is demonstrated for vibrational state densities of methane, where we find comparable sampling efficiency when using curvilinear z-matrix and rectilinear Cartesian normal mode coordinates. In agreement with past work, we find that anharmonicity increases the vibrational state density of methane by a factor of ˜2 at its dissociation threshold. For the vinyl radical, we find a significant (˜10×) improvement in sampling efficiency when using curvilinear z-matrix coordinates relative to Cartesian normal mode coordinates. We attribute this improved efficiency, in part, to a more natural curvilinear coordinate description of the double well associated with the H2C-C-H wagging motion. The anharmonicity correction for the vinyl radical state density is ˜1.4 at its dissociation threshold. Finally, we demonstrate that with trivial parallelizations of the Monte Carlo step, tractable calculations can be made for the vinyl radical using direct ab initio potential energy surface evaluations and a composite QCISD(T)/MP2 method.
Kamarchik, Eugene; Jasper, Ahren W
2013-05-21
An algorithm is presented for calculating fully anharmonic vibrational state counts, state densities, and partition functions for molecules using Monte Carlo integration of classical phase space. The algorithm includes numerical evaluations of the elements of the Jacobian and is general enough to allow for sampling in arbitrary curvilinear or rectilinear coordinate systems. Invariance to the choice of coordinate system is demonstrated for vibrational state densities of methane, where we find comparable sampling efficiency when using curvilinear z-matrix and rectilinear Cartesian normal mode coordinates. In agreement with past work, we find that anharmonicity increases the vibrational state density of methane by a factor of ∼2 at its dissociation threshold. For the vinyl radical, we find a significant (∼10×) improvement in sampling efficiency when using curvilinear z-matrix coordinates relative to Cartesian normal mode coordinates. We attribute this improved efficiency, in part, to a more natural curvilinear coordinate description of the double well associated with the H2C-C-H wagging motion. The anharmonicity correction for the vinyl radical state density is ∼1.4 at its dissociation threshold. Finally, we demonstrate that with trivial parallelizations of the Monte Carlo step, tractable calculations can be made for the vinyl radical using direct ab initio potential energy surface evaluations and a composite QCISD(T)/MP2 method.
Liu, Qian; Chen, Yi-Ping Phoebe; Li, Jinyan
2014-01-07
Many studies are aimed at identifying dense clusters/subgraphs from protein-protein interaction (PPI) networks for protein function prediction. However, the prediction performance based on the dense clusters is actually worse than a simple guilt-by-association method using neighbor counting ideas. This indicates that the local topological structures and properties of PPI networks are still open to new theoretical investigation and empirical exploration. We introduce a novel topological structure called k-partite cliques of protein interactions-a functionally coherent but not-necessarily dense subgraph topology in PPI networks-to study PPI networks. A k-partite protein clique is a maximal k-partite clique comprising two or more nonoverlapping protein subsets between any two of which full interactions are exhibited. In the detection of PPI's maximal k-partite cliques, we propose to transform PPI networks into induced K-partite graphs where edges exist only between the partites. Then, we present a maximal k-partite clique mining (MaCMik) algorithm to enumerate maximal k-partite cliques from K-partite graphs. Our MaCMik algorithm is then applied to a yeast PPI network. We observed interesting and unusually high functional coherence in k-partite protein cliques-the majority of the proteins in k-partite protein cliques, especially those in the same partites, share the same functions, although k-partite protein cliques are not restricted to be dense compared with dense subgraph patterns or (quasi-)cliques. The idea of k-partite protein cliques provides a novel approach of characterizing PPI networks, and so it will help function prediction for unknown proteins.
Some exact results on the Potts model partition function in a magnetic field
NASA Astrophysics Data System (ADS)
Chang, Shu-Chiuan; Shrock, Robert
2009-09-01
We consider the Potts model in a magnetic field on an arbitrary graph G. Using a formula by F Y Wu for the partition function Z of this model as a sum over spanning subgraphs of G, we prove some properties of Z concerning factorization, monotonicity and zeros. A generalization of the Tutte polynomial is presented that corresponds to this partition function. In this context, we formulate and discuss two weighted graph-coloring problems. We also give a general structural result for Z for cyclic strip graphs.
Reducing the 4d index to the S 3 partition function
NASA Astrophysics Data System (ADS)
Gadde, Abhijit; Yan, Wenbin
2012-12-01
The superconformal index of a 4 d gauge theory is computed by a matrix integral arising from localization of the supersymmetric path integral on S 3 × S 1. As the radius of the circle goes to zero, it is natural to expect that the 4 d path integral becomes the partition function of dimensionally reduced gauge theory on S 3. We show that this is indeed the case and recover the matrix integral of Kapustin, Willett and Yaakov from the matrix integral that computes the superconformal index. Remarkably, the superconformal index of the "parent" 4 d theory can be thought of as the q-deformation of the 3 d partition function.
Partitioned log-rank tests for the overall homogeneity of hazard rate functions.
Liu, Yukun; Yin, Guosheng
2016-03-19
In survival analysis, it is routine to test equality of two survival curves, which is often conducted by using the log-rank test. Although it is optimal under the proportional hazards assumption, the log-rank test is known to have little power when the survival or hazard functions cross. To test the overall homogeneity of hazard rate functions, we propose a group of partitioned log-rank tests. By partitioning the time axis and taking the supremum of the sum of two partitioned log-rank statistics over different partitioning points, the proposed test gains enormous power for cases with crossing hazards. On the other hand, when the hazards are indeed proportional, our test still maintains high power close to that of the optimal log-rank test. Extensive simulation studies are conducted to compare the proposed test with existing methods, and three real data examples are used to illustrate the commonality of crossing hazards and the advantages of the partitioned log-rank tests.
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.
Exact Potts model partition function on strips of the triangular lattice
NASA Astrophysics Data System (ADS)
Chang, Shu-Chiuan; Shrock, Robert
2000-10-01
In this paper 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 strip graphs, of width Ly=2 and arbitrary length, of the triangular lattice 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 the graphs, and the thermodynamics is discussed. 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. Comparisons are made with our previous exact calculation of Potts model partition functions for the corresponding strips of the square lattice. Our present calculations yield, as special cases, several quantities of graph-theoretic interest.
Partition function and astronomical observation of interstellar isomers: Is there a link?
NASA Astrophysics Data System (ADS)
Etim, Emmanuel E.; Arunan, Elangannan
2017-02-01
The unsuccessful astronomical searches for some important astrophysical and astrobiological molecules have been linked to the large partition function of these molecules. This letter reports an extensive investigation of the relationship between partition function and astronomical observation of interstellar isomers using high level quantum chemical calculations. 120 molecules from 30 different isomeric groups have been considered. Partition function and thermodynamic stabilities are determined for each set of isomeric species. From the results, there is no direct correlation between partition function and astronomical observation of the same isomeric species. Though interstellar formations processes are generally controlled by factors like kinetics, thermodynamics, formation and destruction pathways. However, the observation of the isomers seems to correlate well with thermodynamics. For instance, in all the groups considered, the astronomically detected isomers are the thermodynamically most stable molecules in their respective isomeric groups. The implications of these results in accounting for the limited number of known cyclic interstellar molecules, unsuccessful searches for amino acid and the possible molecules for astronomical observations are discussed.
Kuo, Yu-Chieh; Chen, Yu-Cheng; Yang, Jeng-How; Tsai, Perng-Jy; Wang, Lin-Chi; Chang-Chien, Guo-Ping
2012-03-30
This study was aimed at developing an approach for correcting the gas and particle partitioning of PCDD/F congeners for samples collected from the flue gas of an iron ore sinter plant. An iron ore sinter plant equipped with an electrostatic precipitator (EP) and a selective catalytic reduction (SCR) was selected. Flue gas samples were collected at EP inlet, EP outlet and SCR outlet. Both particle- and gas-phase PCDD/Fs were analyzed for each collected sample. PCDD/F contents in EP ashes (EP(ash)) were also analyzed and used to correct the gas and particle partitioning of PCDD/F congeners of the collected flue gas samples. Results show that PCDD/Fs in the flue gas were dominated by the gas-phase. Before correction, the removal efficiencies for the gas- and particle-phase PCDD/Fs for EP were -58.1% and 64.3%, respectively, and SCR were 39.4% and 83.9%, respectively. The above results were conflict with the expected results for both EP and SCR indicating the need for correcting the gas and particle partitioning of PCDD/F congeners for all collected flue gas samples. After correction, the removal efficiencies become more reasonable for EP (=4.22% and 97.7%, respectively), and SCR (=54.7% and 62.0%, respectively). The above results confirm the effectiveness of the approach developed by this study. Copyright Â© 2012 Elsevier B.V. All rights reserved.
Niu, Yiming; Wang, Jiayi; Zhang, Chi; Chen, Yiqiang
2017-04-15
The objective of this study was to develop a micro-plate based colorimetric assay for rapid and high-throughput detection of copper in animal feed. Copper ion in animal feed was extracted by trichloroacetic acid solution and reduced to cuprous ion by hydroxylamine. The cuprous ion can chelate with 2,2'-bicinchoninic acid to form a Cu-BCA complex which was detected with high sensitivity by micro-plate reader at 354nm. The whole assay procedure can be completed within 20min. To eliminate matrix interference, a statistical partitioning correction approach was proposed, which makes the detection of copper in complex samples possible. The limit of detection was 0.035μg/mL and the detection range was 0.1-10μg/mL of copper in buffer solution. Actual sample analysis indicated that this colorimetric assay produced results consistent with atomic absorption spectrometry analysis. These results demonstrated that the developed assay can be used for rapid determination of copper in animal feed.
Soft Clustering Criterion Functions for Partitional Document Clustering
2004-05-26
of the corresponding clusters. We represent the documents using the vector- space model [35]. In this model, each document d is considered to be a...vector in the space of the distinct terms present in the collection. We employ the tf-idf term-weighting scheme that represents each document d as the...produce balanced clusters. In this paper, due to space constraints, we focus on only four out of these seven criterion functions, which are referred to as
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.
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.
Optimal gene partition into operons correlates with gene functional order
NASA Astrophysics Data System (ADS)
Zaslaver, Alon; Mayo, Avi; Ronen, Michal; Alon, Uri
2006-09-01
Gene arrangement into operons varies between bacterial species. Genes in a given system can be on one operon in some organisms and on several operons in other organisms. Existing theories explain why genes that work together should be on the same operon, since this allows for advantageous lateral gene transfer and accurate stoichiometry. But what causes the frequent separation into multiple operons of co-regulated genes that act together in a pathway? Here we suggest that separation is due to benefits made possible by differential regulation of each operon. We present a simple mathematical model for the optimal distribution of genes into operons based on a balance of the cost of operons and the benefit of regulation that provides 'just-when-needed' temporal order. The analysis predicts that genes are arranged such that genes on the same operon do not skip functional steps in the pathway. This prediction is supported by genomic data from 137 bacterial genomes. Our work suggests that gene arrangement is not only the result of random historical drift, genome re-arrangement and gene transfer, but has elements that are solutions of an evolutionary optimization problem. Thus gene functional order may be inferred by analyzing the operon structure across different genomes.
Conformal Orbifold Partition Functions from Topologically Massive Gauge Theory
NASA Astrophysics Data System (ADS)
Castelo Ferreira, Pedro; Kogan, Ian I.; Szabo, Richard J.
2002-04-01
We continue the development of the topological membrane approach to open and unoriented string theories. We study orbifolds of topologically massive gauge theory defined on the geometry [0,1] × Σ, where Σ is a generic compact Riemann surface. The orbifold operations are constructed by gauging the discrete symmetries of the bulk three-dimensional field theory. Multi-loop bosonic string vacuum amplitudes are thereby computed as bulk correlation functions of the gauge theory. It is shown that the three-dimensional correlators naturally reproduce twisted and untwisted sectors in the case of closed worldsheet orbifolds, and Neumann and Dirichlet boundary conditions in the case of open ones. The bulk wavefunctions are used to explicitly construct the characters of the underlying extended Kac-Moody group for arbitrary genus. The correlators for both the original theory and its orbifolds give the expected modular invariant statistical sums over the characters.
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.
Multifractal analysis of Chinese stock volatilities based on the partition function approach
NASA Astrophysics Data System (ADS)
Jiang, Zhi-Qiang; Zhou, Wei-Xing
2008-08-01
We have performed a detailed multifractal analysis on the 1-min volatility of two indexes and 1139 stocks in the Chinese stock markets based on the partition function approach. The partition function χq(s) scales as a power law with respect to the box size s. The scaling exponents τ(q) form a nonlinear function of q. Statistical tests based on bootstrapping show that the extracted multifractal nature is significant at the 1% significance level. The individual securities can be well modeled by the p-model in turbulence with p=0.40±0.02. Based on the idea of ensemble averaging (including quenched and annealed average), we treat each stock exchange as a whole and confirm the existence of multifractal nature in the Chinese stock markets.
Supersymmetric partition functions and the three-dimensional A-twist
NASA Astrophysics Data System (ADS)
Closset, Cyril; Kim, Heeyeon; Willett, Brian
2017-03-01
We study three-dimensional N=2 supersymmetric gauge theories on M_{g,p} , an oriented circle bundle of degree p over a closed Riemann surface, Σ g . We compute the M_{g,p} supersymmetric partition function and correlation functions of supersymmetric loop operators. This uncovers interesting relations between observables on manifolds of different topologies. In particular, the familiar supersymmetric partition function on the round S 3 can be understood as the expectation value of a so-called "fibering operator" on S 2 ×S 1 with a topological twist. More generally, we show that the 3d N=2 supersymmetric partition functions (and supersymmetric Wilson loop correlation functions) on M_{g,p} are fully determined by the two-dimensional A-twisted topological field theory obtained by compactifying the 3d theory on a circle. We give two complementary derivations of the result. We also discuss applications to F-maximization and to three-dimensional supersymmetric dualities.
Missing mass approximations for the partition function of stimulus driven Ising models.
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 N pat the number of unique patterns in the data, contrasting with the O(L2 (N) ) 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.
Missing mass approximations for the partition function of stimulus driven Ising models
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
Structure Functions at Low Q^2: Target Mass Corrections
Wally Melnitchouk
2007-05-30
We discuss recent developments in the study of structure functions at low Q^2, focusing in particular on the issue of target mass corrections (TMC) to nucleon structure functions. We summarize the standard TMC implementation, and contrast this with a new formulation which has the correct kinematic threshold behavior at finite Q^2 in the x -> 1 limit.
Correction for the STIS echelle blaze function
NASA Technical Reports Server (NTRS)
Heap, Sara R.; Brown, Thomas M.
1997-01-01
Using the Early Release Observation of 9 Comae, we demonstrate an iterative method for correcting Space Telescope Imaging Spectrograph (STIS) echelle spectra for the effects of the echelle ripple. This analytic approach allows the actual spectrum of interest to be used in the determination of its calibration. The late F star 9 Comae is not an ideal candidate for this method, due to the many absorption lines present in its E230M spectrum, yet, given this difficulty, the method still works quite well.
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.
Partition functions with spin in AdS2 via quasinormal mode methods
NASA Astrophysics Data System (ADS)
Keeler, Cynthia; Lisbão, Pedro; Ng, Gim Seng
2016-10-01
We extend the results of [1], computing one loop partition functions for massive fields with spin half in AdS2 using the quasinormal mode method proposed by Denef, Hartnoll, and Sachdev [2]. We find the finite representations of SO(2, 1) for spin zero and spin half, consisting of a highest weight state | h> and descendants with non-unitary values of h. These finite representations capture the poles and zeroes of the one loop determinants. Together with the asymptotic behavior of the partition functions (which can be easily computed using a large mass heat kernel expansion), these are sufficient to determine the full answer for the one loop determinants. We also discuss extensions to higher dimensional AdS2 n and higher spins.
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.
Partition Functions of the Light Elements (H to Na), A Revision
NASA Astrophysics Data System (ADS)
Milone, Luis A.; Merlo, David C.
1998-07-01
As the extensive calculations of atomic partition functions (APFs) made by Traving, Baschek and Holweger, Irwin, and Sauval and Tatum, have been widely used in the literature, the aim of this paper is to analyze whether the numerical values derived from their approximations are homogeneous and accurate, and which are their limitations. Irwin, and Sauval and Tatum, made their calculations for a lowering of the ionization energy Δχ =0.1 eV, and within a limited range of temperature; we found here, that in the solar atmosphere 0.005 ≤ Δχ ≤ 0.154 eV for a neutral atom (0.008 ≤ Δχ ≤ 0.245 eV for a singly ionized atom), whereas in a B-star atmosphere Δχ may become as large as 0.416 eV. Therefore, it is quite clear that the selection of a unique value for Δχ, may result in a poor determination of the APF-value. The representation of APFs made by Traving et al. has no limitation on temperature range, it gives the correct result for Δχ ≤ Δχlimit (Δχlimit being a function of the element and its ionization stage) and has the advantage of being computed in single numerical precision. One limitation it has is practical: if used in the analysis of the excitation and ionization equilibrium of a medium with many elements present, the full calculations require excessive computer time; other shortcomings were also found for the Traving et al. formulae, e.g., owing to overestimation of the ionization energy for Li I, Be II, B III, etc., too many terms are added up in the APF computation, and the value so obtained is larger than the right one if Δχ ≤ 0.01 eV. In a broad sense, it is shown that the representations of APFs made by Traving et al., Irwin, and Sauval and Tatum, are quite homogeneous and accurate; some exceptions are analyzed.
Rovibrational energies, partition functions and equilibrium fractionation of the CO2 isotopologues
NASA Astrophysics Data System (ADS)
Cerezo, J.; Bastida, A.; Requena, A.; Zúñiga, J.
2014-11-01
Rovibrational energy levels, partition functions and relative abundances of the stable isotopologues of CO2 in gas phase at equilibrium are calculated using an empirical Morse-cosine potential energy surface (PES) refined by fitting to the updated pure (l2 = 0) vibrational frequencies observed for the main 12C16O2 isotopologue. The rovibrational energy levels are calculated variationally using a system of optimized hyperspherical normal coordinates, and from these the vibrational terms Gv and rotational constants Bv of the isotopologues are determined. The refined potential surface is shown to be clearly superior to the original potential surface, with the former reproducing the observed values of the spectroscopic constants Gv and Bv with accuracies of about 0.1 cm-1 and 0.00020 cm-1, respectively, for levels with l2 ≥ 0 up to 10,000 cm-1 above the ground state. The internal partition functions of the isotopologues are calculated by approximated direct summation over the rovibrational energies and compared with both previous partition sums and values obtained from analytical expressions based on the harmonic oscillator and rigid rotor models. The partition functions calculated by approximated direct summation are then used to determine the abundances of the CO2 isotopologues at thermodynamic equilibrium using the method developed by Wang et al. [74]. Significant variations in the relative abundances of some of the CO2 multiple substituted isotopologues at terrestrial temperatures with respect to those provided by the classical harmonic-based Urey theory are found, which may be of relevance in geochemical processes.
Long-Range Corrected Hybrid Density Functionals with Damped Atom-Atom Dispersion Corrections
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.
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).
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.
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.
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.
A novel brain partition highlights the modular skeleton shared by structure and function
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
A novel brain partition highlights the modular skeleton shared by structure and function.
Diez, Ibai; Bonifazi, Paolo; Escudero, Iñaki; Mateos, Beatriz; Muñoz, Miguel A; Stramaglia, Sebastiano; Cortes, Jesus M
2015-06-03
Elucidating the intricate relationship between brain structure and function, both in healthy and pathological conditions, is a key challenge for modern neuroscience. Recent progress in neuroimaging has helped advance our understanding of this important issue, with diffusion images providing information about structural connectivity (SC) and functional magnetic resonance imaging shedding light on resting state functional connectivity (rsFC). Here, we adopt a systems approach, relying on modular hierarchical clustering, to study together SC and rsFC datasets gathered independently from healthy human subjects. Our novel approach allows us to find a common skeleton shared by structure and function from which a new, optimal, brain partition can be extracted. We describe the emerging common structure-function modules (SFMs) in detail and compare them with commonly employed anatomical or functional parcellations. Our results underline the strong correspondence between brain structure and resting-state dynamics as well as the emerging coherent organization of the human brain.
Parrish, Robert M; Parker, Trent M; Sherrill, C David
2014-10-14
Recently, we introduced an effective atom-pairwise partition of the many-body symmetry-adapted perturbation theory (SAPT) interaction energy decomposition, producing a method known as atomic SAPT (A-SAPT) [Parrish, R. M.; Sherrill, C. D. J. Chem. Phys. 2014, 141, 044115]. A-SAPT provides ab initio atom-pair potentials for force field development and also automatic visualizations of the spatial contributions of noncovalent interactions, but often has difficulty producing chemically useful partitions of the electrostatic energy, due to the buildup of oscillating partial charges on adjacent functional groups. In this work, we substitute chemical functional groups in place of atoms as the relevant local quasiparticles in the partition, resulting in a functional-group-pairwise partition denoted as functional-group SAPT (F-SAPT). F-SAPT assigns integral sets of local occupied electronic orbitals and protons to chemical functional groups and linking σ bonds. Link-bond contributions can be further assigned to chemical functional groups to simplify the analysis. This approach yields a SAPT partition between pairs of functional groups with integral charge (usually neutral), preventing oscillations in the electrostatic partition. F-SAPT qualitatively matches chemical intuition and the cut-and-cap fragmentation technique but additionally yields the quantitative many-body SAPT interaction energy. The conceptual simplicity, chemical utility, and computational efficiency of F-SAPT is demonstrated in the context of phenol dimer, proflavine(+)-DNA intercalation, and a cucurbituril host-guest inclusion complex.
Self-interaction corrections in density functional theory
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.
Accurate partition function for acetylene, 12C2H2, and related thermodynamical quantities.
Amyay, B; Fayt, A; Herman, M
2011-12-21
The internal partition function (Q(int)) of ethyne (acetylene), (12)C(2)H(2), is calculated by explicit summation of the contribution of all individual vibration-rotation energy levels up to 15,000 cm(-1). The corresponding energies are predicted from a global model and constants reproducing within 3σ all 18,415 published vibration-rotation lines in the literature involving vibrational states up to 8900 cm(-1), as produced by Amyay et al. [J. Mol. Spectrosc. 267, 80 (2011)]. Values of Q(int), with distinct calculations for para and ortho species are provided from 1 to 2000 K, in step of 1 K. The total internal partition function at 298.15 K is 104.224387(47) or 416.89755(19), with the nuclear degeneracy spin factors taken as 1/4:3/4 (astronomer convention) or 1:3 (atmospheric convention), respectively, for para:ortho species. The Helmholtz function, Gibbs enthalpy function, entropy, and specific heat at constant pressure are also calculated over the same temperature range. Accuracies as well as the missing contribution of the vinylidene isomer of acetylene in the calculations are discussed.
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.
NASA Astrophysics Data System (ADS)
Black, Jay R.; Kavner, Abby; Schauble, Edwin A.
2011-02-01
The goal of this study is to determine reduced partition function ratios for a variety of species of zinc, both as a metal and in aqueous solutions in order to calculate equilibrium stable isotope partitioning. We present calculations of the magnitude of Zn stable-isotope fractionation ( 66,67,68Zn/ 64Zn) between aqueous species and metallic zinc using measured vibrational spectra (fit from neutron scattering studies of metallic zinc) and a variety of electronic structure models. The results show that the reduced metal, Zn(0), will be light in equilibrium with oxidized Zn(II) aqueous species, with the best estimates for the Zn(II)-Zn(0) fractionation between hexaquo species and metallic zinc being Δ 66/64Zn aq-metal ˜ 1.6‰ at 25 °C, and Δ 66/64Zn aq-metal ˜ 0.8‰ between the tetrachloro zinc complex and metallic zinc at 25 °C using B3LYP/aug-cc-pVDZ level of theory and basis set. To examine the behavior of zinc in various aqueous solution chemistries, models for Zn(II) complex speciation were used to determine which species are thermodynamically favorable and abundant under a variety of different conditions relevant to natural waters, experimental and industrial solutions. The optimal molecular geometries for [Zn(H 2O) 6] 2+, [Zn(H 2O) 6]·SO 4, [ZnCl 4] 2- and [Zn(H 2O) 3(C 3H 5O(COO) 3)] - complexes in various states of solvation, protonation and coordination were calculated at various levels of electronic structure theory and basis set size. Isotopic reduced partition function ratios were calculated from frequency analyses of these optimized structures. Increasing the basis set size typically led to a decrease in the calculated reduced partition function ratios of ˜0.5‰ with values approaching a plateau using the aug-cc-pVDZ basis set or larger. The widest range of species were studied at the B3LYP/LAN2DZ/6-31G ∗ level of theory and basis-set size for comparison. Aqueous zinc complexes where oxygen is bound to the metal center tended to have the
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.
Do, Hainam; Hirst, Jonathan D; Wheatley, Richard J
2012-04-19
It is challenging to compute the partition function (Q) for systems with enormous configurational spaces, such as fluids. Recently, we developed a Monte Carlo technique (an energy partitioning method) for computing Q [ J. Chem. Phys. 2011 , 135 , 174105 ]. In this paper, we use this approach to compute the partition function of a binary fluid mixture (carbon dioxide + methane); this allows us to obtain the Helmholtz free energy (F) via F = -k(B)T ln Q and the Gibbs free energy (G) via G = F + pV. We then utilize G to obtain the coexisting mole fraction curves. The chemical potential of each species is also obtained. At the vapor-liquid equilibrium condition, the chemical potential of methane significantly increases, while that of carbon dioxide slightly decreases, as the pressure increases along an isotherm. Since Q is obtained from the density of states, which is independent of the temperature, equilibrium thermodynamic properties at any condition can be obtained by varying the total composition and volume of the system. Our methodology can be adapted to explore the free energies of other binary mixtures in general and of those containing CO(2) in particular. Since the method gives access to the free energy and chemical potentials, it will be useful in many other applications.
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.
Poulin, David; Wocjan, Pawel
2009-11-27
We present a quantum algorithm to prepare the thermal Gibbs state of interacting quantum systems. This algorithm sets a universal upper bound D{sup {alpha}} on the thermalization time of a quantum system, where D is the system's Hilbert space dimension and {alpha}<=(1/2) is proportional to the Helmholtz free energy density. We also derive an algorithm to evaluate the partition function of a quantum system in a time proportional to the system's thermalization time and inversely proportional to the targeted accuracy squared.
LETTER TO THE EDITOR: The partition function in the Wigner Kirkwood expansion
NASA Astrophysics Data System (ADS)
Matinyan, Sergei G.; Müller, Berndt
2006-05-01
We study the semiclassical Wigner-Kirkwood (WK) expansion of the partition function Z(t) for arbitrary even homogeneous potentials, starting from the Bloch equation. As is well known, the phase-space kernel of Z satisfies the so-called Uhlenbeck-Beth equation, which depends on the gradients of the potential. We perform a chain of transformations to obtain novel forms of this equation that invite analogies with various physical phenomena and formalisms, such as diffusion processes, the Fokker-Planck equation and supersymmetric quantum mechanics.
Theory of a two-level system interacting with a degenerate electron gas. I. Partition function
NASA Astrophysics Data System (ADS)
Vladár, K.; Zawadowski, A.; Zimányi, Gergely T.
1988-02-01
The problem of the two-level system (TLS) interacting with a free-electron gas is considered. In a previous work Yu and Anderson treated that problem by taking into account the screening by the conduction electrons described by an arbitrarily large phase shift. The present paper is devoted to a generalization of their result by including weak electron-assisted TLS transition processes. Generalizing the Yuval-Anderson technique, the partition function is derived, which has the form of the partition function of a one-dimensional Coulomb gas with logarithmic interactions. The charges introduced depend on the phase shifts and on the electron spin and orbital quantum numbers corresponding to the incoming and outgoing electrons in the related electron-TLS scattering processes. Additionally charged dipoles are introduced to describe those processes in which the scattered electrons do not change their quantum number. Special care is paid to the formal divergencies occurring in these processes if the long-time asymptotic expressions are used for the conduction-electron Green's functions. In this way, going beyond the charge-charge interaction, charge-dipole and dipole-dipole interactions are introduced. The next paper deals with the derivation of the scaling equations, which are derived by eliminating the short-time behavior.
Partition functions in even dimensional AdS via quasinormal mode methods
NASA Astrophysics Data System (ADS)
Keeler, Cynthia; Ng, Gim Seng
2014-06-01
In this note, we calculate the one-loop determinant for a massive scalar (with conformal dimension Δ) in even-dimensional AdS d+1 space, using the quasinormal mode method developed in [1] by Denef, Hartnoll, and Sachdev. Working first in two dimensions on the related Euclidean hyperbolic plane H 2, we find a series of zero modes for negative real values of Δ whose presence indicates a series of poles in the one-loop partition function Z(Δ) in the Δ complex plane; these poles contribute temperature-independent terms to the thermal AdS partition function computed in [1]. Our results match those in a series of papers by Camporesi and Higuchi, as well as Gopakumar et al. [2] and Banerjee et al. [3]. We additionally examine the meaning of these zero modes, finding that they Wick-rotate to quasinormal modes of the AdS2 black hole. They are also interpretable as matrix elements of the discrete series representations of SO(2, 1) in the space of smooth functions on S 1. We generalize our results to general even dimensional AdS2 n , again finding a series of zero modes which are related to discrete series representations of SO(2 n, 1), the motion group of H 2 n .
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.
Zaghloul, Mofreh R.
2010-12-15
Potekhin [Phys. Plasmas 17, 124705 (2010)] claims that the inconsistencies in previous models of the well-known occupation probability formalism, which we have pointed out in Zaghloul [Phys. Plasmas 17, 062701 (2010)], are due to omission of the configurational factor from the partition function in our work. We show that this claim is not justified, and thus explain the existence of these inconsistencies in the previous models we referred to in Zaghloul [Phys. Plasmas 17, 062701 (2010)], and reconfirm the correctness of our work and conclusions.
Interaction corrections to the polarization function of graphene
NASA Astrophysics Data System (ADS)
Sodemann, I.; Fogler, M. M.
2012-09-01
The first-order interaction correction to the irreducible polarization function of pristine graphene is studied at arbitrary relation between momentum and frequency. The results are used to calculate the dielectric function and the dynamical conductivity of graphene beyond the standard random-phase approximation. The computed static dielectric constant compares favorably with recent experiments.
CORRECTION OF FUNCTIONAL MISARTICULATION UNDER AN AUTOMATED SELF-CORRECTION SYSTEM. FINAL REPORT.
ERIC Educational Resources Information Center
GARRETT, EDGAR RAY
THE AUTOMATED SPEECH CORRECTION PROGRAM (ASCP) WAS DESIGNED TO TEST THE USE OF PROGRAMED INSTRUCTION IN THE REMEDIATION OF FUNCTIONAL ARTICULATION ERRORS. A SERIES OF PROGRAMED TAPES WHICH TAKE THE STUDENT THROUGH AUDITORY IDENTIFICATION, AUDITORY DISCRIMINATION, PRODUCTION, AND SELF-EVALUATION WERE DESIGNED. SUB-GOALS OF THE EXPERIMENT WERE A…
Partition function zeros and phase transitions of a square-well polymer
NASA Astrophysics Data System (ADS)
Phyo Aung, Pyie; Mark, Taylor
2012-04-01
The zeros of the canonical partition functions for flexible square-well polymer chains have been computed for chains up to length 256 for a range of square-well diameters. We have previously shown that such chain molecules can undergo a coil-globule and globule-crystal transition as well as a direct coil-crystal transition [1]. Here we show that each of these transitions has a well-defined signature in the complex-plane map of the partition function zeros. The freezing transitions are characterized by nearly circular rings of uniformly spaced roots, indicative of a discontinuous transition. The collapse transition is signaled by the coalescence of roots onto an elliptical horse-shoe segment pinching down towards the positive real axis. For sufficiently small square-well diameter the elliptical collapse ring merges with the circular freezing ring yielding the direct coil-crystal transition. The root density of all rings increases with increasing chain length and the leading roots move towards the positive real axis, implying a divergence of the specific heat in the thermodynamic limit (as originally proposed by Yang and Lee).[4pt] [1] M.P. Taylor, W. Paul, and K. Binder, J. Chem. Phys. 131, 114907 (2009).
Partition function zeros and phase transitions of a square-well polymer
NASA Astrophysics Data System (ADS)
Aung, Pyie-Phyo; Taylor, Mark
2012-02-01
The zeros of the canonical partition functions for flexible square-well polymer chains have been computed for chains up to length 256 for a range of square-well diameters. We have previously shown that such chain molecules can undergo a coil-globule and globule-crystal transition as well as a direct coil-crystal transition [1]. Here we show that each of these transitions has a well-defined signature in the complex-plane map of the partition function zeros. The freezing transitions are characterized by nearly circular rings of uniformly spaced roots, indicative of a discontinuous transition. The collapse transition is signaled by the coalescence of roots onto an elliptical horse-shoe segment pinching down towards the positive real axis. For sufficiently small square-well diameter the elliptical collapse ring merges with the circular freezing ring yielding the direct coil-crystal transition. The root density of all rings increases with increasing chain length and the leading roots move towards the positive real axis, implying a divergence of the specific heat in the thermodynamic limit (as originally proposed by Yang and Lee). [4pt] [1] M.P. Taylor, W. Paul, and K. Binder, J. Chem. Phys. 131, 114907 (2009).
Sabour, Mohammad Reza; Moftakhari Anasori Movahed, Saman
2017-02-01
The soil sorption partition coefficient logKoc is an indispensable parameter that can be used in assessing the environmental risk of organic chemicals. In order to predict soil sorption partition coefficient for different and even unknown compounds in a fast and accurate manner, a radial basis function neural network (RBFNN) model was developed. Eight topological descriptors of 800 organic compounds were used as inputs of the model. These 800 organic compounds were chosen from a large and very diverse data set. Generalized Regression Neural Network (GRNN) was utilized as the function in this neural network model due to its capability to adapt very quickly. Hence, it can be used to predict logKoc for new chemicals, as well. Out of total data set, 560 organic compounds were used for training and 240 to test efficiency of the model. The obtained results indicate that the model performance is very well. The correlation coefficients (R2) for training and test sets were 0.995 and 0.933, respectively. The root-mean square errors (RMSE) were 0.2321 for training set and 0.413 for test set. As the results for both training and test set are extremely satisfactory, the proposed neural network model can be employed not only to predict logKoc of known compounds, but also to be adaptive for prediction of this value precisely for new products that enter the market each year.
Partition function zeros and phase transitions for a square-well polymer chain.
Taylor, Mark P; Aung, Pyie Phyo; Paul, Wolfgang
2013-07-01
The zeros of the canonical partition functions for flexible square-well polymer chains have been approximately computed for chains up to length 256 for a range of square-well diameters. We have previously shown that such chain molecules can undergo a coil-globule and globule-crystal transition as well as a direct coil-crystal transition. Here we show that each of these transitions has a well-defined signature in the complex-plane map of the partition function zeros. The freezing transitions are characterized by nearly circular rings of uniformly spaced roots, indicative of a discontinuous transition. The collapse transition is signaled by the appearance of an elliptical horseshoe segment of roots that pinches down towards the positive real axis and defines a boundary to a root-free region of the complex plane. With increasing chain length, the root density on the circular ring and in the space adjacent to the elliptical boundary increases and the leading roots move towards the positive real axis. For finite-length chains, transition temperatures can be obtained by locating the intersection of the ellipse and/or circle of roots with the positive real axis. A finite-size scaling analysis is used to obtain transition temperatures in the long-chain (thermodynamic) limit. The collapse transition is characterized by crossover and specific-heat exponents of φ≈0.76(2) and α≈0.66(2), respectively, consistent with a second-order phase transition.
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
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.
Partitioning heritability by functional annotation using genome-wide association summary statistics
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
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.
NASA Astrophysics Data System (ADS)
Dappen, Werner; Anderson, Lawrence; Mihalas, Dimitri
1987-08-01
We discuss a recent controversy about the Planck-Larkin partition function, and present optical simulations of high-quality spectra from laboratory hydrogen plasmas (Wiese, Kelleher, and Paquette) using several partition function formalisms. We point out that the controversy has arisen from a misunderstanding about the use of the Planck-Larkin partition function. A Planck-Larkin cancellation may still have its place in equations of state that are based on quantum-statistical many-body theory (i.e., the "physical picture"). However, experimental evidence shows that it is inconsistent to use the Planck-Larkin partition function as the internal partition function in simple models of reacting gases (i.e., the "chemical picture"). Moreover, the more sophisticated equations of state of the physical picture will have to be subjected to the same comparison with experimental data. We also address the question of plasma polarization shifts of bound-state energies. We discuss the static-screened Coulomb potential (SSCP) as an atomic potential: from theoretical considerations and observational constraints we conclude that it should not be used. The only useful result of the SSCP potential its prediction of the number of excited be obtained by alternative means, e.g., by an occupation probability formalism.
Application of calcite Mg partitioning functions to the reconstruction of paleocean Mg/Ca
NASA Astrophysics Data System (ADS)
Hasiuk, Franciszek J.; Lohmann, Kyger C.
2010-12-01
Calcite Mg/Ca is usually assumed to vary linearly with solution Mg/Ca, that a constant partition coefficient describes the relationship between these two ratios. Numerous published empirical datasets suggests that this relationship is better described by a power function. We provide a compilation of these literature data for biotic and abiotic calcite in the form of Calcite Mg/Ca = F(Solution Mg/Ca) H, where F and H are empirically determined fitting parameters describing the slope and deviation from linearity, respectively, of the function. This is equivalent to Freundlich sorption behavior controlling Mg incorporation in calcite. Using a power function, instead of a partition coefficient, lowers Phanerozoic seawater Mg/Ca estimates based on echinoderm skeletal material by, on average, 0.5 mol/mol from previous estimates. These functions can also be used to model the primary skeletal calcite Mg/Ca of numerous calcite phases through geologic time. Such modeling suggests that the Mg/Ca of all calcite precipitated from seawater has varied through the Phanerozoic in response to changing seawater Mg/Ca and that the overall range in Mg/Ca measured among various calcite phases would be greatest when seawater Mg/Ca was also high (e.g., "aragonite seas") and lowest when seawater Mg/Ca was low (e.g., "calcite seas"). It follows that, during times of "calcite seas" when the seawater Mg/Ca is presumed to have been lower, deposition of calcite with low Mg contents would have resulted in a depressed drive for diagenetic stabilization of shelfal carbonate and, in turn, lead to greater preservation of crystal and skeletal microfabrics and primary chemistries in biotic and abiotic calcites.
Kawashima, Yukio; Hirao, Kimihiko
2017-03-09
We introduced two methods to correct the singularity in the calculation of long-range Hartree-Fock (HF) exchange for long-range-corrected density functional theory (LC-DFT) calculations in plane-wave basis sets. The first method introduces an auxiliary function to cancel out the singularity. The second method introduces a truncated long-range Coulomb potential, which has no singularity. We assessed the introduced methods using the LC-BLYP functional by applying it to isolated systems of naphthalene and pyridine. We first compared the total energies and the HOMO energies of the singularity-corrected and uncorrected calculations and confirmed that singularity correction is essential for LC-DFT calculations using plane-wave basis sets. The LC-DFT calculation results converged rapidly with respect to the cell size as the other functionals, and their results were in good agreement with the calculated results obtained using Gaussian basis sets. LC-DFT succeeded in obtaining accurate orbital energies and excitation energies. We next applied LC-DFT with singularity correction methods to the electronic structure calculations of the extended systems, Si and SiC. We confirmed that singularity correction is important for calculations of extended systems as well. The calculation results of the valence and conduction bands by LC-BLYP showed good convergence with respect to the number of k points sampled. The introduced methods succeeded in overcoming the singularity problem in HF exchange calculation. We investigated the effect of the singularity correction on the excitation state calculation and found that careful treatment of the singularities is required compared to ground-state calculations. We finally examined the excitonic effect on the band gap of the extended systems. We calculated the excitation energies to the first excited state of the extended systems using a supercell model at the Γ point and found that the excitonic binding energy, supposed to be small for
Relativistic correction to gluon fragmentation function into pseudoscalar quarkonium
NASA Astrophysics Data System (ADS)
Gao, Xiangrui; Jia, Yu; Li, Liuji; Xiong, Xiaonu
2017-02-01
Inspired by the recent measurements of the ηc meson production at LHC experiments, we investigate the relativistic correction effect for the fragmentation functions of gluon/charm quark fragmenting into ηc, which constitute the crucial nonperturbative element for the ηc production at high p T. Employing three distinct methods, we calculate the next-to-leading-order (NLO) relativistic correction to g → ηc fragmentation function in the NRQCD factorization framework, as well as verifying the existing NLO result for the c → ηc fragmentation function. We also study the evolution behavior of these fragmentation functions with the aid of the DGLAP equation. Supported by National Natural Science Foundation of China (11475188, 11261130311, 11575202, 11222549), IHEP Innovation (Y4545170Y2), State Key Lab for Electronics and Particle Detectors
Yang, Jie; Swenson, Nathan G; Zhang, Guocheng; Ci, Xiuqin; Cao, Min; Sha, Liqing; Li, Jie; Ferry Slik, J W; Lin, Luxiang
2015-08-03
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.
NASA Technical Reports Server (NTRS)
Hummer, D. G.; Mihalas, Dimitri
1988-01-01
An equation of state for material in stellar envelopes, subject to the limits of temperature less than about 10 to the 7th K and density less than about .01 g/cu cm is presented. The equation makes it possible to express free energy as the sum of several terms representing effects such as partial degeneracy of the electron, Coulomb interactions among charged particles, finite-volume, hard sphere repulsion, and van der Waals attraction. An occupation probability formalism is used to represent the effects of the plasma in establishing a finite partition function. It is shown that the use of the static screened Coulomb potential to calculate level shifts and to estimate the cutoff of the internal partition function is invalid. For most of the parameter space relevant to stellar envelopes, perturbations arising from the plasma ions are shown to be dominant in establishing the internal partition function.
NASA Technical Reports Server (NTRS)
Hummer, D. G.; Mihalas, Dimitri
1988-01-01
An equation of state for material in stellar envelopes, subject to the limits of temperature less than about 10 to the 7th K and density less than about .01 g/cu cm is presented. The equation makes it possible to express free energy as the sum of several terms representing effects such as partial degeneracy of the electron, Coulomb interactions among charged particles, finite-volume, hard sphere repulsion, and van der Waals attraction. An occupation probability formalism is used to represent the effects of the plasma in establishing a finite partition function. It is shown that the use of the static screened Coulomb potential to calculate level shifts and to estimate the cutoff of the internal partition function is invalid. For most of the parameter space relevant to stellar envelopes, perturbations arising from the plasma ions are shown to be dominant in establishing the internal partition function.
Fluctuations of the partition function in the generalized random energy model with external field
NASA Astrophysics Data System (ADS)
Bovier, Anton; Klimovsky, Anton
2008-12-01
We study Derrida's generalized random energy model (GREM) in the presence of uniform external field. We compute the fluctuations of the ground state and of the partition function in the thermodynamic limit for all admissible values of parameters. We find that the fluctuations are described by a hierarchical structure which is obtained by a certain coarse graining of the initial hierarchical structure of the GREM with external field. We provide an explicit formula for the free energy of the model. We also derive some large deviation results providing an expression for the free energy in a class of models with Gaussian Hamiltonians and external field. Finally, we prove that the coarse-grained parts of the system emerging in the thermodynamic limit tend to have a certain optimal magnetization, as prescribed by the strength of the external field and by parameters of the GREM.
On the Exact Evaluation of Certain Instances of the Potts Partition Function by Quantum Computers
NASA Astrophysics Data System (ADS)
Geraci, Joseph; Lidar, Daniel A.
2008-05-01
We present an efficient quantum algorithm for the exact evaluation of either the fully ferromagnetic or anti-ferromagnetic q-state Potts partition function Z for a family of graphs related to irreducible cyclic codes. This problem is related to the evaluation of the Jones and Tutte polynomials. We consider the connection between the weight enumerator polynomial from coding theory and Z and exploit the fact that there exists a quantum algorithm for efficiently estimating Gauss sums in order to obtain the weight enumerator for a certain class of linear codes. In this way we demonstrate that for a certain class of sparse graphs, which we call Irreducible Cyclic Cocycle Code (ICCCɛ) graphs, quantum computers provide a polynomial speed up in the difference between the number of edges and vertices of the graph, and an exponential speed up in q, over the best classical algorithms known to date.
NASA Astrophysics Data System (ADS)
Chang, Shu-Chiuan; Shrock, Robert
2001-03-01
We present exact calculations of the zero-temperature partition function for the q-state Potts antiferromagnet (equivalently, the chromatic polynomial) for families of arbitrarily long strip graphs of the square and triangular lattices with width Ly=4 and boundary conditions that are doubly periodic or doubly periodic with reversed orientation (i.e., of torus or Klein bottle type). These boundary conditions have the advantage of removing edge effects. In the limit of infinite length, we calculate the exponent of the entropy, W( q) and determine the continuous locus B where it is singular. We also give results for toroidal strips involving “crossing subgraphs”; these make possible a unified treatment of torus and Klein bottle boundary conditions and enable us to prove that for a given strip, the locus B is the same for these boundary conditions.
The star-triangle relation, lens partition function, and hypergeometric sum/integrals
NASA Astrophysics Data System (ADS)
Gahramanov, Ilmar; Kels, Andrew P.
2017-02-01
The aim of the present paper is to consider the hyperbolic limit of an elliptic hypergeometric sum/integral identity, and associated lattice model of statistical mechanics previously obtained by the second author. The hyperbolic sum/integral identity obtained from this limit, has two important physical applications in the context of the so-called gauge/YBE correspondence. For statistical mechanics, this identity is equivalent to a new solution of the star-triangle relation form of the Yang-Baxter equation, that directly generalises the Faddeev-Volkov models to the case of discrete and continuous spin variables. On the gauge theory side, this identity represents the duality of lens ({S}_b^3/{Z}_r) partition functions, for certain three-dimensional N=2 supersymmetric gauge theories.
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.
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.
Semantics and correctness proofs for programs with partial functions
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.
Identifying microproduction inaccuracies with Knudsen number depending correction functions
NASA Astrophysics Data System (ADS)
Groll, R.; Gomez, J.
2016-11-01
The pressure drop of a transonic Laval nozzle depends on the rarefaction of the gas flow. So relative deviations of the numerical data are a measure for describing the influence of the rarefaction of the gas flow. This deviation is predicted by using a second-order modeling approximation for the Knudsen number depending correction function in the slip-flow regime. The production accuracy is able to be read in these deviation functions because of a deviation from the analytical solutions of the slip-flow influence. With the usage of experimental data the correction function can be calibrated through elimination of the error resulting from the accuracy. The investigated case is a micronozzle flow with Knudsen numbers of slip-flow regime near the nozzle throat in vacuum environment. Compared gases are neon, argon, krypton and xenon.
Duan, Jianmin; Bolger, Gordon; Garneau, Michel; Amad, Ma'an; Batonga, Joëlle; Montpetit, Hélène; Otis, François; Jutras, Martin; Lapeyre, Nicole; Rhéaume, Manon; Kukolj, George; White, Peter W; Bethell, Richard C; Cordingley, Michael G
2012-10-01
Pharmacokinetic-pharmacodynamic (PK-PD) data analyses from early hepatitis C virus (HCV) clinical trials failed to show a good correlation between the plasma inhibitory quotient (IQ) and antiviral activity of different classes of directly acting antiviral agents (DAAs). The present study explored whether use of the liver partition coefficient-corrected IQ (LCIQ) could improve the PK-PD relationship. Animal liver partition coefficients (Kp(liver)) were calculated from liver to plasma exposure ratios. In vitro hepatocyte partition coefficients (Kp(hep)) were determined by the ratio of cellular to medium drug concentrations. Human Kp(liver) was predicted using an in vitro-in vivo proportionality method: the species-averaged animal Kp(liver) multiplied by the ratio of human Kp(hep) over those in animals. LCIQ was calculated using the IQ multiplied by the predicted human Kp(liver). Our results demonstrated that the in vitro-in vivo proportionality approach provided the best human Kp(liver) prediction, with prediction errors of <45% for all 5 benchmark drugs evaluated (doxorubicin, verapamil, digoxin, quinidine, and imipramine). Plasma IQ values correlated poorly (r(2) of 0.48) with maximum viral load reduction and led to a corresponding 50% effective dose (ED(50)) IQ of 42, with a 95% confidence interval (CI) of 0.1 to 148534. In contrast, the LCIQ-maximum VLR relationship fit into a typical sigmoidal curve with an r(2) value of 0.95 and an ED(50) LCIQ of 121, with a 95% CI of 83 to 177. The present study provides a novel human Kp(liver) prediction model, and the LCIQ correlated well with the viral load reductions observed in short-term HCV monotherapy of different DAAs and provides a valuable tool to guide HCV drug discovery.
Dispersion corrections to density functionals for water aromatic interactions.
Zimmerli, Urs; Parrinello, Michele; Koumoutsakos, Petros
2004-02-08
We investigate recently published methods for extending density functional theory to the description of long-range dispersive interactions. In all schemes an empirical correction consisting of a C6r(-6) term is introduced that is damped at short range. The coefficient C6 is calculated either from average molecular or atomic polarizabilities. We calculate geometry-dependent interaction energy profiles for the water benzene cluster and compare the results with second-order Møller-Plesset calculations. Our results indicate that the use of the B3LYP functional in combination with an appropriate mixing rule and damping function is recommended for the interaction of water with aromatics.
Assessment of a long-range corrected hybrid functional
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.
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.
Schmidt, Markus H; Swang, Theodore W; Hamilton, Ian M; Best, Janet A
2017-01-01
Metabolic rate reduction has been considered the mechanism by which sleep conserves energy, similar to torpor or hibernation. This mechanism of energy savings is in conflict with the known upregulation (compared to wake) of diverse functions during sleep and neglects a potential role in energy conservation for partitioning of biological operations by behavioral state. Indeed, energy savings as derived from state-dependent resource allocations have yet to be examined. A mathematical model is presented based on relative rates of energy deployment for biological processes upregulated during either wake or sleep. Using this model, energy savings from sleep-wake cycling over constant wakefulness is computed by comparing stable limit cycles for systems of differential equations. A primary objective is to compare potential energy savings derived from state-dependent metabolic partitioning versus metabolic rate reduction. Additionally, energy conservation from sleep quota and the circadian system are also quantified in relation to a continuous wake condition. As a function of metabolic partitioning, our calculations show that coupling of metabolic operations with behavioral state may provide comparatively greater energy savings than the measured decrease in metabolic rate, suggesting that actual energy savings derived from sleep may be more than 4-fold greater than previous estimates. A combination of state-dependent metabolic partitioning and modest metabolic rate reduction during sleep may enhance energy savings beyond what is achievable through metabolic partitioning alone; however, the relative contribution from metabolic partitioning diminishes as metabolic rate is decreased during the rest phase. Sleep quota and the circadian system further augment energy savings in the model. Finally, we propose that state-dependent resource allocation underpins both sleep homeostasis and the optimization of daily energy conservation across species. This new paradigm identifies an
Ravin, N; Lane, D
1999-11-01
A locus close to one end of the linear N15 prophage closely resembles the sop operon which governs partition of the F plasmid; the promoter region contains similar operator sites, and the two putative gene products have extensive amino acid identity with the SopA and -B proteins of F. Our aim was to ascertain whether the N15 sop homologue functions in partition, to identify the centromere site, and to examine possible interchangeability of function with the F Sop system. When expressed at a moderate level, N15 SopA and -B proteins partly stabilize mini-F which lacks its own sop operon but retains the sopC centromere. The stabilization does not depend on increased copy number. Likewise, an N15 mutant with most of its sop operon deleted is partly stabilized by F Sop proteins and fully stabilized by its own. Four inverted repeat sequences similar to those of sopC were located in N15. They are distant from the sop operon and from each other. Two of these were shown to stabilize a mini-F sop deletion mutant when N15 Sop proteins were provided. Provision of the SopA homologue to plasmids with a sopA deletion resulted in further destabilization of the plasmid. The N15 Sop proteins exert effective, but incomplete, repression at the F sop promoter. We conclude that the N15 sop locus determines stable inheritance of the prophage by using dispersed centromere sites. The SopB-centromere and SopA-operator interactions show partial functional overlap between N15 and F. SopA of each plasmid appears to interact with SopB of the other, but in a way that is detrimental to plasmid maintenance.
Hui, Dafeng; Luo, Yiqi; Katul, Gabriel
2003-05-01
Interannual variability (IAV) in net ecosystem exchange of carbon (NEE) is a critical factor in projections of future ecosystem changes. However, our understanding of IAV is limited because of the difficulty in isolating its numerous causes. We proposed that IAV in NEE is primarily caused by climatic variability, through its direct effects on photosynthesis and respiration and through its indirect effects on carbon fluxes (i.e., the parameters that govern photosynthesis and respiration), hereafter called functional change. We employed a homogeneity-of-slopes model to identify the functional change contributing to IAV in NEE and nighttime ecosystem respiration (RE). The model uses multiple regression analysis to relate NEE and RE with climatic variables for individual years and for all years. If the use of different slopes for each year significantly improves the model fitting compared to the use of one slope for all years, we consider that functional change exists, at least on annual time scales. With the functional change detected, we then partition the observed variation in NEE or RE to four components, namely, the functional change, the direct effect of interannual climatic variability, the direct effect of seasonal climatic variation, and random error. Application of this approach to a data set collected at the Duke Forest AmeriFlux site from August 1997 to December 2001 indicated that functional change, interannual climatic variability, seasonal climatic variation and random error explained 9.9, 8.9, 59.9 and 21.3%, respectively, of the observed variation in NEE and 13.1, 5.0, 38.1 and 43.8%, respectively, of the observed variation in RE.
Hierarchical Partitioning of Metazoan Protein Conservation Profiles Provides New Functional Insights
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
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.
NASA Astrophysics Data System (ADS)
Bilal, Adel; Leduc, Laetitia
2015-07-01
We study two-dimensional quantum gravity on arbitrary genus Riemann surfaces in the Kähler formalism where the basic quantum field is the (Laplacian of the) Kähler potential. We do a careful first-principles computation of the fixed-area partition function Z [ A ] up to and including all two-loop contributions. This includes genuine two-loop diagrams as determined by the Liouville action, one-loop diagrams resulting from the non-trivial measure on the space of metrics, as well as one-loop diagrams involving various counterterm vertices. Contrary to what is often believed, several such counterterms, in addition to the usual cosmological constant, do and must occur. We consistently determine the relevant counterterms from a one-loop computation of the full two-point Green's function of the Kähler field. Throughout this paper we use the general spectral cutoff regularization developed recently and which is well-suited for multi-loop computations on curved manifolds. At two loops, while all "unwanted" contributions to ln (Z [ A ] / Z [A0 ]) correctly cancel, it appears that the finite coefficient of ln (A /A0) does depend on the finite part of a certain counterterm coefficient, i.e. on the finite renormalization conditions one has to impose. There exists a choice that reproduces the famous KPZ-scaling, but it seems to be only one consistent choice among others. Maybe, this hints at the possibility that other renormalization conditions could eventually provide a way to circumvent the famous c = 1 barrier.
NASA Astrophysics Data System (ADS)
Williams, Floyd L.
2012-09-01
We consider some applications (old and new) of the Patterson-Selberg zeta function to 3D gravity with a negative cosmological constant. We also consider 2D black hole vacua with a parabolic generator of their holonomy. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical in honour of Stuart Dowker's 75th birthday devoted to ‘Applications of zeta functions and other spectral functions in mathematics and physics’.
Peeler, D. K.; Taylor, A. S.; Edwards, T.B.
2005-06-26
error only reflects that the particular constraint system being used is overly conservative (i.e., its application restricts access to glasses that have an acceptable measured durability response). A Type II error results in a more serious misclassification that could result in allowing the transfer of a Slurry Mix Evaporator (SME) batch to the melter, which is predicted to produce a durable product based on the specific system applied but in reality does not meet the defined ''acceptability'' criteria. More specifically, a nondurable product could be produced in DWPF. Given the presence of Type II errors, the Index System approach was deemed inadequate for further implementation consideration at the DWPF. The second approach (the JMP partitioning process) was purely data driven and empirically derived--glass science was not a factor. In this approach, the collection of composition--durability data in ComPro was sequentially partitioned or split based on the best available specific criteria and variables. More specifically, the JMP software chose the oxide (Al{sub 2}O{sub 3} for this dataset) that most effectively partitions the PCT responses (NL [B]'s)--perhaps not 100% effective based on a single oxide. Based on this initial split, a second request was made to split a particular set of the ''Y'' values (good or bad PCTs based on the 10 g/L limit) based on the next most critical ''X'' variable. This ''splitting'' or ''partitioning'' process was repeated until an AGCR was defined based on the use of only 3 oxides (Al{sub 2}O{sub 3}, CaO, and MgO) and critical values of > 3.75 wt% Al{sub 2}O{sub 3}, {ge} 0.616 wt% CaO, and < 3.521 wt% MgO. Using this set of criteria, the ComPro database was partitioned in which no Type II errors were committed. The automated partitioning function screened or removed 978 of the 2406 ComPro glasses which did cause some initial concerns regarding excessive conservatism regardless of its ability to identify an AGCR. However, a preliminary
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.
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.
Reliability correction for functional connectivity: Theory and implementation.
Mueller, Sophia; Wang, Danhong; Fox, Michael D; Pan, Ruiqi; Lu, Jie; Li, Kuncheng; Sun, Wei; Buckner, Randy L; Liu, Hesheng
2015-11-01
Network properties can be estimated using functional connectivity MRI (fcMRI). However, regional variation of the fMRI signal causes systematic biases in network estimates including correlation attenuation in regions of low measurement reliability. Here we computed the spatial distribution of fcMRI reliability using longitudinal fcMRI datasets and demonstrated how pre-estimated reliability maps can correct for correlation attenuation. As a test case of reliability-based attenuation correction we estimated properties of the default network, where reliability was significantly lower than average in the medial temporal lobe and higher in the posterior medial cortex, heterogeneity that impacts estimation of the network. Accounting for this bias using attenuation correction revealed that the medial temporal lobe's contribution to the default network is typically underestimated. To render this approach useful to a greater number of datasets, we demonstrate that test-retest reliability maps derived from repeated runs within a single scanning session can be used as a surrogate for multi-session reliability mapping. Using data segments with different scan lengths between 1 and 30 min, we found that test-retest reliability of connectivity estimates increases with scan length while the spatial distribution of reliability is relatively stable even at short scan lengths. Finally, analyses of tertiary data revealed that reliability distribution is influenced by age, neuropsychiatric status and scanner type, suggesting that reliability correction may be especially important when studying between-group differences. Collectively, these results illustrate that reliability-based attenuation correction is an easily implemented strategy that mitigates certain features of fMRI signal nonuniformity.
Asymptotic prime partitions of integers
NASA Astrophysics Data System (ADS)
Bartel, Johann; Bhaduri, R. K.; Brack, Matthias; Murthy, M. V. N.
2017-05-01
In this paper, we discuss P (n ) , the number of ways a given integer n may be written as a sum of primes. In particular, an asymptotic form Pas(n ) valid for n →∞ is obtained analytically using standard techniques of quantum statistical mechanics. First, the bosonic partition function of primes, or the generating function of unrestricted prime partitions in number theory, is constructed. Next, the density of states is obtained using the saddle-point method for Laplace inversion of the partition function in the limit of large n . This gives directly the asymptotic number of prime partitions Pas(n ) . The leading term in the asymptotic expression grows exponentially as √{n /ln(n ) } and agrees with previous estimates. We calculate the next-to-leading-order term in the exponent, proportional to ln[ln(n )]/ln(n ) , and we show that an earlier result in the literature for its coefficient is incorrect. Furthermore, we also calculate the next higher-order correction, proportional to 1 /ln(n ) and given in Eq. (43), which so far has not been available in the literature. Finally, we compare our analytical results with the exact numerical values of P (n ) up to n ˜8 ×106 . For the highest values, the remaining error between the exact P (n ) and our Pas(n ) is only about half of that obtained with the leading-order approximation. But we also show that, unlike for other types of partitions, the asymptotic limit for the prime partitions is still quite far from being reached even for n ˜107 .
NASA Astrophysics Data System (ADS)
Wendland, D.; Ballenegger, V.; Alastuey, A.
2014-11-01
We compute two- and three-body cluster functions that describe contributions of composite entities, like hydrogen atoms, ions H-, H_2^+, 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.
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.
Biological diversity can be divided into: alpha (α, local), beta (β, difference in assemblage composition among locals), and gamma (γ, total diversity). We assessed the partitioning of taxonomic diversity of Ephemeroptera, Plecoptera and Trichoptera (EPT) and of ...
Biological diversity can be divided into: alpha (α, local), beta (β, difference in assemblage composition among locals), and gamma (γ, total diversity). We assessed the partitioning of taxonomic diversity of Ephemeroptera, Plecoptera and Trichoptera (EPT) and of ...
Partition-function zeros of spherical spin glasses and their relevance to chaos
NASA Astrophysics Data System (ADS)
Obuchi, Tomoyuki; Takahashi, Kazutaka
2012-03-01
We investigate the partition-function zeros of the many-body interacting spherical spin glass, the so-called p-spin spherical model, with respect to the complex temperature in the thermodynamic limit. We use the replica method and extend the procedure of the replica symmetry breaking ansatz to be applicable in the complex-parameter case. We derive the phase diagrams in the complex-temperature plane and calculate the density of zeros in each phase. Near the imaginary axis away from the origin, there is a replica symmetric phase having a large density. On the other hand, we observe no density in the spin-glass phases, irrespective of the replica symmetry breaking. We speculate that this suggests the absence of the temperature chaos. To confirm this, we investigate the multiple many-body interacting case which is known to exhibit the chaos effect. The result shows that the density of zeros actually takes finite values in the spin-glass phase, even on the real axis. These observations indicate that the density of zeros is more closely connected to the chaos effect than the replica symmetry breaking.
The oxygen isotope partition function ratio of water and the structure of liquid water
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.
Exact Potts model partition functions on wider arbitrary-length strips of the square lattice
NASA Astrophysics Data System (ADS)
Chang, Shu-Chiuan; Shrock, Robert
2001-07-01
We present exact calculations of the partition function of the q-state Potts model for general q and temperature on strips of the square lattice of width Ly=3 vertices and arbitrary length Lx with periodic longitudinal boundary conditions, of the following types: (i) (FBC y, PBC x) = cyclic, (ii) (FBC y,TPBC x) = Möbius, (iii) (PBC y,PBC x) = toroidal, and (iv) (PBC y,TPBC x) = Klein bottle, where FBC and ( T) PBC refer to free and (twisted) periodic boundary conditions. Results for the Ly=2 torus and Klein bottle strips are also included. In the infinite-length limit the thermodynamic properties are discussed and some general results are given for low-temperature behavior on strips of arbitrarily great width. We determine the submanifold in the C2 space of q and temperature where the free energy is singular for these strips. Our calculations are also used to compute certain quantities of graph-theoretic interest.
Partition function and thermodynamic parameters of the all-particle cosmic-ray flux
NASA Astrophysics Data System (ADS)
Tomaschitz, Roman
2016-11-01
The all-particle cosmic-ray energy spectrum is studied in the 1 GeV-1011 GeV interval, the relativistic nuclei being treated as a free multi-component gas in stationary non-equilibrium. A phase-space derivation of the spectral number density, partition function and entropy is given, and an analytic expression for the flux density of the all-particle spectrum is semi-empirically obtained from a wideband spectral fit. The all-particle spectrum is the additive superposition of four strongly overlapping peaks with exponential cutoffs at the spectral breaks. The analytic flux density covers the mentioned interval ranging over eleven decades and accurately reproduces the spectral fine-structure, such as two weak spectral breaks between knee and ankle emerging in the IceTop-73 and KASCADE-Grande data sets. In the low-energy range below 104 GeV, the all-particle flux is approximated by adding the proton and helium flux densities obtained from fits to the AMS-02 and CREAM spectra, the contribution of heavier nuclei being negligible in this energy range. Estimates of the thermodynamic parameters (number count, internal energy, entropy and pressure) of the all-particle flux and the partial fluxes generating the spectral peaks are derived.
Exact partition functions for deformed N=2 theories with N_f=4 flavours
NASA Astrophysics Data System (ADS)
Beccaria, Matteo; Fachechi, Alberto; Macorini, Guido; Martina, Luigi
2016-12-01
We consider the Ω-deformed N=2 SU(2) gauge theory in four dimensions with N f = 4 massive fundamental hypermultiplets. The low energy effective action depends on the deformation parameters ɛ 1 , ɛ 2, the scalar field expectation value a, and the hypermultiplet masses m = ( m 1 , m 2 , m 3 , m 4). Motivated by recent findings in the N={2}^{*} theory, we explore the theories that are characterized by special fixed ratios ɛ 2 /ɛ 1 and m /ɛ 1 and propose a simple condition on the structure of the multi-instanton contributions to the prepotential determining the effective action. This condition determines a finite set Π N of special points such that the prepotential has N poles at fixed positions independent on the instanton number. In analogy with what happens in the N={2}^{*} gauge theory, the full prepotential of the Π N theories may be given in closed form as an explicit function of a and the modular parameter q appearing in special combinations of Eisenstein series and Jacobi theta functions with well defined modular properties. The resulting finite pole partition functions are related by AGT correspondence to special 4-point spherical conformal blocks of the Virasoro algebra. We examine in full details special cases where the closed expression of the block is known and confirms our Ansatz. We systematically study the special features of Zamolodchikov's recursion for the Π N conformal blocks. As a result, we provide a novel effective recursion relation that can be exactly solved and allows to prove the conjectured closed expressions analytically in the case of the Π1 and Π2 conformal blocks.
Simple spin correction of unrestricted density-functional calculation
NASA Astrophysics Data System (ADS)
Ovchinnikov, Alexander A.; Labanowski, Jan K.
1996-06-01
The unrestricted Hartree-Fock and unrestricted Kohn-Sham calculations generally result in spin-contaminated solutions. Moreover, the energies from these calculations cannot be directly compared with the results of corresponding restricted calculations since the latter yield higher energies due to restrictions imposed on the form of the wave function. We present here a simple method of correcting the mixed spin energies resulting from unrestricted Hartree-Fock or density-functional theory calculations and removing the foreign spin components. The method allows for elimination of higher-multiplet components from the given mixed spin state solution by performing unrestricted calculations at the same fixed geometry for the higher multiplets and the state under consideration. The performance of the method is illustrated with several examples of density-functional calculations of radical species. The current method is also variational in nature and can be further extended in a self-consistent field fashion.
Short- and long-range corrected hybrid density functionals with the D3 dispersion corrections
NASA Astrophysics Data System (ADS)
Wang, Chih-Wei; Hui, Kerwin; Chai, Jeng-Da
2016-11-01
We propose a short- and long-range corrected (SLC) hybrid scheme employing 100% Hartree-Fock exchange at both zero and infinite interelectronic distances, wherein three SLC hybrid density functionals with the D3 dispersion corrections (SLC-LDA-D3, SLC-PBE-D3, and SLC-B97-D3) are developed. SLC-PBE-D3 and SLC-B97-D3 are shown to be accurate for a very diverse range of applications, such as core ionization and excitation energies, thermochemistry, kinetics, noncovalent interactions, dissociation of symmetric radical cations, vertical ionization potentials, vertical electron affinities, fundamental gaps, and valence, Rydberg, and long-range charge-transfer excitation energies. Relative to ωB97X-D, SLC-B97-D3 provides significant improvement for core ionization and excitation energies and noticeable improvement for the self-interaction, asymptote, energy-gap, and charge-transfer problems, while performing similarly for thermochemistry, kinetics, and noncovalent interactions.
A soft damping function for dispersion corrections with less overfitting.
Ucak, Umit V; Ji, Hyunjun; Singh, Yashpal; Jung, Yousung
2016-11-07
The use of damping functions in empirical dispersion correction schemes is common and widespread. These damping functions contain scaling and damping parameters, and they are usually optimized for the best performance in practical systems. In this study, it is shown that the overfitting problem can be present in current damping functions, which can sometimes yield erroneous results for real applications beyond the nature of training sets. To this end, we present a damping function called linear soft damping (lsd) that suffers less from this overfitting. This linear damping function damps the asymptotic curve more softly than existing damping functions, attempting to minimize the usual overcorrection. The performance of the proposed damping function was tested with benchmark sets for thermochemistry, reaction energies, and intramolecular interactions, as well as intermolecular interactions including nonequilibrium geometries. For noncovalent interactions, all three damping schemes considered in this study (lsd, lg, and BJ) roughly perform comparably (approximately within 1 kcal/mol), but for atomization energies, lsd clearly exhibits a better performance (up to 2-6 kcal/mol) compared to other schemes due to an overfitting in lg and BJ. The number of unphysical parameters resulting from global optimization also supports the overfitting symptoms shown in the latter numerical tests.
A soft damping function for dispersion corrections with less overfitting
NASA Astrophysics Data System (ADS)
Ucak, Umit V.; Ji, Hyunjun; Singh, Yashpal; Jung, Yousung
2016-11-01
The use of damping functions in empirical dispersion correction schemes is common and widespread. These damping functions contain scaling and damping parameters, and they are usually optimized for the best performance in practical systems. In this study, it is shown that the overfitting problem can be present in current damping functions, which can sometimes yield erroneous results for real applications beyond the nature of training sets. To this end, we present a damping function called linear soft damping (lsd) that suffers less from this overfitting. This linear damping function damps the asymptotic curve more softly than existing damping functions, attempting to minimize the usual overcorrection. The performance of the proposed damping function was tested with benchmark sets for thermochemistry, reaction energies, and intramolecular interactions, as well as intermolecular interactions including nonequilibrium geometries. For noncovalent interactions, all three damping schemes considered in this study (lsd, lg, and BJ) roughly perform comparably (approximately within 1 kcal/mol), but for atomization energies, lsd clearly exhibits a better performance (up to 2-6 kcal/mol) compared to other schemes due to an overfitting in lg and BJ. The number of unphysical parameters resulting from global optimization also supports the overfitting symptoms shown in the latter numerical tests.
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.
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)
NASA Astrophysics Data System (ADS)
King, S. Christopher; Leblanc, James F.; Pacey, Philip D.
1988-07-01
An exact analytic expression has been derived for the classical partition function, Qc, of a two-dimensional rotation hindered by a sinusoidal potential with a double minimum. The expression transforms smoothly between the classical partition function for free rotation, Qfc, valid where the barrier to rotation, V2, is much less than the thermal energy, kBT, and the classical partition function for doubly degenerate harmonic vibrations, valid where V2 is greater than kBT. Numerical results have been compared to exact and approximate calculations of the quantal partition function. An approximate quantal expression, Qb, generally agrees with the exact quantal results within 10% when V2 is greater than 4 kBT. Qc agrees better with the exact quantal results when V2 is less than 4 kBT. However, when Qfc is unity or less and the barrier is small, both Qb and Qc diverge from the exact quantal results. The Pitzer-Gwinn interpolation method gives satisfactory results when Qfc is greater than five, but does not work as well as Qc itself for low barriers. Qc has been applied to a variational transition state theory calculation of the rate constant for H + CH 3→CH 4. Quantum chemical electronic energies have been fitted to a sinusoidal function for the rocking motion and to Morse and Lippincott functions for the C…H stretching motion. Analytic expressions have been deduced for the critical C…H distance and for the rate constant. The results have been compared with previous theoretical work and with experiment.
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.
The correct renal function evaluation in patients with thyroid dysfunction.
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.
Corrected confidence bands for functional data using principal components.
Goldsmith, J; Greven, S; Crainiceanu, C
2013-03-01
Functional principal components (FPC) analysis is widely used to decompose and express functional observations. Curve estimates implicitly condition on basis functions and other quantities derived from FPC decompositions; however these objects are unknown in practice. In this article, we propose a method for obtaining correct curve estimates by accounting for uncertainty in FPC decompositions. Additionally, pointwise and simultaneous confidence intervals that account for both model- and decomposition-based variability are constructed. Standard mixed model representations of functional expansions are used to construct curve estimates and variances conditional on a specific decomposition. Iterated expectation and variance formulas combine model-based conditional estimates across the distribution of decompositions. A bootstrap procedure is implemented to understand the uncertainty in principal component decomposition quantities. Our method compares favorably to competing approaches in simulation studies that include both densely and sparsely observed functions. We apply our method to sparse observations of CD4 cell counts and to dense white-matter tract profiles. Code for the analyses and simulations is publicly available, and our method is implemented in the R package refund on CRAN. Copyright © 2013, The International Biometric Society.
Corrected Confidence Bands for Functional Data Using Principal Components
Goldsmith, J.; Greven, S.; Crainiceanu, C.
2014-01-01
Functional principal components (FPC) analysis is widely used to decompose and express functional observations. Curve estimates implicitly condition on basis functions and other quantities derived from FPC decompositions; however these objects are unknown in practice. In this article, we propose a method for obtaining correct curve estimates by accounting for uncertainty in FPC decompositions. Additionally, pointwise and simultaneous confidence intervals that account for both model- and decomposition-based variability are constructed. Standard mixed model representations of functional expansions are used to construct curve estimates and variances conditional on a specific decomposition. Iterated expectation and variance formulas combine model-based conditional estimates across the distribution of decompositions. A bootstrap procedure is implemented to understand the uncertainty in principal component decomposition quantities. Our method compares favorably to competing approaches in simulation studies that include both densely and sparsely observed functions. We apply our method to sparse observations of CD4 cell counts and to dense white-matter tract profiles. Code for the analyses and simulations is publicly available, and our method is implemented in the R package refund on CRAN. PMID:23003003
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.
Gillespie, Dirk
2013-10-01
An algorithm to approximately calculate the partition function (and subsequently ensemble averages) and density of states of lattice spin systems through non-Monte-Carlo random sampling is developed. This algorithm (called the sampling-the-mean algorithm) can be applied to models where the up or down spins at lattice nodes interact to change the spin states of other lattice nodes, especially non-Ising-like models with long-range interactions such as the biological model considered here. Because it is based on the Central Limit Theorem of probability, the sampling-the-mean algorithm also gives estimates of the error in the partition function, ensemble averages, and density of states. Easily implemented parallelization strategies and error minimizing sampling strategies are discussed. The sampling-the-mean method works especially well for relatively small systems, systems with a density of energy states that contains sharp spikes or oscillations, or systems with little a priori knowledge of the density of states.
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.
Carter, Stuart; Sharma, Amit R; Bowman, Joel M
2012-10-21
Large-scale, rovibrational variational calculations are performed for ethylene, using the potential energy surface published by Avila and Carrington [J. Chem. Phys. 135, 064101 (2011)]. Energies for J = 0 are in very good agreement with their benchmark results. Corresponding energies for J = 1 and J = 2 are also given. Calculations with a slightly reduced basis permit energies to J = 40, allowing a reliable determination of the partition function at 296 K. Using a new ab initio dipole moment surface, reported here, the infrared spectra of five dipole-allowed fundamentals are calculated. Both the partition function and infrared spectra are shown to be in excellent agreement with those in the experimental HITRAN database, with the exception of one band, which we believe is partially mis-assigned in HITRAN.
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.
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.
Source water partitioning as a means of characterizing hydrologic function in mangroves
Drexler, J.Z.; De Carlo, E. W.
2002-01-01
Mangrove ecosystems rely on seawater, rain-derived flow, and groundwater for hydrologic sustenance, flushing, and inflow of nutrients and sediments. The relative contribution of these source waters and their variability through time and space can provide key information concerning the hydrologic function of ecosystems. We used hydrologic tracers to partition source waters and trace their movements in the Enipoas stream, a river-dominated mangrove ecosystem on the island of Pohnpei, Federated States of Micronesia (FSM) and in the Yela watershed, an interior mangrove ecosystem on the island of Kosrae, FSM. The Enipoas site was characterized as a salt wedge estuary whose source water contributions alternated between predominantly seawater and rain-derived flow, depending on the tide. The source waters in the interior Yela site were also predominantly seawater and rain-derived flow, however the relative contribution of each was much more stable. The mean groundwater contribution was 5% (SD = 5.5) for the Enipoas site and 20% (SD = 11.0) for the Yela site. Although a small contributor to flow, groundwater was a steady source of freshwater for both systems. Hydrologic linkages between mangroves and adjacent ecosystems were demonstrated by the temporal and spatial distribution of source waters. The 0.8 km Enipoas estuary, with its highly dynamic bi-directional flows, transported source waters along a hydrologic continuum comprised of coral reef, mangroves, and palm forest. In the interior mangroves of the Yela watershed, the presence of rain-derived flow and groundwater demonstrated a hydraulic connection between the mangroves and an upstream freshwater swamp. Interior mangroves with such linkages avoid stresses such as desiccation and heightened salinity, and thus are more productive than those with little or no freshwater flows.
Effect of partition board color on mood and autonomic nervous function.
Sakuragi, Sokichi; Sugiyama, Yoshiki
2011-12-01
The purpose of this study was to evaluate the effects of the presence or absence (control) of a partition board and its color (red, yellow, blue) on subjective mood ratings and changes in autonomic nervous system indicators induced by a video game task. The increase in the mean Profile of Mood States (POMS) Fatigue score and mean Oppressive feeling rating after the task was lowest with the blue partition board. Multiple-regression analysis identified oppressive feeling and error scores on the second half of the task as statistically significant contributors to Fatigue. While explanatory variables were limited to the physiological indices, multiple-regression analysis identified a significant contribution of autonomic reactivity (assessed by heart rate variability) to Fatigue. These results suggest that a blue partition board would reduce task-induced subjective fatigue, in part by lowering the oppressive feeling of being enclosed during the task, possibly by increasing autonomic reactivity.
NASA Astrophysics Data System (ADS)
Dolan, Louise; Sun, Yang
2015-06-01
We compute the partition function of four-dimensional abelian gauge theory on a general four-torus T 4 with flat metric using Dirac quantization. In addition to an symmetry, it possesses symmetry that is electromagnetic S-duality. We show explicitly how this S-duality of the 4 d abelian gauge theory has its origin in symmetries of the 6 d (2 , 0) tensor theory, by computing the partition function of a single fivebrane compactified on T 2 times T 4, which has symmetry. If we identify the couplings of the abelian gauge theory with the complex modulus of the T 2 torus , then in the small T 2 limit, the partition function of the fivebrane tensor field can be factorized, and contains the partition function of the 4 d gauge theory. In this way the symmetry of the 6d tensor partition function is identified with the S-duality symmetry of the 4d gauge partition function. Each partition function is the product of zero mode and oscillator contributions, where the acts suitably. For the 4d gauge theory, which has a Lagrangian, this product redistributes when using path integral quantization.
Alvarez-Paggi, Damian; Zitare, Ulises A; Szuster, Jonathan; Morgada, Marcos N; Leguto, Alcides J; Vila, Alejandro J; Murgida, Daniel H
2017-07-26
Manipulation of the partition function (Q) of the redox center CuA from cytochrome c oxidase is attained by tuning the accessibility of a low lying alternative electronic ground state and by perturbation of the electrostatic potential through point mutations, loop engineering and pH variation. We report clear correlations of the entropic and enthalpic contributions to redox potentials with Q and with the identity and hydrophobicity of the weak axial ligand, respectively.
NASA Astrophysics Data System (ADS)
Shrock, Robert; Xu, Yan
2010-12-01
We present exact results on the partition function of the q-state Potts model on various families of graphs G in a generalized external magnetic field that favors or disfavors spin values in a subset I s ={1,…, s} of the total set of possible spin values, Z( G, q, s, v, w), where v and w are temperature- and field-dependent Boltzmann variables. We remark on differences in thermodynamic behavior between our model with a generalized external magnetic field and the Potts model with a conventional magnetic field that favors or disfavors a single spin value. Exact results are also given for the interesting special case of the zero-temperature Potts antiferromagnet, corresponding to a set-weighted chromatic polynomial Ph( G, q, s, w) that counts the number of colorings of the vertices of G subject to the condition that colors of adjacent vertices are different, with a weighting w that favors or disfavors colors in the interval I s . We derive powerful new upper and lower bounds on Z( G, q, s, v, w) for the ferromagnetic case in terms of zero-field Potts partition functions with certain transformed arguments. We also prove general inequalities for Z( G, q, s, v, w) on different families of tree graphs. As part of our analysis, we elucidate how the field-dependent Potts partition function and weighted-set chromatic polynomial distinguish, respectively, between Tutte-equivalent and chromatically equivalent pairs of graphs.
Leading Non-Gaussian Corrections for Diffusion Orientation Distribution Function
Jensen, Jens H.; Helpern, Joseph A.; Tabesh, Ali
2014-01-01
An analytical representation of the leading non-Gaussian corrections for a class of diffusion orientation distribution functions (dODFs) is presented. This formula is constructed out of the diffusion and diffusional kurtosis tensors, both of which may be estimated with diffusional kurtosis imaging (DKI). By incorporating model-independent non-Gaussian diffusion effects, it improves upon the Gaussian approximation used in diffusion tensor imaging (DTI). This analytical representation therefore provides a natural foundation for DKI-based white matter fiber tractography, which has potential advantages over conventional DTI-based fiber tractography in generating more accurate predictions for the orientations of fiber bundles and in being able to directly resolve intra-voxel fiber crossings. The formula is illustrated with numerical simulations for a two-compartment model of fiber crossings and for human brain data. These results indicate that the inclusion of the leading non-Gaussian corrections can significantly affect fiber tractography in white matter regions, such as the centrum semiovale, where fiber crossings are common. PMID:24738143
2015-07-01
Lai Y-S, Biedermann P, Ekpo UF, et al. Spatial distribution of schistosomiasis and treatment needs in sub-Saharan Africa: a systematic review and geostatistical analysis. Lancet Infect Dis 2015; published online May 22. http://dx.doi.org/10.1016/S1473-3099(15)00066-3—Figure 1 of this Article should have contained a box stating ‘100 references added’ with an arrow pointing inwards, rather than a box stating ‘199 records excluded’, and an asterisk should have been added after ‘1473 records extracted into GNTD’. Additionally, the positioning of the ‘§ and ‘†’ footnotes has been corrected in table 1. These corrections have been made to the online version as of June 4, 2015.
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.
NASA Astrophysics Data System (ADS)
Odabasi, Mustafa; Cetin, Eylem; Sofuoglu, Aysun
Octanol-air partition coefficients ( KOA) for 14 polycyclic aromatic hydrocarbons (PAHs) were determined as a function of temperature using the gas chromatographic retention time method. log KOA values at 25° ranged over six orders of magnitude, between 6.34 (acenaphthylene) and 12.59 (dibenz[ a,h]anthracene). The determined KOA values were within factor of 0.7 (dibenz[ a,h]anthracene) to 15.1 (benz[ a]anthracene) of values calculated as the ratio of octanol-water partition coefficient to dimensionless Henry's law constant. Supercooled liquid vapor pressures ( PL) of 13 PAHs were also determined using the gas chromatographic retention time technique. Activity coefficients in octanol calculated using KOA and PL ranged between 3.2 and 6.2 indicating near-ideal solution behavior. Atmospheric concentrations measured in this study in Izmir, Turkey were used to investigate the partitioning of PAHs between particle and gas-phases. Experimental gas-particle partition coefficients ( Kp) were compared to the predictions of KOA absorption and KSA (soot-air partition coefficient) models. Octanol-based absorptive partitioning model predicted lower partition coefficients especially for relatively volatile PAHs. Ratios of measured/modeled partition coefficients ranged between 1.1 and 15.5 (4.5±6.0, average±SD) for KOA model. KSA model predictions were relatively better and measured to modeled ratios ranged between 0.6 and 5.6 (2.3±2.7, average±SD).
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.
Hemoadsorption corrects hyperresistinemia and restores anti-bacterial neutrophil function.
Bonavia, Anthony; Miller, Lauren; Kellum, John A; Singbartl, Kai
2017-12-01
-dependent manner. Hemoadsorption with AC reduced serum concentrations of resistin and restored neutrophil migration and generation of ROS to normal levels. Hemoadsorption with CC also corrected hyperresistinemia and reconstituted normal intracellular bacterial clearance. Septic hyperresistinemia strongly correlates with inhibition of neutrophil migration in vitro. Hyperresistinemia itself reversibly impairs neutrophil intracellular bacterial clearance and ROS generation. Hemoadsorption therapy with a clinically approved device corrects hyperresistinemia and neutrophil dysfunction. It may therefore provide a therapeutic option to improve neutrophil function during septic hyperresistinemia and ultimately alleviate immunosuppression in this disease state.
Metallophilic interactions from dispersion-corrected density-functional theory
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.
Kamiyama, Chiho; Oikawa, Shimpei; Hikosaka, Kouki
2014-12-01
Species niches are expected to differ between different functional groups and between species with different functional traits. However, it is still unclear how functional traits contribute to niche separation between species coexisting in a community and between sites along environmental gradients. We studied seasonal changes in light partitioning among coexisting species belonging to different functional groups in moorland plant communities at different altitudes. We estimated the lifetime light absorption per unit invested leaf biomass (ΦLleafmass) as a measure of the benefit/cost ratio of light acquisition. Evergreen species absorbed more light in spring, whereas deciduous species absorbed more light in summer. A similar tradeoff was also found between short and tall species within each functional group. As a result, evergreen and shorter species had comparable ΦLleafmass values to those of deciduous and taller species. Evergreen species had higher ΦLleafmass at higher altitudes relative to deciduous species, suggesting that evergreen habit is more advantageous for the lifetime light interception at higher altitudes. Our results demonstrate that phenological tradeoffs for light partitioning can contribute to the coexistence of species with different functional traits. Our results also reveal that the most advantageous traits differ depending on environment. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.
Predicting functional associations from metabolism using bi-partite network algorithms.
Veeramani, Balaji; Bader, Joel S
2010-07-14
Metabolic reconstructions contain detailed information about metabolic enzymes and their reactants and products. These networks can be used to infer functional associations between metabolic enzymes. Many methods are based on the number of metabolites shared by two enzymes, or the shortest path between two enzymes. Metabolite sharing can miss associations between non-consecutive enzymes in a serial pathway, and shortest-path algorithms are sensitive to high-degree metabolites such as water and ATP that create connections between enzymes with little functional similarity. We present new, fast methods to infer functional associations in metabolic networks. A local method, the degree-corrected Poisson score, is based only on the metabolites shared by two enzymes, but uses the known metabolite degree distribution. A global method, based on graph diffusion kernels, predicts associations between enzymes that do not share metabolites. Both methods are robust to high-degree metabolites. They out-perform previous methods in predicting shared Gene Ontology (GO) annotations and in predicting experimentally observed synthetic lethal genetic interactions. Including cellular compartment information improves GO annotation predictions but degrades synthetic lethal interaction prediction. These new methods perform nearly as well as computationally demanding methods based on flux balance analysis. We present fast, accurate methods to predict functional associations from metabolic networks. Biological significance is demonstrated by identifying enzymes whose strong metabolic correlations are missed by conventional annotations in GO, most often enzymes involved in transport vs. synthesis of the same metabolite or other enzyme pairs that share a metabolite but are separated by conventional pathway boundaries. More generally, the methods described here may be valuable for analyzing other types of networks with long-tailed degree distributions and high-degree hubs.
Wu, Di; Köster, Jan Reent; Cárdenas, Laura M; Brüggemann, Nicolas; Lewicka-Szczebak, Dominika; Bol, Roland
2016-03-15
The aim of this study was to determine the impact of isotope fractionation associated with N2O reduction during soil denitrification on N2O site preference (SP) values and hence quantify the potential bias on SP-based N2O source partitioning. The N2O SP values (n = 431) were derived from six soil incubation studies in N2-free atmosphere, and determined by isotope ratio mass spectrometry (IRMS). The N2 and N2O concentrations were measured directly by gas chromatography. Net isotope effects (NIE) during N2O reduction to N2 were compensated for using three different approaches: a closed-system model, an open-system model and a dynamic apparent NIE function. The resulting SP values were used for N2O source partitioning based on a two end-member isotopic mass balance. The average SP0 value, i.e. the average SP values of N2O prior to N2O reduction, was recalculated with the closed-system model, resulting in -2.6 ‰ (±9.5), while the open-system model and the dynamic apparent NIE model gave average SP0 values of 2.9 ‰ (±6.3) and 1.7 ‰ (±6.3), respectively. The average source contribution of N2O from nitrification/fungal denitrification was 18.7% (±21.0) according to the closed-system model, while the open-system model and the dynamic apparent NIE function resulted in values of 31.0% (±14.0) and 28.3% (±14.0), respectively. Using a closed-system model with a fixed SP isotope effect may significantly overestimate the N2O reduction effect on SP values, especially when N2O reduction rates are high. This is probably due to soil inhomogeneity and can be compensated for by the application of a dynamic apparent NIE function, which takes the variable reduction rates in soil micropores into account. Copyright © 2016 John Wiley & Sons, Ltd.
Marine microalgae growth and carbon partitioning as a function of nutrient availability.
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.
1991-09-25
In Temperature taking - getting it right' (Nursing Standard December 12 1990), the author erroneously referred to TcmpaDOT thermometers as using liquid crystal indicators. They in fact function through a colour change, using a mix of two organic chemicals.
Han, Shu-ying; Qiao, Jun-qin; Zhang, Yun-yang; Yang, Li-li; Lian, Hong-zhen; Ge, Xin; Chen, Hong-yuan
2011-03-01
n-Octanol/water partition coefficients (P) for DDTs and dicofol were determined by reversed-phase high performance liquid chromatography (RP-HPLC) on a C(18) column using methanol-water mixture as mobile phase. A dual-point retention time correction (DP-RTC) was proposed to rectify chromatographic retention time (t(R)) shift resulted from stationary phase aging. Based on this correction, the relationship between logP and logk(w), the logarithm of the retention factor extrapolated to pure water, was investigated for a set of 12 benzene homologues and DDT-related compounds with reliable experimental P as model compounds. A linear regression logP=(1.10±0.04) logk(w) - (0.60±0.17) was established with correlation coefficient R(2) of 0.988, cross-validated correlation coefficient R(cv)(2) of 0.983 and standard deviation (SD) of 0.156. This model was further validated using four verification compounds, naphthalene, biphenyl, 2,2-bis(4-chlorophenyl)-1,1-dichloroethane (p,p'-DDD) and 2,2-bis(4-chlorophenyl)-1,1-dichloroethene (p,p'-DDE) with similar structure to DDT. The RP-HPLC-determined P values showed good consistency with shake-flask (SFM) or slow-stirring (SSM) results, especially for highly hydrophobic compounds with logP in the range of 4-7. Then, the P values for five DDT-related compounds, 2-(2-chlorophenyl)-2-(4-chlorophenyl)-1,1,1-trichloroethane (o,p'-DDT), 2-(2-chlorophenyl)-2-(4-chlorophenyl)-1,1-dichloroethane (o,p'-DDD), 2-(2-chlorophenyl)-2-(4-chlorophenyl)-1,1-dichloroethene (o,p'-DDE), and 2,2,2-trichloro-1,1-bis(4-chlorophenyl)ethanol (dicofol) and its main degradation product 4,4'-dichlorobenzophenone (p,p'-DBP) were evaluated by the improved RP-HPLC method for the first time. The excellent precision with SD less than 0.03 proved that the novel DP-RTC protocol can significantly increases the determination accuracy and reliability of P by RP-HPLC.
Galgani, J. E.; Mizgier, M. L.; Mari, A.; Ravussin, E.
2014-01-01
Background Glucose-stimulated insulin secretion correlates inversely with the degree of whole-body insulin sensitivity suggesting a crosstalk between peripheral organs and pancreas. Such sensing mechanism could be mediated by changes in glucose flux (uptake, oxidation or storage) in peripheral tissues that may drive insulin secretion. Aim To relate whole-body non-protein respiratory quotient (npRQ), an index of macronutrient oxidative partitioning, with insulin secretion and β-cell function in non-diabetic individuals. Methods Macronutrient oxidation was measured after an overnight fast and for 4 hours after a 75-g oral glucose tolerance test (OGTT) in 30 participants (15/15 males/females; 35±12 y; 27±4 kg/m2). Furthermore, npRQ was assessed for 24 hours in a metabolic chamber. Insulin secretion was estimated by deconvolution of serum C-peptide concentration (fasting and 4-h OGTT) and from 24-h urinary C-peptide excretion corrected for energy intake (metabolic chamber). β-cell function parameters were obtained by mathematical modelling, while insulin sensitivity was determined by a euglycemic-hyperinsulinemic clamp (120 mU·m−2·min). Results Insulin secretion (from 24-h urinary C-peptide) correlated inversely with 24-h npRQ (r=−0.61; p=0.001), even after controlling for insulin sensitivity, energy balance, age and body mass index (r=−0.52; p=0.01). In turn, insulin secretion (from serum C-peptide) was not associated with fasting or OGTT npRQ. However, fasting npRQ was positively correlated with rate sensitivity (r=0.40; p<0.05) and marginally with glucose sensitivity (r=0.34; p=0.08). Conclusion Macronutrient oxidative partitioning, specifically glucose oxidation, might play a role on the regulation of insulin secretion. Further studies should aim at identifying the signals linking these processes. PMID:25176602
Zaghloul, Mofreh R
2004-02-01
The system of coupled nonlinear Saha equations supplemented by electroneutrality and conservation of nuclei for complex plasma mixtures is reformulated into a reduced form, which allows the development of an efficient numerical algorithm to solve the set of nonlinear equations. The efficient algorithm is based on the solution of an equivalent single transcendental equation. Nonideality corrections have been taken into consideration in terms of depression of ionization potentials and truncated partition functions. Implementing this simple efficient methodology simplifies the problem and considerably reduces the computational effort needed to compute the detailed plasma composition for different cases. The algorithm is analytically known to be safe, fast, and efficient. It also shows no numerical instabilities, no convergence problems, and no accuracy limitations or lack of change problems, which have been reported in the literature. A nontrivial sample problem has been worked in detail showing the usefulness of the method for applied and industrial plasma physicists. Effects of the nonideality corrections and the exclusion of excited states are quantified and presented. A criterion for the validity of the assumption of local thermodynamic equilibrium is applied to the results from the sample problem to show the region of the temperature-density phase space over which the assumption is valid.
NASA Astrophysics Data System (ADS)
Biggs, Norman; Shrock, Robert
1999-11-01
We present exact calculations of the zero-temperature partition function for the q-state Potts antiferromagnet (or, equivalently, the chromatic polynomial) for two families of arbitrarily long strip graphs of the square lattice with periodic boundary conditions in the transverse direction and (i) periodic and (ii) twisted periodic boundary conditions in the longitudinal direction, so that the strip graphs are embedded on (i) a torus and (ii) a Klein bottle. In the limit of infinite length, we calculate the exponent of the entropy, W(q), show it to be the same for (i) and (ii), and determine its analytic structure.
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. Copyright © 2012 Wiley Periodicals, Inc.
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
Transfer matrices for the partition function of the Potts model on cyclic and Möbius lattice strips
NASA Astrophysics Data System (ADS)
Chang, Shu-Chiuan; Shrock, Robert
2005-03-01
We present a method for calculating transfer matrices for the q-state Potts model partition functions Z(G,q,v), for arbitrary q and temperature variable v, on cyclic and Möbius strip graphs G of the square (sq), triangular (tri), and honeycomb (hc) lattices of width Ly vertices and of arbitrarily great length Lx vertices. For the cyclic case we express the partition function as Z(Λ,Ly×Lx,q,v)=∑d=0Ly c Tr[(T)m], where Λ denotes lattice type, c are specified polynomials of degree d in q, T is the transfer matrix in the degree- d subspace, and m=Lx (Lx/2) for Λ=sq, tri ( hc), respectively. An analogous formula is given for Möbius strips. We exhibit a method for calculating T for arbitrary Ly. Explicit results for arbitrary Ly are given for T with d=Ly and Ly-1. In particular, we find very simple formulas the determinant det(T), and trace Tr(T). Corresponding results are given for the equivalent Tutte polynomials for these lattice strips and illustrative examples are included. We also present formulas for self-dual cyclic strips of the square lattice.
Two-loop QED corrections to the Altarelli-Parisi splitting functions
NASA Astrophysics Data System (ADS)
de Florian, Daniel; Sborlini, Germán F. R.; Rodrigo, Germán
2016-10-01
We compute the two-loop QED corrections to the Altarelli-Parisi (AP) splitting functions by using a deconstructive algorithmic Abelianization of the well-known NLO QCD corrections. We present explicit results for the full set of splitting kernels in a basis that includes the leptonic distribution functions that, starting from this order in the QED coupling, couple to the partonic densities. Finally, we perform a phenomenological analysis of the impact of these corrections in the splitting functions.
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.
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.
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
Ravin, Nikolai V; Rech, Jérôme; Lane, David
2008-05-01
The mitotic stability of the linear plasmid-prophage N15 of Escherichia coli depends on a partition system closely related to that of the F plasmid SopABC. The two Sop systems are distinguished mainly by the arrangement of their centromeric SopB-binding sites, clustered in F (sopC) and dispersed in N15 (IR1 to IR4). Because two of the N15 inverted repeat (IR) sites are located close to elements presumed (by analogy with phage lambda) to regulate late gene expression during the lytic growth of N15, we asked whether Sop partition functions play a role in this process. In N15, a putative Q antiterminator gene is located 6 kb upstream of the probable major late promoter and two intrinsic terminator-like sequences, in contrast to lambda, where the Q gene is adjacent to the late promoter. Northern hybridization and lacZ reporter activity confirmed the identity of the N15 late promoter (p52), demonstrated antiterminator activity of the Q analogue, and located terminator sequences between p52 and the first open reading frame. Following prophage induction, N15 mutated in IR2 (downstream from gene Q) or IR3 (upstream of p52) showed a pronounced delay in lysis relative to that for wild-type N15. Expression of ir3(-)-p52::lacZ during N15 wild-type lytic growth was strongly reduced relative to the equivalent ir3(+) fusion. The provision of Q protein and the IR2 and SopAB proteins in trans to ir3(+)-p52::lacZ increased expression beyond that seen in the absence of any one of these factors. These results indicate that the N15 Sop system has a dual role: partition and regulation of late gene transcription during lytic growth.
Vansteenkiste, P; Van Neck, D; Van Speybroeck, V; Waroquier, M
2006-01-28
Large-amplitude motions, particularly internal rotations, are known to affect substantially thermodynamic functions and rate constants of reactions in which flexible molecules are involved. Up to now all methods for computing the partition functions of these motions rely on the Pitzer approximation of more than 50 years ago, in which the large-amplitude motion is treated in complete independence of the other (vibrational) degrees of freedom. In this paper an extended hindered-rotor model (EHR) is developed in which the vibrational modes, treated harmonically, are correctly separated from the large-amplitude motion and in which relaxation effects (the changes in the kinetic-energy matrix and potential curvature) are taken into account as one moves along the large-amplitude path. The model also relies on a specific coordinate system in which the Coriolis terms vanish at all times in the Hamiltonian. In this way an increased level of consistency between the various internal modes is achieved, as compared with the more usual hindered-rotor (HR) description. The method is illustrated by calculating the entropies and heat capacities on 1,3-butadiene and 1-butene (with, respectively, one and two internal rotors) and the rate constant for the addition reaction of a vinyl radical to ethene. We also discuss various variants of the one-dimensional hindered-rotor scheme existing in the literature and its relation with the EHR model. It is argued why in most cases the HR approach is already quite successful.
NASA Astrophysics Data System (ADS)
Prayitno, T. B.
2014-03-01
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.
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.
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.
The 'heritability' of domestication and its functional partitioning in the pig.
Pérez-Enciso, M; de Los Campos, G; Hudson, N; Kijas, J; Reverter, A
2017-02-01
We propose to estimate the proportion of variance explained by regression on genome-wide markers (or genomic heritability) when wild/domestic status is considered the phenotype of interest. This approach differs from the standard Fst in that it can accommodate genetic similarity between individuals in a general form. We apply this strategy to complete genome data from 47 wild and domestic pigs from Asia and Europe. When we partitioned the total genomic variance into components associated to subsets of single nucleotide polymorphisms (SNPs) defined in terms of their annotation, we found that potentially deleterious non-synonymous mutations (9566 SNPs) explained as much genetic variance as the whole set of 25 million SNPs. This suggests that domestication may have affected protein sequence to a larger extent than regulatory or other kinds of mutations. A pathway-guided analysis revealed ovarian steroidogenesis and leptin signaling as highly relevant in domestication. The genomic regression approach proposed in this study revealed molecular processes not apparent through typical differentiation statistics. We propose that at least some of these processes are likely new discoveries because domestication is a dynamic process of genetic selection, which may not be completely characterized by a static metric like Fst. Nevertheless, and despite some particularly influential mutation types or pathways, our analyses tend to rule out a simplistic genetic basis for the domestication process: neither a single pathway nor a unique set of SNPs can explain the process as a whole.
Wong, Kin-Yiu; Gao, Jiali
2008-09-09
In this paper, we describe an automated integration-free path-integral (AIF-PI) method, based on Kleinert's variational perturbation (KP) theory, to treat internuclear quantum-statistical effects in molecular systems. We have developed an analytical method to obtain the centroid potential as a function of the variational parameter in the KP theory, which avoids numerical difficulties in path-integral Monte Carlo or molecular dynamics simulations, especially at the limit of zero-temperature. Consequently, the variational calculations using the KP theory can be efficiently carried out beyond the first order, i.e., the Giachetti-Tognetti-Feynman-Kleinert variational approach, for realistic chemical applications. By making use of the approximation of independent instantaneous normal modes (INM), the AIF-PI method can readily be applied to many-body systems. Previously, we have shown that in the INM approximation, the AIF-PI method is accurate for computing the quantum partition function of a water molecule (3 degrees of freedom) and the quantum correction factor for the collinear H(3) reaction rate (2 degrees of freedom). In this work, the accuracy and properties of the KP theory are further investigated by using the first three order perturbations on an asymmetric double-well potential, the bond vibrations of H(2), HF, and HCl represented by the Morse potential, and a proton-transfer barrier modeled by the Eckart potential. The zero-point energy, quantum partition function, and tunneling factor for these systems have been determined and are found to be in excellent agreement with the exact quantum results. Using our new analytical results at the zero-temperature limit, we show that the minimum value of the computed centroid potential in the KP theory is in excellent agreement with the ground state energy (zero-point energy) and the position of the centroid potential minimum is the expectation value of particle position in wave mechanics. The fast convergent property
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
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.
On Complex Zeros of the q-Potts Partition Function for a Self-dual Family of Graphs
NASA Astrophysics Data System (ADS)
Billiot, J.-M.; Corset, F.; Fontenas, E.
2010-06-01
This paper deals with the location of the complex zeros of q-Potts partition function for a class of self-dual graphs. For this class of graphs, as the form of the eigenvalues is known, the regions of the complex plane can be focused on the sets where there is only one dominant eigenvalue in particular containing the positive half plane. Thus, in these regions, the analyticity of the free energy per site can be derived easily. Next, some examples of graphs with their Tutte polynomial having few eigenvalues are given. The case of the cycle with an edge having a high order of multiplicity is presented in detail. In particular, we show that the well known conjecture of Chen et al. is false in the finite case. Furthermore we obtain a sequence of self-dual graphs for which the unit circle does not belong to the accumulation sets of the zeros.
Wang, Nan; Ma, Jie; Jin, Dan; Yu, Bin
2017-01-01
Aim. The purpose of this study was to investigate the relationship between upper limbs' three functional partitions and the golden curve. Materials and Methods. We measured 30 subjects' right or left upper limb data and investigate the relationship between them and the golden curve by use of SPSS version 20.0 statistical software (SPSS, Inc., Chicago, Illinois), one-sample t-test. Results. There are four points on human's upper limbs which have no difference with the four points on the golden curve. And there is one point of which the difference is obvious. But we still could draw the conclusion that human upper limbs are accordant with the golden curve. Conclusion. Human upper limbs are accordant with the golden curve.
NASA Astrophysics Data System (ADS)
Rocha, J. C. S.; Mól, L. A. S.; Costa, B. V.
2016-12-01
Using the two dimensional XY -(S(O(3))) model as a test case, we show that analysis of the Fisher zeros of the canonical partition function can provide signatures of a transition in the Berezinskii-Kosterlitz-Thouless (BKT) universality class. Studying the internal border of zeros in the complex temperature plane, we found a scenario in complete agreement with theoretical expectations which allow one to uniquely classify a phase transition as in the BKT class of universality. We obtain TBKT in excellent accordance with previous results. A careful analysis of the behavior of the zeros for both regions Re(T) ≤TBKT and Re(T) >TBKT in the thermodynamic limit shows that Im(T) goes to zero in the former case and is finite in the last one.
Lee, Jae Hwan; Kim, Seung-Yeon; Lee, Julian
2013-05-01
We study distributions of the partition function zeros in the complex temperature plane for a square-lattice homopolymer with nearest-neighbor (NN) and next-nearest-neighbor (NNN) interactions. The dependence of distributions on the ratio of NN and NNN interaction strengths R is examined. The finite-size scaling of the zeros is performed to obtain the crossover exponent, which is shown to be independent of R within error bars, suggesting that all of these models belong to the same universality class. The transition temperatures are also computed by the zeros to obtain the phase diagram, and the results confirm that the model with stronger NNN interaction exhibits stronger effects of cooperativity.
Zaghloul, Mofreh R.
2010-06-15
The problem of formulating a thermodynamically consistent finite internal partition function in nonideal hydrogen plasma systems is investigated and analyzed within the chemical picture revealing inaccuracies and inconsistencies buried in widely used formulations in the literature. The analysis carried out here, though performed for the simplest case of pure nonideal hydrogen plasma, shows all specific features of the problem and is extendable to the general case of a complex multicomponent plasma mixture. A criterion for the separability of the configurational component of the free energy is presented and an accurate and consistent formulation of the problem is introduced. The presented criterion and the introduced consistent formulation of the problem clear ambiguities in other formulations in the literature and provide a better understanding of the problem. An illustrative example is worked out showing simplicity and effectiveness of the proposed consistent formulation and the importance of terms essential for thermodynamic consistency, which are commonly neglected by other authors in the literature.
Ma, Jie
2017-01-01
Aim. The purpose of this study was to investigate the relationship between upper limbs' three functional partitions and the golden curve. Materials and Methods. We measured 30 subjects' right or left upper limb data and investigate the relationship between them and the golden curve by use of SPSS version 20.0 statistical software (SPSS, Inc., Chicago, Illinois), one-sample t-test. Results. There are four points on human's upper limbs which have no difference with the four points on the golden curve. And there is one point of which the difference is obvious. But we still could draw the conclusion that human upper limbs are accordant with the golden curve. Conclusion. Human upper limbs are accordant with the golden curve. PMID:28232941
Maji, Jaya; Bhattacharjee, Somendra M
2012-10-01
We study the melting of three-stranded DNA by using the real-space renormalization group and exact recursion relations. The prediction of an unusual Efimov-analog three-chain bound state, that appears at the critical melting of two-chain DNA, is corroborated by the zeros of the partition function. The distribution of the zeros has been studied in detail for various situations. We show that the Efimov DNA can occur even if the three-chain (i.e., three-monomer) interaction is repulsive in nature. In higher dimensions, a striking result that emerged in this repulsive zone is a continuous transition from the critical state to the Efimov DNA.
Prospective motion correction for functional MRI using sparsity and Kalman filtering
NASA Astrophysics Data System (ADS)
Weller, Daniel S.; Noll, Douglas C.; Fessler, Jeffrey A.
2013-09-01
We propose a novel algorithm to adaptively correct head motion during functional magnetic resonance imaging scans. Our method combines a Kalman-filter-like motion tracker and a registration cost function based on a sparse residual image model. Using simulated data, we compare a time series correlation analysis of our prospectively corrected reconstruction against the same analysis using post-scan motion correction provided by standard software. Our experiments demonstrate our prospective correction method is capable of mitigating motion effects and improving the sensitivity and specificity of the correlation analysis, without relying on costly external tracking hardware or separate navigational data that would take extra time to acquire during each time frame.
Video-rate optical flow corrected intraoperative functional fluorescence imaging.
Koch, Maximilian; Glatz, Jürgen; Ermolayev, Vladimir; de Vries, Elisabeth G E; van Dam, Gooitzen M; Englmeier, Karl-Hans; Ntziachristos, Vasilis
2014-04-01
Intraoperative fluorescence molecular imaging based on targeted fluorescence agents is an emerging approach to improve surgical and endoscopic imaging and guidance. Short exposure times per frame and implementation at video rates are necessary to provide continuous feedback to the physician and avoid motion artifacts. However, fast imaging implementations also limit the sensitivity of fluorescence detection. To improve on detection sensitivity in video rate fluorescence imaging, we considered herein an optical flow technique applied to texture-rich color images. This allows the effective accumulation of fluorescence signals over longer, virtual exposure times. The proposed correction scheme is shown to improve signal-to-noise ratios both in phantom experiments and in vivo tissue imaging.
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
Different functional states of ram spermatozoa analysed by partition in an aqueous two-phase system.
Grasa, P; Martí, J I; Muiño-Blanco, T; Cebrián-Pérez, J A
2003-09-25
The surface of spermatozoa plays a critical role in many stages involved in fertilisation. The plasma membrane undergoes important alterations in the male and female reproductive tract, which result in the ability of spermatozoa to fertilise eggs. One of these membrane modifications is sperm capacitation, a process by which sperm interacts with the zona pellucida receptors leading to the acrosome reaction. It has been proposed that the freezing process induces capacitation-like changes to spermatozoa, and that this premature capacitation could explain the reduction in longevity and fertilising capacity of cryopreserved mammalian spermatozoa. Our research focused on the relationship between membrane alterations occurring throughout freezing-thawing and the processes of capacitation and acrosome reaction. We used centrifugal countercurrent distribution (CCCD) analysis to compare the partition behaviour of ram spermatozoa that was either subjected to cold-shock or frozen-thawed with capacitated and acrosome reacted samples. In addition, the effect of the induced acrosome reaction on membrane integrity of ram spermatozoa was studied using biochemical markers and electron microscopy scanning. The CCCD analysis revealed important similarities between the surface characteristics of capacitated and cold-shocked sperm as well as between acrosome-reacted and frozen-thawed sperm. Cold-shocked and capacitated sperm showed an increased cell affinity for the lower dextran-rich phase as well as a decreased heterogeneity. Likewise, the induction of the acrosome reaction resulted in a loss of viability and an important decrease in cell surface heterogeneity compared to the untreated-control sample. Similar surface changes were found when semen samples were frozen with either Fiser or milk-yolk extender. These results confirm those obtained for membrane integrity by fluorescence markers. Thus, the high cell viability value found in the control sample (74.5%) was greatly decreased
Quantum partition functions from classical distributions: Application to rare-gas clusters
NASA Astrophysics Data System (ADS)
Calvo, F.; Doye, J. P. K.; Wales, D. J.
2001-05-01
We investigate the thermodynamic behavior of quantum many-body systems using several methods based on classical calculations. These approaches are compared for the melting of Lennard-Jones (LJ) clusters, where path-integral Monte Carlo (PIMC) results are also available. First, we examine two quasiclassical approaches where the classical potential is replaced by effective potentials accounting for quantum corrections of low order in ℏ. Of the Wigner-Kirkwood and Feynman-Hibbs effective potentials, only the latter is found to be in quantitative agreement with quantum simulations. However, both potentials fail to describe even qualitatively the low-temperature regime, where quantum effects are strong. Our second approach is based on the harmonic superposition approximation, but with explicit quantum oscillators. In its basic form, this approach is in good qualitative agreement with PIMC results, and becomes more accurate at low temperatures. By including anharmonic corrections in the form of temperature-dependent frequency shifts, the agreement between the quantum superposition and the PIMC results becomes quantitative for the caloric curve of neon clusters. The superposition method is then applied to larger clusters to study the influence of quantum delocalization on the melting and premelting of LJ19, LJ31, LJ38, and LJ55. The quantum character strongly affects the thermodynamics via changes in the ground state structure due to increasing zero-point energies. Finally, we focus on the lowest temperature range, and we estimate the Debye temperatures of argon clusters and their size variation. A strong sensitivity to the cluster structure is found, especially when many surface atoms reorganize as in the anti-Mackay/Mackay transition. In the large size regime, the Debye temperature smoothly rises to its bulk limit, but still depends slightly on the growth sequence considered.
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.
Menon, Prahlad G; Ludwig, Daniel; Lacomis, Joan; Schwartzman, David; Toma, Catalin
2014-12-01
Preliminary clinical experience with a percutaneous endoventricular partitioning device (Parachute®, CardioKinetix Inc., Menlo Park, CA, USA) suggests that it ameliorates global LV dysfunction and heart failure symptoms in selected patients who have suffered previous anterior myocardial infarction. Less is known of its effect on regional LV function. To gain insight into device effect on regional LV function by analysis of cardiac computed tomographic (CT) images obtained before and after device implantation. Comparative analysis of pre and 6 months post-implantation contrast-enhanced CT images from 6 subjects enrolled in the phase 1 Parachute clinical trials, including regional LV volume and systolic excursion, as well as device motion. After implantation, a significant reduction in volume of the "dynamic" LV compartment (that which was not excluded by the device) was accompanied by a significant reduction in dykinetic motion and a trend toward an improved ejection fraction. Penetration of contrast into the excluded compartment was still present at 6 months, however the apical motion was significantly less dyskinetic in 3 subjects and unchanged in the other 3. Overall device surface motion was inward in systole, a significant improvement relative to the overall dyskinetic LV apex pre-implantation. Device motion was spatially heterogeneous, which appeared to be dependent on the motility of the myocardium that anchored its individual splines. Our data suggest that the Parachute device acts as a functional impediment to flow and stretch, effectively depressurizing the apical segment. © 2014, Wiley Periodicals, Inc.
Wodrich, Matthew D; Jana, Daniel F; Schleyer, Paul von Ragué; Corminboeuf, Clémence
2008-11-13
Energies of alkanes computed with many popular and even newer density functionals are flawed by systematic errors, which become considerable with larger molecules. The same energies, however, are well described by post-Hartree-Fock methods. Similar DFT shortcomings are well documented for cases involving descriptions of intermolecular van der Waals complexes. One solution to the density functional problem is the addition of an empirical correction term, which more accurately models the known R (-6) dependence of van der Waals energies. Here, we present the first empirical correction to DFT parametrized to reproduce experimental energies associated with intramolecular interactions in alkanes. Our training set used only three reactions involving simple linear and branched alkanes and provides a remarkable improvement over conventional DFT methods and empirical corrections optimized for intermolecular interactions. In contrast to many standard density functionals, the intramolecular empirical correction correctly predicts the lowest energy alkane isomer in addition to performing satisfactorily for describing the interaction energies of intermolecular complexes.
Multicenter-type corrections to standard DFT exchange and correlation functionals
NASA Astrophysics Data System (ADS)
Tavernelli, Ivano; Lin, I.-Chun; Rothlisberger, Ursula
2009-01-01
We propose to express corrections to the standard approximations of the exchange-correlation functionals in the form of multiatom-centered functionals that can be related to the atoms-in-molecules theory of Bader and a multicenter density expansion. Unlike conventional functionals, the variables of these multicenter functionals are the positions and identities of the nuclei, which can unambiguously be determined from the topology of the electronic density. The proposed multicenter correction is used to provide a theoretical basis for the dispersion-corrected atom-centered potential (DCACP) approach used to improve van der Waals interactions in conventional density functional theory. Convergence to the correct long-range asymptotic behavior of the multicenter expansion for DCACPs is demonstrated in the test case of the H2 van der Waals dimer.
A correction to a highly accurate voight function algorithm
NASA Technical Reports Server (NTRS)
Shippony, Z.; Read, W. G.
2002-01-01
An algorithm for rapidly computing the complex Voigt function was published by Shippony and Read. Its claimed accuracy was 1 part in 10^8. It was brought to our attention by Wells that Shippony and Read was not meeting its claimed accuracy for extremely small but non zero y values. Although true, the fix to the code is so trivial to warrant this note for those who use this algorithm.
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…
Timothy S. McCay; Matthew J. Lovallo; W. Mark Ford; Michael A. Menzel; Michael A. Menzel
2004-01-01
We examined the representation of shrew species within assemblages at 197 sites in the southern Appalachian Mountains, USA. Assemblages were classified according to representation of functional groups, including fossorial, small epigeal, and large epigeal. Average (9?SD) species richness was 2.99?1.0 and assemblages averaged 0.8 species in the fossorial and large...
How pulmonary function changes after pectus excavatum correction surgery.
Kuru, Pinar; Dudakli, Asli; Mursaloglu, Hakan; Arikan, Hazal; Oktay, Aysu; Yuksel, Mustafa
2015-10-01
We aimed to determine the effects of minimally invasive repair of pectus excavatum on pulmonary function and quality of life. Minimally invasive pectus excavatum repair was undertaken in 80 patients with a mean age of 16.91 ± 4.37 years (range 7-30 years) and a mean Haller index of 4.07 ± 1.39; 85% of the patients were male. They and their parents completed the Nuss Questionnaire Modified for Adults, and pulmonary function tests were performed on the patients before and 6 months after the operation. The mean Nuss score was 31.06 ± 6.78 before the operation and it increased to 37.1 ± 8.31 (p = 0.000) 6 months after the operation. Forced vital capacity decreased from 3.70 ± 1.23 to 3.48 ± 1.03 L (p = 0.05) postoperatively. The percentage of expected forced vital capacity decreased from 83.21% ± 16.97% to 76.52% ± 20.98% (p = 0.01). There was no significant change in forced expiratory volume in 1 s. The mean ratio of forced expiratory volume in 1 s to forced vital capacity was 86% preoperatively and it increased to 91% postoperatively (p = 0.000). Minimally invasive pectus excavatum repair has a positive impact on the quality of life of pectus excavatum patients, but a negative impact on forced vital capacity. Follow-up studies are needed to assess the long-term changes in pulmonary function after this operation. © The Author(s) 2015.
Does Bicarbonate Correct Coagulation Function Impaired by Acidosis in Swine?
2006-07-01
L bicarbonate to a pH of 7.4 (A-Bi, n 6). Blood samples were taken at base - line, 15 minutes after acidosis induction, and 15 minutes after...Behring, Deerfield, IL). Plasma fibrinogen concentra- tion was determined by BCS Coagulation System based on fibrinogen functional activities in the...0.05). Hct decreased from 31 1% to 28 1% in A-LR and from 29 1% to 25 1% in A-Bi (p 0.05). Arterial base excess (BE) dropped from 7.1 0.7
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
Dudovitz, Rebecca N; Izadpanah, Nilufar; Chung, Paul J.; Slusser, Wendelin
2015-01-01
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
Dudovitz, Rebecca N; Izadpanah, Nilufar; Chung, Paul J; Slusser, Wendelin
2016-05-01
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. 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. 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. 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.
Approach to a correct function of stuffing boxes
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.
[Correcting influence of music on the students' functional state].
Gevorkian, É S; Minasian, S M; Abraamian, É T; Adamian, Ts I
2013-01-01
The influence of listening to classical music on integral indices of the activity of the regulatory mechanisms of the heart rhythm in students after teaching load was tested with the method of variational pulsometry accordingly to R.M Baevsky procedure. Registration and analysis of ECG was realized on Pentium 4 in three experimental situations: before the start of lessons (norm), after lessons, after listening to the music. Two types of response of students 'functional state to the teaching load: sympathetic and parasympathetic have been established. After teaching load music therapy session was found to led to the shift of levels of all examined indices of heart rhythm toward the original data (norm), most expressed in students with a sympathetic response type.
Proton fragmentation functions considering finite-mass corrections
NASA Astrophysics Data System (ADS)
Moosavi Nejad, S. M.; Soleymaninia, M.; Maktoubian, A.
2016-10-01
We present new sets of proton fragmentation functions (FFs) describing the production of protons from the gluon and each of the quarks, obtained by the NLO QCD fits to all relevant data sets of single-inclusive electron-positron annihilation. Specifically, we determine their uncertainties using the Gaussian method for error estimation. Our analysis is in good agreement with the e + e - annihilation data. We also include finite-mass effects of the proton in our calculations, a topic to which very little attention is paid in the literature. Proton mass effects turn out to be appreciable for gluon and light quark FFs. The inclusion of finite-mass effects tends to improve the overall description of the data by reducing the minimized χ2 values significantly. As an application, we apply the extracted FFs to make predictions for the scaled-energy distribution of protons inclusively produced in top quark decays at next-to-leading order, relying on the universality and scaling violations of FFs.
Dispersion- and Exchange-Corrected Density Functional Theory for Sodium Ion Hydration.
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.
Zarillo, G.A.; Liu, T.C.; Tsien, H.S.; Zimmerman, M.S.
1985-02-01
Recent geomorphic evidence from the inner shelf and shoreface to the east of Long Island's barrier island system indicates that reworking of glacial outwash deposits at the inner shelf-shoreface transition, as sea level rises, may be supplying much of the sediment needed to maintain barrier island to the west. A conceptual model describing sediment dispersal from outwash source areas was developed from this hypothesis. It was reasoned that outwash sediments ranging from silts to coarse gravels would be subject to differential transport paths across and along the shoreface upon reworking. Coarser grain sizes would move onshore toward the intertidal beach, whereas finer sediments would move offshore. Sand of intermediate grain size would be concentrated in the surf zone and move alongshore in wave-generated longshore currents. To test this model, 400 samples from the beach and shoreface of Long Island were analyzed for grain-size frequency distribution and each grain-size class was examined for frequency of occurrence in the cross-shore and alongshore directions. On a spatially averaged basis, grain-size classes displayed peak abundance in specific zones across the shoreface as predicted by the model, but alongshore trends could not be recognized among the noisy data. Therefore, empirical orthogonal functions (EOF) were used to examine uncorrelated modes of variability in the occurrence of each grain-size class in the alongshore direction. The first function, representing more than 60% of the variability among the data, showed that grain sizes subject to longshore transport in the surf zone increase in frequency in the alongshore direction relative to coarser grain sizes. Results also show that peak concentrations of coarse sediments correspond to zones subject to frequent overwashing. It is concluded that EOF analysis of individual grain-size classes holds promise for extracting trends from noisy data sets.
NASA Technical Reports Server (NTRS)
Phinney, W. C.
1992-01-01
As a prelude to determinations of the content of total iron as FeO(T) in melts in equilibrium with calcic anorthosites, the partition coefficients (Ds) for FeO(T) between calcic plagioclase and basaltic melt were determined, as a function of oxygen fugacity (f(O2)), for a basaltic composition that occurs as matrices for plagioclase megacrysts. Results showed that, at the liquidus conditions, the value of D for FeO(T) between calcic plagioclase and tholeiitic basalt changed little (from 0.030 to 0.044) between the very low f(O2) of the iron-wustite buffer and that of the quartz-fayalite-magnetite (QFM) buffer. At fugacities above QFM, the value for D increased rapidly to 0.14 at the magnetite-hematite buffer and to 0.33 in air. The increase in D results from the fact that, at f(O2) below QFM, nearly all of the Fe is in the Fe(2+) state; above QFM, the Fe(3+)/Fe(2+) ratio in the melt increases rapidly, causing more Fe to enter the plagioclase which accepts Fe(3+) more readily than Fe(2+).
NASA Technical Reports Server (NTRS)
Phinney, W. C.
1992-01-01
As a prelude to determinations of the content of total iron as FeO(T) in melts in equilibrium with calcic anorthosites, the partition coefficients (Ds) for FeO(T) between calcic plagioclase and basaltic melt were determined, as a function of oxygen fugacity (f(O2)), for a basaltic composition that occurs as matrices for plagioclase megacrysts. Results showed that, at the liquidus conditions, the value of D for FeO(T) between calcic plagioclase and tholeiitic basalt changed little (from 0.030 to 0.044) between the very low f(O2) of the iron-wustite buffer and that of the quartz-fayalite-magnetite (QFM) buffer. At fugacities above QFM, the value for D increased rapidly to 0.14 at the magnetite-hematite buffer and to 0.33 in air. The increase in D results from the fact that, at f(O2) below QFM, nearly all of the Fe is in the Fe(2+) state; above QFM, the Fe(3+)/Fe(2+) ratio in the melt increases rapidly, causing more Fe to enter the plagioclase which accepts Fe(3+) more readily than Fe(2+).
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).
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
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.
Partition-DFT on the water dimer.
Gómez, Sara; Nafziger, Jonathan; Restrepo, Albeiro; Wasserman, Adam
2017-02-21
As is well known, the ground-state symmetry group of the water dimer switches from its equilibrium Cs-character to C2h-character as the distance between the two oxygen atoms of the dimer decreases below RO-O∼2.5 Å. For a range of RO-O between 1 and 5 Å, and for both symmetries, we apply Partition Density Functional Theory (PDFT) to find the unique monomer densities that sum to the correct dimer densities while minimizing the sum of the monomer energies. We calculate the work involved in deforming the isolated monomer densities and find that it is slightly larger for the Cs geometry for all RO-O. We discuss how the PDFT densities and the corresponding partition potentials support the orbital-interaction picture of hydrogen-bond formation.
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
Partnering dispersion corrections with modern parameter-free double-hybrid density functionals.
Sancho-García, J C; Brémond, É; Savarese, M; Pérez-Jiménez, A J; Adamo, C
2017-03-09
The PBE-QIDH and SOS1-PBE-QIDH double-hybrid density functionals are merged with a pair of dispersion corrections, namely the pairwise additive D3(BJ) and the non-local correlation functional VV10, leading to the corresponding dispersion-corrected models. The parameters adjusting each of the dispersion corrections to the functionals are obtained by fitting to well-established energy datasets (e.g. S130) used as a benchmark, giving rise to functionals spanning covalent and non-covalent binding forces. The application of the models to challenging systems out of the training set, like those comprising the L7 database of large supramolecular complexes, or the S66x8 dataset of stretched and elongated intermolecular distances, reveals the high accuracy of the coupling.
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.
Mielke, Steven L; Truhlar, Donald G
2015-01-28
We present an improved version of our "path-by-path" enhanced same path extrapolation scheme for Feynman path integral (FPI) calculations that permits rapid convergence with discretization errors ranging from O(P(-6)) to O(P(-12)), where P is the number of path discretization points. We also present two extensions of our importance sampling and stratified sampling schemes for calculating vibrational-rotational partition functions by the FPI method. The first is the use of importance functions for dihedral angles between sets of generalized Jacobi coordinate vectors. The second is an extension of our stratification scheme to allow some strata to be defined based only on coordinate information while other strata are defined based on both the geometry and the energy of the centroid of the Feynman path. These enhanced methods are applied to calculate converged partition functions by FPI methods, and these results are compared to ones obtained earlier by vibrational configuration interaction (VCI) calculations, both calculations being for the Jordan-Gilbert potential energy surface. The earlier VCI calculations are found to agree well (within ∼1.5%) with the new benchmarks. The FPI partition functions presented here are estimated to be converged to within a 2σ statistical uncertainty of between 0.04% and 0.07% for the given potential energy surface for temperatures in the range 300-3000 K and are the most accurately converged partition functions for a given potential energy surface for any molecule with five or more atoms. We also tabulate free energies, enthalpies, entropies, and heat capacities.
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.
Loureiro, Dana B; Braia, Mauricio; Romanini, Diana; Tubio, Gisela
2017-01-01
The structure and catalytic activity of xylanase from Thermomyces lanuginosus were studied in different media (containing polyethylene glycol -PEG- or salt) at different temperatures. The aim was to study how the native structure of the enzyme is affected to understand the partitioning behavior of xylanase in PEG/sodium citrate (PEG/NaCit) aqueous two-phase systems. The presence of PEGs of different molar masses slightly altered the native structure of xylanase, although its catalytic activity was not affected. All the polymers assayed protect the native structure (and catalytic activity) of xylanase against temperature, except for PEG1000. Surface hydrophobicity experiments showed that xylanase favorable interacts with PEGs. Partitioning experiments confirmed this result and demonstrated that PEG1000/NaCit is the best system to partition xylanase from Thermomyces lanuginosus, since the Kp was 17.7 ± 0.3. Copyright © 2016 Elsevier Inc. All rights reserved.
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.
NASA Astrophysics Data System (ADS)
Nocera, A.; Alvarez, G.
2016-11-01
Frequency-dependent correlations, such as the spectral function and the dynamical structure factor, help illustrate condensed matter experiments. Within the density matrix renormalization group (DMRG) framework, an accurate method for calculating spectral functions directly in frequency is the correction-vector method. The correction vector can be computed by solving a linear equation or by minimizing a functional. This paper proposes an alternative to calculate the correction vector: to use the Krylov-space approach. This paper then studies the accuracy and performance of the Krylov-space approach, when applied to the Heisenberg, the t-J, and the Hubbard models. The cases studied indicate that the Krylov-space approach can be more accurate and efficient than the conjugate gradient, and that the error of the former integrates best when a Krylov-space decomposition is also used for ground state DMRG.
None, None
2016-11-21
Frequency-dependent correlations, such as the spectral function and the dynamical structure factor, help illustrate condensed matter experiments. Within the density matrix renormalization group (DMRG) framework, an accurate method for calculating spectral functions directly in frequency is the correction-vector method. The correction vector can be computed by solving a linear equation or by minimizing a functional. Our paper proposes an alternative to calculate the correction vector: to use the Krylov-space approach. This paper also studies the accuracy and performance of the Krylov-space approach, when applied to the Heisenberg, the t-J, and the Hubbard models. The cases we studied indicate that themore » Krylov-space approach can be more accurate and efficient than the conjugate gradient, and that the error of the former integrates best when a Krylov-space decomposition is also used for ground state DMRG.« less
None, None
2016-11-21
Frequency-dependent correlations, such as the spectral function and the dynamical structure factor, help illustrate condensed matter experiments. Within the density matrix renormalization group (DMRG) framework, an accurate method for calculating spectral functions directly in frequency is the correction-vector method. The correction vector can be computed by solving a linear equation or by minimizing a functional. Our paper proposes an alternative to calculate the correction vector: to use the Krylov-space approach. This paper also studies the accuracy and performance of the Krylov-space approach, when applied to the Heisenberg, the t-J, and the Hubbard models. The cases we studied indicate that the Krylov-space approach can be more accurate and efficient than the conjugate gradient, and that the error of the former integrates best when a Krylov-space decomposition is also used for ground state DMRG.
Nocera, A; Alvarez, G
2016-11-01
Frequency-dependent correlations, such as the spectral function and the dynamical structure factor, help illustrate condensed matter experiments. Within the density matrix renormalization group (DMRG) framework, an accurate method for calculating spectral functions directly in frequency is the correction-vector method. The correction vector can be computed by solving a linear equation or by minimizing a functional. This paper proposes an alternative to calculate the correction vector: to use the Krylov-space approach. This paper then studies the accuracy and performance of the Krylov-space approach, when applied to the Heisenberg, the t-J, and the Hubbard models. The cases studied indicate that the Krylov-space approach can be more accurate and efficient than the conjugate gradient, and that the error of the former integrates best when a Krylov-space decomposition is also used for ground state DMRG.
NASA Astrophysics Data System (ADS)
Chang, Shu-Chiuan; Shrock, Robert
2006-05-01
We present a method for calculating transfer matrices for the q-state Potts model partition functions Z(G,q,v), for arbitrary q and temperature variable v, on strip graphs G of the square (sq), triangular (tri), and honeycomb (hc) lattices of width Ly vertices and of arbitrarily great length Lx vertices, subject to toroidal and Klein-bottle boundary conditions. For the toroidal case we express the partition function as Z(Λ,Ly×Lx,q,v)=∑d=0Ly ∑ bj(d)(λ)m, where Λ denotes lattice type, bj(d) are specified polynomials of degree d in q, λ are eigenvalues of the transfer matrix T in the degree- d subspace, and m=Lx ( Lx/2) for Λ=sq,tri (hc), respectively. An analogous formula is given for Klein-bottle strips. We exhibit a method for calculating T for arbitrary Ly. In particular, we find some very simple formulas for the determinant det(T), and trace Tr(T). Illustrative examples of our general results are given, including new calculations of transfer matrices for Potts model partition functions on strips of the square, triangular, and honeycomb lattices with toroidal or Klein-bottle boundary conditions.
NASA Astrophysics Data System (ADS)
Brandenburg, J. G.; Bates, J. E.; Sun, J.; Perdew, J. P.
2016-09-01
The strongly constrained and appropriately normed (SCAN) semilocal density functional [J. Sun, A. Ruzsinszky, and J. P. Perdew, Phys. Rev. Lett. 115, 036402 (2015), 10.1103/PhysRevLett.115.036402] obeys all 17 known exact constraints for meta-generalized-gradient approximations (meta-GGAs), and it includes some medium-range correlation effects. Long-range London dispersion interactions are still missing, but they can be accounted for via an appropriate correction scheme. In this study, we combine SCAN with an efficient London dispersion correction and show that lattice energies of simple organic crystals can be improved with the applied correction by 50%. The London-dispersion corrected SCAN meta-GGA outperforms all other tested London-dispersion corrected meta-GGAs for molecular geometries. Our method yields mean absolute deviations (MADs) for main group bond lengths that are consistently below 1 pm, rotational constants with MADs of 0.2%, and noncovalent distances with MADs below 1%. For a large database of general main group thermochemistry and kinetics (˜800 chemical species), one of the lowest weighted mean absolute deviations for long-range corrected meta-GGA functionals is achieved. Noncovalent interactions are of average quality, and hydrogen bonded systems in particular seem to suffer from overestimated polarization related to the self-interaction error of SCAN. We also discuss some consequences of numerical sensitivity encountered for meta-GGAs.
Next-to leading order analysis of target mass corrections to structure functions and asymmetries
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.
Software Partitioning Technologies
2001-05-29
1 Software Partitioning Technologies Tim Skutt Smiths Aerospace 3290 Patterson Ave. SE Grand Rapids, MI 49512-1991 (616) 241-8645 skutt_timothy...Limitation of Abstract UU Number of Pages 12 2 Agenda n Software Partitioning Overview n Smiths Software Partitioning Technology n Software Partitioning...Partition Level OS Core Module Level OS Timers MMU I/O API Layer Partitioning Services 6 Smiths Software Partitioning Technology n Smiths has developed
One loop corrections on fragmentation function of 1S wave charmed mesons
NASA Astrophysics Data System (ADS)
Sepahvand, Reza; Dadfar, Sareh
2017-04-01
We present the contribution of the next to leading order (NLO) corrections in fragmentation a c-quark to 1S wave charmed mesons. These corrections are calculated by using the dimensional regularization method. We use two slicing methods that allow the phase space integrals to be evaluated in 4 dimensions. Technical details are discussed about virtual and real corrections in this scheme. Our numerical calculations show the NLO corrections to D mesons fragmentation function (FF) enhance the fragmentation probability (FP). The production ratio of vector mesons D* and D+* to all states is estimated. At NLO, it is obtained a bit smaller than the one at LO. Finally our analytic results are compared with available experimental data for D0 and D+* mesons.
Functional Gene Correction for Cystic Fibrosis in Lung Epithelial Cells Generated From Patient iPSCs
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
2015-01-01
SUMMARY Lung disease is a major cause of death in the USA, with current therapeutic approaches only serving 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 (iPSC) 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 iPSC 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
NASA Astrophysics Data System (ADS)
Bubin, Sergiy; Stanke, Monika; Adamowicz, Ludwik
2017-06-01
In our previous work S. Bubin et al., Chem. Phys. Lett. 647, 122 (2016), 10.1016/j.cplett.2016.01.056, it was established that complex explicitly correlated one-center all-particle Gaussian functions (CECGs) provide effective basis functions for very accurate nonrelativistic molecular non-Born-Oppenheimer calculations. In this work, we advance the molecular CECGs approach further by deriving and implementing algorithms for calculating the leading relativistic corrections within this approach. The algorithms are tested in the calculations of the corrections for all 23 bound pure vibrational states of the HD+ ion.
Spin-history artifact during functional MRI: potential for adaptive correction.
Yancey, Sadie E; Rotenberg, David J; Tam, Fred; Chiew, Mark; Ranieri, Shawn; Biswas, L; Anderson, Kevan J T; Baker, S Nicole; Wright, Graham A; Graham, Simon J
2011-08-01
Functional magnetic resonance imaging (fMRI) is limited by sensitivity to millimetre-scale head motion. Adaptive correction is a strategy to adjust the imaging plane in response to measured head motion, thereby suppressing motion artifacts. This strategy should correct for motion in all six degrees of freedom and also holds promise for through-plane motion that creates "spin-history" artifact that cannot easily be removed by postprocessing methods. Improved quantitative understanding of the MRI signal behavior associated with spin-history artifact would be useful for implementing adaptive correction robustly. A numerical simulation was developed to predict MRI artifact signal amplitude in a single-slice for simple motions, implemented with and without adaptive correction, and compared with experiment by imaging a phantom at 3.0 T. Functional MRI was also performed of a human volunteer to illustrate adaptive correction in the presence of spin-history artifact. Good agreement was achieved between simulation and experimental results. Although time-averaged artifact signal amplitude was observed to correlate linearly with motion speed, artifact time-courses were nonlinearly related to motion waveforms. In addition, experimental results demonstrated effective adaptive correction of spin-history artifact when the phantom underwent complex motions. Adaptive correction during human fMRI suppressed spin-history artifacts and spurious activations associated with task-correlated motion. Overall, this work suggests that adaptive correction, especially when implemented with minimal lag between motion measurement and scan plane update, may help to expand the populations for which fMRI can be performed robustly.
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
Lensing corrections to features in the angular two-point correlation function and power spectrum
LoVerde, Marilena; Hui, Lam; Gaztanaga, Enrique
2008-01-15
It is well known that magnification bias, the modulation of galaxy or quasar source counts by gravitational lensing, can change the observed angular correlation function. We investigate magnification-induced changes to the shape of the observed correlation function w({theta}), and the angular power spectrum C{sub l}, paying special attention to the matter-radiation equality peak and the baryon wiggles. Lensing effectively mixes the correlation function of the source galaxies with that of the matter correlation at the lower redshifts of the lenses distorting the observed correlation function. We quantify how the lensing corrections depend on the width of the selection function, the galaxy bias b, and the number count slope s. The lensing correction increases with redshift and larger corrections are present for sources with steep number count slopes and/or broad redshift distributions. The most drastic changes to C{sub l} occur for measurements at high redshifts (z > or approx. 1.5) and low multipole moment (l < or approx. 100). For the source distributions we consider, magnification bias can shift the location of the matter-radiation equality scale by 1%-6% at z{approx}1.5 and by z{approx}3.5 the shift can be as large as 30%. The baryon bump in {theta}{sup 2}w({theta}) is shifted by < or approx. 1% and the width is typically increased by {approx}10%. Shifts of > or approx. 0.5% and broadening > or approx. 20% occur only for very broad selection functions and/or galaxies with (5s-2)/b > or approx. 2. However, near the baryon bump the magnification correction is not constant but is a gently varying function which depends on the source population. Depending on how the w({theta}) data is fitted, this correction may need to be accounted for when using the baryon acoustic scale for precision cosmology.
Ensemble density variational methods with self- and ghost-interaction-corrected functionals
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.
Second-order corrections to the wave function at the origin in muonic hydrogen and pionium
Ivanov, Vladimir G.; Korzinin, Evgeny Yu.; Karshenboim, Savely G.
2009-07-15
Nonrelativistic second-order corrections to the wave function at the origin in muonic and exotic atoms are considered. The corrections are due to the electronic vacuum polarization. Such corrections are of interest due to various effective approaches, which take into account QED and hadronic effects. The wave function at the origin plays a key role in the calculation of the pionium lifetime, various finite nuclear size effects, and the hyperfine splitting. The results are obtained for the 1s and 2s states in pionic and muonic hydrogen and deuterium and in pionium, a bound system of {pi}{sup +} and {pi}{sup -}. Applications to the hyperfine structure and the Lamb shift in muonic hydrogen are also considered.
String corrections to four point functions in the AdS/CFT correspondence
NASA Astrophysics Data System (ADS)
Brodie, John H.; Gutperle, Michael
1999-01-01
In a string calculation to order α'3, we compute an eight-derivative four-dilaton term in the type IIB effective action. Following the AdS prescription, we compute the order (gYM2Nc)-3/2 correction to the four-point correlation function involving the operator trF2 in four dimensional N=4 super Yang-Mills using the string corrected type IIB action extending the work of Freedman et al. (hep-th/9808006). In the limit where two of the Yang-Mills operators approach each other, we find that our correction to the four-point correlation functions develops a logarithmic singularity. We discuss the possible cancellation of this logarithmic singularities by conjecturing new terms in the type IIB effective action.
Brandenburg, Jan Gerit; Grimme, Stefan
2014-06-05
The ambitious goal of organic crystal structure prediction challenges theoretical methods regarding their accuracy and efficiency. Dispersion-corrected density functional theory (DFT-D) in principle is applicable, but the computational demands, for example, to compute a huge number of polymorphs, are too high. Here, we demonstrate that this task can be carried out by a dispersion-corrected density functional tight binding (DFTB) method. The semiempirical Hamiltonian with the D3 correction can accurately and efficiently model both solid- and gas-phase inter- and intramolecular interactions at a speed up of 2 orders of magnitude compared to DFT-D. The mean absolute deviations for interaction (lattice) energies for various databases are typically 2-3 kcal/mol (10-20%), that is, only about two times larger than those for DFT-D. For zero-point phonon energies, small deviations of <0.5 kcal/mol compared to DFT-D are obtained.
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.
Steinmann, Stephan N; Csonka, Gábor; Corminboeuf, Clémence
2009-11-10
Density functionals fail to provide a consistent description of weak intra- (i.e., short-range) and inter- (i.e., long-range) molecular interactions arising from nonoverlapping electron densities. An efficient way to correct the long-range errors is to add an empirical atom pair wise interaction-correction, inspired by the Lennard-Jones potential (R(-6) dependence). We show that the universal damping function of Tang and Toennies (TT) that includes higher-order correction terms (R(-8) and R(-10) dependent) reduces the intramolecular errors more efficiently, without altering the long-range correction. For general applicability, the TT damping function is augmented by a Fermi damping to prevent corrections at covalent distances. The performance of the new dD10 correction was tested in combination with three nonempirical GGAs (PBE, PBEsol, RGE2) on 64 illustrative reaction energies featuring both intra- and intermolecular interactions. With only two empirical parameters, PBE-dD10 outperforms the computationally more demanding and most recent functionals such as M06-2X or B2PLYP-D (MAD = 3.78 and 1.95 kcal mol(-1), respectively). At the cc-pVTZ level, PBE-dD10 (MAD = 1.24 kcal mol(-1)) considerably reduces common DFT errors successfully balancing intra- (short-range) and inter- (long-range) molecular interactions. While REG2-dD10 performs closely to PBE-dD10 (MAD = 1.48 kcal mol(-1)), the overall MAD of PBEsol-dD10 is again slightly higher (MAD = 1.76 kcal mol(-1)).
Correction of base deficits in deceased organ donors: effects on immediate renal allograft function.
Shen, G K; Recicar, J F; Hovsepian, R V; Salisbury, J A; Niles, P A
2004-11-01
Fluid status in the brain-dead donor is often difficult to assess. We hypothesized that using base deficit as a measure of tissue perfusion will facilitate fluid management in these donors, thereby improving renal allograft function. Consecutive donors over a 12-month period were prospectively studied. In Group I, resuscitation was based on maintaining normal blood pressure and urine output. In Group II, additional parameters of resuscitation included the correction of base deficit. Immediate renal allograft function was examined in the 48 recipients. Delayed graft function occurred in 48% of Group I, and in 19% of Group II recipients. Creatinine clearance on day 7, calculated by the Cockroft-Gault formula, was 29 +/- 6 mL/min in Group I versus 41 +/- 8 mL/min in Group II. We conclude that correcting base deficit is an extremely useful approach to expedite organ recovery and potentially improve function of transplanted kidneys.
Laymon, Charles M; Bowsher, James E
2013-02-01
In dual modality PET/CT, CT data are used to generate the attenuation correction applied in the reconstruction of the PET emission image. This requires converting the CT image into a 511-keV attenuation map. Algorithms for making this transformation require assumptions about the makeup of material within the patient. Anomalous material such as contrast agent administered to enhance the CT scan confounds conversion algorithms and has been observed to result in inaccuracies, i.e., inconsistencies with the true 511-keV attenuation present at the time of the PET emission scan. These attenuation artifacts carry through to the final attenuation-corrected PET emission image and can resemble diseased tissue. We propose an approach to correcting this problem that employs the attenuation information carried by the PET emission data. A likelihood-based algorithm for identifying and correcting of contrast is presented and tested. The algorithm exploits the fact that contrast artifacts manifest as too-high attenuation values in an otherwise high quality attenuation image. In a separate study, the performance of the loglikelihood as an objective-function component of a detection/correction algorithm, independent of any particular algorithm was mapped out for several imaging scenarios as a function of statistical noise. Both the full algorithm and the loglikelihood performed well in studies with simulated data. Additional studies including those with patient data are required to fully understand their capabilities.
Bhattacharjee, Anirban; Hofer, Thomas S; Rode, Bernd M
2008-11-28
Three-body distribution functions are calculated for metal ions in an aqueous medium in order to investigate and characterise solvent structure reorganization. Based on the existing formulation of three body correlation function, a local density correction is introduced to enable a comparison of different sub-regions within a solvate as well as different systems, thus taking into account the varying density arising from the influence of the solute.
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.
Acidosis and correction of acidosis does not affect rFVIIa function in swine
Darlington, Daniel N; Kheirabadi, Bijan S; Scherer, Michael R; Martini, Wenjun Z; Cap, Andrew P; Dubick, Michael A
2012-01-01
Background: Hemorrhagic shock and trauma are associated with acidosis and altered coagulation. A fall in pH has been reported to attenuate the activity of recombinant activated Factor VII (rFVIIa) in vitro. However, it is not known if acidosis induced by hemorrhagic shock or infusion of HCl attenuates FVIIa activity in vivo. The purpose of this study was to determine if acidosis, induced by two methods, affects recombinant FVIIa (rFVIIa) activity in swine, and if correction of the pH restores rFVIIa activity to normal. Methods: Acidosis was induce in anesthetized swine in two separate models: 1) HCl infusion (n=10) and 2) hemorrhage/hypoventilation (n=8). Three groups per model were used: Control (pH7.4), Acidosis (arterial pH7.1) and Acidosis-Corrected (bicarbonate infusion to return pH from 7.1 to 7.4). Pigs were then injected with rFVIIa (90 μg/kg) or vehicle (saline) at target pH and arterial blood samples were taken for measurement of coagulation function, including Thromboelastography -TEG, Thrombin Generation, Activated Clotting Time, Prothrombin Time, activated Partial Thromboplastin Time, Fibrinogen Concentration and Platelet count before and 5min after injection of rFVIIa. Results: Acidosis led to a hypocoagulation as measured by almost all coagulation parameters in both models. Furthermore, the change in coagulation function produced after infusion of rFVIIa was not different between control, acidosis and acidosis-corrected groups for all coagulation parameters measured. Conclusion: Acidosis associated with hemorrhagic shock or HCl infusion led to a hypocoagulation that was not corrected with bicarbonate infusion. Furthermore, acidosis did not affect rFVIIa function, and correction of the acidosis with bicarbonate had no effect on rFVIIa function in these models. This suggests that in vivo acidosis did not diminish rFVIIa function. PMID:23272296
Corrective osteotomy in forearm fracture malunion improves functional outcome in adults.
Chia, D S Y; Lim, Y J; Chew, W Y C
2011-02-01
Malunions of forearm fractures in adults can present with limitation of forearm rotation, or as distal radioulnar joint instability with functional impairment. This contrasts with paediatric patients in whom malunions of similar severities are often better tolerated. We did a retrospective review of six adult patients after corrective forearm osteotomy for symptomatic malunited forearm shaft fractures. The corrective operations were done between 7 and 168 months after initial injury, using oblique or wedge osteotomies. Median follow-up was 22.5 months. The patients recovered well, with statistically significant improvement in forearm rotation and Disabilities of the Arm, Shoulder, and Hand (DASH) scores. No significant complications occurred.
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.
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.
Yousaf, Kazim E; Brothers, Edward N
2010-03-09
An empirical dispersion correction is added to the range-separated hybrid density functionals HSE and HISS via parametrization versus a standard test bed of weakly bound complexes. The performance of the resulting HSE-D and HISS-D functionals is evaluated by calculating the equilibrium bond length, harmonic frequency, and dissociation energy for a number of rare gas dimers, and the lattice constants, band gaps, and sublimation energies of the rare gas solids. Both HSE-D and HISS-D are shown to provide accurate results for both molecules and extended systems, suggesting that the combination of a screened hybrid functional with an empirical dispersion correction provides an accurate, widely applicable method for use in solid-state and gas-phase electronic structure theory.
Reaction energetics on long-range corrected density functional theory: Diels-Alder reactions.
Singh, Raman K; Tsuneda, Takao
2013-02-15
The possibility of quantitative reaction analysis on the orbital energies of long-range corrected density functional theory (LC-DFT) is presented. First, we calculated the Diels-Alder reaction enthalpies that have been poorly given by conventional functionals including B3LYP functional. As a result, it is found that the long-range correction drastically improves the reaction enthalpies. The barrier height energies were also computed for these reactions. Consequently, we found that dispersion correlation correction is also crucial to give accurate barrier height energies. It is, therefore, concluded that both long-range exchange interactions and dispersion correlations are essentially required in conventional functionals to investigate Diels-Alder reactions quantitatively. After confirming that LC-DFT accurately reproduces the orbital energies of the reactant and product molecules of the Diels-Alder reactions, the global hardness responses, the halves of highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) energy gaps, along the intrinsic reaction coordinates of two Diels-Alder reactions were computed. We noticed that LC-DFT results satisfy the maximum hardness rule for overall reaction paths while conventional functionals violate this rule on the reaction pathways. Furthermore, our results also show that the HOMO-LUMO gap variations are close to the reaction enthalpies for these Diels-Alder reactions. Based on these results, we foresee quantitative reaction analysis on the orbital energies. Copyright © 2012 Wiley Periodicals, Inc.
Correction of dispersion and the betatron functions in the CEBAF accelerator
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.
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
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.
An improved theoretical approach to the empirical corrections of density functional theory
NASA Astrophysics Data System (ADS)
Lii, Jenn-Huei; Hu, Ching-Han
2012-02-01
An empirical correction to density functional theory (DFT) has been developed in this study. The approach, called correlation corrected atomization-dispersion (CCAZD), involves short- and long-range terms. Short-range correction consists of bond ( 1,2-) and angle ( 1,3-) interactions, which remedies the deficiency of DFT in describing the proto-branching stabilization effects. Long-range correction includes a Buckingham potential function aiming to account for the dispersion interactions. The empirical corrections of DFT were parameterized to reproduce reported Δ H f values of the training set containing alkane, alcohol and ether molecules. The Δ H f of the training set molecules predicted by the CCAZD method combined with two different DFT methods, B3LYP and MPWB1K, with a 6-31G* basis set agreed well with the experimental data. For 106 alkane, alcohol and ether compounds, the average absolute deviations (AADs) in Δ H f were 0.45 and 0.51 kcal/mol for B3LYP- and MPWB1K-CCAZD, respectively. Calculations of isomerization energies, rotational barriers and conformational energies further validated the CCAZD approach. The isomerization energies improved significantly with the CCAZD treatment. The AADs for 22 energies of isomerization reactions were decreased from 3.55 and 2.44 to 0.55 and 0.82 kcal/mol for B3LYP and MPWB1K, respectively. This study also provided predictions of MM4, G3, CBS-QB3 and B2PLYP-D for comparison. The final test of the CCAZD approach on the calculation of the cellobiose analog potential surface also showed promising results. This study demonstrated that DFT calculations with CCAZD empirical corrections achieved very good agreement with reported values for various chemical reactions with a small basis set as 6-31G*.
Khalili-Mahani, Najmeh; Chang, Catie; van Osch, Matthias J; Veer, Ilya M; van Buchem, Mark A; Dahan, Albert; Beckmann, Christian F; van Gerven, Joop M A; Rombouts, Serge A R B
2013-01-15
Growing interest in pharmacological resting state fMRI (RSfMRI) necessitates developing standardized and robust analytical approaches that are insensitive to spurious correlated physiological signals. However, in pharmacological experiments physiological variations constitute an important aspect of the pharmacodynamic/pharmacokinetic profile of drug action; therefore retrospective corrective methods that discard physiological signals as noise may not be suitable. Previously, we have shown that template-based dual regression analysis is a sensitive method for model-free and objective detection of drug-specific effects on functional brain connectivity. In the current study, the robustness of this standard approach to physiological variations in a placebo controlled, repeated measures pharmacological RSfMRI study of morphine and alcohol in 12 healthy young men is tested. The impact of physiology-related variations on statistical inferences has been studied by: 1) modeling average physiological rates in higher level group analysis; 2) Regressing out the instantaneous respiration variation (RV); 3) applying retrospective image correction (RETROICOR) in the preprocessing stage; and 4) performing combined RV and heart rate correction (RVHRCOR) by regressing out physiological pulses convolved with canonical respiratory and cardiac hemodynamic response functions. Results indicate regional sensitivity of the BOLD signal to physiological variations, especially in the vicinity of large vessels, plus certain brain structures that are reported to be involved in physiological regulation, such as posterior cingulate, precuneus, medial prefrontal and insular cortices, as well as the thalamus, cerebellum and the brainstem. The largest impact of "correction" on final statistical test outcomes resulted from including the average respiration frequency and heart rate in the higher-level group analysis. Overall, the template-based dual regression method seems robust against physical
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
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.
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.
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.
Correction function in the Lidar equation and the solution techniques for CO2 Lidar date reduction
NASA Technical Reports Server (NTRS)
Zhao, Y.; Lea, T. K.; Schotland, R. M.
1986-01-01
For lidar systems with long laser pulses the unusual behavior of the near-range signals causes serious difficulties and large errors in reduction. The commonly used lidar equation is no longer applicable since the convolution of the laser pulse with the atmospheric parameter distributions should be taken into account. It is important to give more insight into this problem and find the solution techniques. Starting from the original equation, a general form is suggested for the single scattering lidar equation where a correction function Cr is introduced. The correction Function Cr(R) derived from the original equation indicates the departure from the normal lidar equation. Examples of Cr(R) for a coaxial CO2 lidar system are presented. The Differential Absorption Lidar (DIAL) errors caused by the differences of Cr(R) for H2O measurements are plotted against height.
NASA Astrophysics Data System (ADS)
Perdew, John P.
Three size-consistency principles of electronic structure theory are set forth. "Separability" and "extensivity" are respected even by local or semilocal density functional approximations, which succeed for that and other reasons. The strong tendency of a separated subsystem to reject fractional electron number is a consequence of the derivative discontinuity of the energy; this "integer preference" is probably not respected by any practical density functional approximation. However, all three size-consistency principles are obeyed by theories which construct the energy from localized orbitals. The self-interaction correction (SIC) to the local spin density approximation favors localized orbitals for most systems. If this fails for metals, then SIC gives rise to a "false surface energy". The self-interaction correction is reviewed, along with its exact-theory "doppelganger", the derivative discontinuity. The latter reveals the physical content of the exact Kohn-Sham orbital energies and resolves the "band-gap problem".
Brandenburg, Jan Gerit; Grimme, Stefan
2014-01-01
We present and evaluate dispersion corrected Hartree-Fock (HF) and Density Functional Theory (DFT) based quantum chemical methods for organic crystal structure prediction. The necessity of correcting for missing long-range electron correlation, also known as van der Waals (vdW) interaction, is pointed out and some methodological issues such as inclusion of three-body dispersion terms are discussed. One of the most efficient and widely used methods is the semi-classical dispersion correction D3. Its applicability for the calculation of sublimation energies is investigated for the benchmark set X23 consisting of 23 small organic crystals. For PBE-D3 the mean absolute deviation (MAD) is below the estimated experimental uncertainty of 1.3 kcal/mol. For two larger π-systems, the equilibrium crystal geometry is investigated and very good agreement with experimental data is found. Since these calculations are carried out with huge plane-wave basis sets they are rather time consuming and routinely applicable only to systems with less than about 200 atoms in the unit cell. Aiming at crystal structure prediction, which involves screening of many structures, a pre-sorting with faster methods is mandatory. Small, atom-centered basis sets can speed up the computation significantly but they suffer greatly from basis set errors. We present the recently developed geometrical counterpoise correction gCP. It is a fast semi-empirical method which corrects for most of the inter- and intramolecular basis set superposition error. For HF calculations with nearly minimal basis sets, we additionally correct for short-range basis incompleteness. We combine all three terms in the HF-3c denoted scheme which performs very well for the X23 sublimation energies with an MAD of only 1.5 kcal/mol, which is close to the huge basis set DFT-D3 result.
[Correction of posture disorders and scoliosis in schoolchildren using functional biofeedback].
Bogdanov, O V; Nikolaeva, N I; Mikhaĭlenok, E L
1990-01-01
A novel technique is offered for correction of postural defects and early manifestations of scoliosis in schoolchildren using methods of functional biofeedback training. The technique allowed the patient to use the biofeedback signals informing on the degree of asymmetry in bioelectric activity of paravertebral muscles in static active straightening of the vertebral column. The data revealed a steady decrease in asymmetric activity indices in muscles erecting the column. This provided a physiological basis for a high clinical efficiency of the technique.
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.
Molecular density functional theory for water with liquid-gas coexistence and correct pressure
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.
Molecular density functional theory for water with liquid-gas coexistence and correct pressure.
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.
Molecular density functional theory for water with liquid-gas coexistence and correct pressure
NASA Astrophysics Data System (ADS)
Jeanmairet, Guillaume; Levesque, Maximilien; Sergiievskyi, Volodymyr; Borgis, Daniel
2015-04-01
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.
Head Motion and Correction Methods in Resting-state Functional MRI.
Goto, Masami; Abe, Osamu; Miyati, Tosiaki; Yamasue, Hidenori; Gomi, Tsutomu; Takeda, Tohoru
2016-01-01
Resting-state functional magnetic resonance imaging (RS-fMRI) is used to investigate brain functional connectivity at rest. However, noise from human physiological motion is an unresolved problem associated with this technique. Following the unexpected previous result that group differences in head motion between control and patient groups caused group differences in the resting-state network with RS-fMRI, we reviewed the effects of human physiological noise caused by subject motion, especially motion of the head, on functional connectivity at rest detected with RS-fMRI. The aim of the present study was to review head motion artifact with RS-fMRI, individual and patient population differences in head motion, and correction methods for head motion artifact with RS-fMRI. Numerous reports have described new methods [e.g., scrubbing, regional displacement interaction (RDI)] for motion correction on RS-fMRI, many of which have been successful in reducing this negative influence. However, the influence of head motion could not be entirely excluded by any of these published techniques. Therefore, in performing RS-fMRI studies, head motion of the participants should be quantified with measurement technique (e.g., framewise displacement). Development of a more effective correction method would improve the accuracy of RS-fMRI analysis.
NASA Astrophysics Data System (ADS)
Lisson, Jerold B.; Mounts, Darryl I.; Fehniger, Michael J.
1992-08-01
Localized wavefront performance analysis (LWPA) is a system that allows the full utilization of the system optical transfer function (OTF) for the specification and acceptance of hybrid imaging systems. We show that LWPA dictates the correction of wavefront errors with the greatest impact on critical imaging spatial frequencies. This is accomplished by the generation of an imaging performance map-analogous to a map of the optic pupil error-using a local OTF. The resulting performance map a function of transfer function spatial frequency is directly relatable to the primary viewing condition of the end-user. In addition to optimizing quality for the viewer it will be seen that the system has the potential for an improved matching of the optical and electronic bandpass of the imager and for the development of more realistic acceptance specifications. 1. LOCAL WAVEFRONT PERFORMANCE ANALYSIS The LWPA system generates a local optical quality factor (LOQF) in the form of a map analogous to that used for the presentation and evaluation of wavefront errors. In conjunction with the local phase transfer function (LPTF) it can be used for maximally efficient specification and correction of imaging system pupil errors. The LOQF and LPTF are respectively equivalent to the global modulation transfer function (MTF) and phase transfer function (PTF) parts of the OTF. The LPTF is related to difference of the average of the errors in separated regions of the pupil. Figure
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.
Long-range corrected density functional theory with linearly-scaled HF exchange
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.
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.
Code of Federal Regulations, 2010 CFR
2010-07-01
... used for other functions, such as automated verification and audits. If you request delegation of error correction functions for production reports or royalty reports, or both, you must perform at least...
NASA Technical Reports Server (NTRS)
Papike, J. J.; Le, L.; Burger, P. V.; Shearer, C. K.; Bell, A. S.; Jones, J.
2013-01-01
Our research on valence state partitioning began in 2005 with a review of Cr, Fe, Ti, and V partitioning among crystallographic sites in olivine, pyroxene, and spinel [1]. That paper was followed by several on QUE94201 melt composition and specifically on Cr, V, and Eu partitioning between pyroxene and melt [2-5]. This paper represents the continuation of our examination of the partitioning of multivalent V between olivine, spinel, and melt in martian olivine-phyric basalts of Y980459 composition [6, 7]. Here we introduce a new, potentially powerful oxybarometer, V partitioning between spinel and olivine, which can be used when no melt is preserved in the meteorite. The bulk composition of QUE94201 was ideal for our study of martian pyroxene-phyric basalts and specifically the partitioning between pyroxene-melt for Cr, V, and Eu. Likewise, bulk composition Y980459 is ideal for the study of martian olivine-phyric basalts and specifically for olivine-melt, spinel-melt, and spinel-olivine partitioning of V as a function of oxygen fugacity.
Functional correction of dystrophin actin binding domain mutations by genome editing.
Kyrychenko, Viktoriia; Kyrychenko, Sergii; Tiburcy, Malte; Shelton, John M; Long, Chengzu; Schneider, Jay W; Zimmermann, Wolfram-Hubertus; Bassel-Duby, Rhonda; Olson, Eric N
2017-09-21
Dystrophin maintains the integrity of striated muscles by linking the actin cytoskeleton with the cell membrane. Duchenne muscular dystrophy (DMD) is caused by mutations in the dystrophin gene (DMD) that result in progressive, debilitating muscle weakness, cardiomyopathy, and a shortened lifespan. Mutations of dystrophin that disrupt the amino-terminal actin-binding domain 1 (ABD-1), encoded by exons 2-8, represent the second-most common cause of DMD. In the present study, we compared three different strategies for CRISPR/Cas9 genome editing to correct mutations in the ABD-1 region of the DMD gene by deleting exons 3-9, 6-9, or 7-11 in human induced pluripotent stem cells (iPSCs) and by assessing the function of iPSC-derived cardiomyocytes. All three exon deletion strategies enabled the expression of truncated dystrophin protein and restoration of cardiomyocyte contractility and calcium transients to varying degrees. We show that deletion of exons 3-9 by genomic editing provides an especially effective means of correcting disease-causing ABD-1 mutations. These findings represent an important step toward eventual correction of common DMD mutations and provide a means of rapidly assessing the expression and function of internally truncated forms of dystrophin-lacking portions of ABD-1.
Hara, Mariko; Verkman, A. S.
2003-01-01
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
Correcting moments of in situ particle distribution functions for spacecraft electrostatic charging
NASA Astrophysics Data System (ADS)
Lavraud, Benoit; Larson, Davin E.
2016-09-01
We first introduce previous works on spacecraft electrostatic charging and its effects on particle measurements and the calculation of moments from three-dimensional distribution functions. We illustrate the fact that the lack of use, or misuse, of Liouville's theorem may lead to misinterpretations and inappropriate corrections to those effects. We emphasize in particular that its appropriate use naturally accounts for what is often called the "sheath focusing effect" in moment calculation. In the case of a "perfect" particle detector we show that there exists a trivial and essentially exact formulation for the calculation of moments of particle distribution functions that accounts for the spacecraft potential and that is particularly useful for onboard moment calculations. The main limitations, but that are not specific to this formulation, are inaccuracies in angle information (from blurring of acceptance angles at low energies or spacecraft-skimming trajectory effects) and those arising from the detector properties (resolution, cutoffs, photoelectrons, etc.). We discuss this correction in the context of previous works and remind that it primarily affects low-energy measurements and for populations whose temperature is comparable to the potential. Based on spacecraft observations, we show that this correction is most needed for regimes such as that of solar wind electrons but also for cold ions as often observed, for instance, in the magnetosphere near the Earth's magnetopause.
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.
Guseva, M V; Kamenskii, A A; Gusev, V B
2013-06-01
Choline diet promotes improvement of the brain cognitive functions in rats with moderate-to-severe traumatic brain injury. In previous studies, the rats received choline being standard (0.2%) or choline-supplemented (2%) diet for 2 weeks prior to and 2 weeks after experimental brain injury. To the end of the experiments (in 4 weeks), the post-traumatic disturbances in the cognitive functions were observed in both groups, although they were less pronounced than in the rats kept on the choline-supplemented diet. Based on original mathematical model, this paper proposes a method to calculate the most efficient use of choline to correct the brain cognitive functions. In addition to evaluating the cognitive functions, the study assessed expression of α7 nicotinic acetylcholine receptors, the amount of consumed food and water, and the dynamics of body weight.
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
NASA Astrophysics Data System (ADS)
Hart, Stanley R.; Gaetani, Glenn A.
2016-07-01
We have measured the partition coefficient of Pb (KdPb) between FeS melt and basalt melt at temperatures of 1250-1523 °C, pressures of 1.0-3.5 GPa and oxygen fugacities at iron-wustite and wustite-magnetite. The total observed range of KdPb is 4.0-66.6, with a strong negative dependence on pressure and a strong negative dependence on FeO of the silicate melt (Fe+2 only). The FeO control was constrained over a wide range of FeO (4.2-39.5%). We found that the effect of oxygen fugacity can be subsumed under the FeO control parameter. Prior work has established the lack of a significant effect of temperature (Kiseeva and Wood, 2015; Li and Audétat, 2015). Our data are parameterized as: KdPb = 4.8 + (512 - 119*P in GPa)*(1/FeO - 0.021). We also measured a single value of KdPb between clinopyroxene and basalt melt at 2.0 GPa of 0.020 ± 0.001. This experimental data supports the "natural" partitioning of Pb measured on sulfide globules in MORB (Patten et al., 2013), but not the low KdPb of ∼3 inferred from sulfides in abyssal peridotites by Warren and Shirey (2012). It also quantitatively affirms the modeling of Hart and Gaetani (2006) with respect to using sulfide to buffer the canonical Nd/Pb ratio for MORB and OIB (Hofmann, 2003). For the low FeO and pressure of segregation typical of MORB, KdPb ∼ 45, and the Nd/Pb ratio of erupted basalts will be the same as the Nd/Pb ratio of the mantle source. The remaining puzzle is why MORB and OIB have the same Nd/Pb when they clearly have different FeO and pressure of melt segregation.
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.
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
Burov, Stanislav; Figliozzi, Patrick; Lin, Binhua; Rice, Stuart A; Scherer, Norbert F; Dinner, Aaron R
2017-01-10
We present a general method for detecting and correcting biases in the outputs of particle-tracking experiments. Our approach is based on the histogram of estimated positions within pixels, which we term the single-pixel interior filling function (SPIFF). We use the deviation of the SPIFF from a uniform distribution to test the veracity of tracking analyses from different algorithms. Unbiased SPIFFs correspond to uniform pixel filling, whereas biased ones exhibit pixel locking, in which the estimated particle positions concentrate toward the centers of pixels. Although pixel locking is a well-known phenomenon, we go beyond existing methods to show how the SPIFF can be used to correct errors. The key is that the SPIFF aggregates statistical information from many single-particle images and localizations that are gathered over time or across an ensemble, and this information augments the single-particle data. We explicitly consider two cases that give rise to significant errors in estimated particle locations: undersampling the point spread function due to small emitter size and intensity overlap of proximal objects. In these situations, we show how errors in positions can be corrected essentially completely with little added computational cost. Additional situations and applications to experimental data are explored in SI Appendix In the presence of experimental-like shot noise, the precision of the SPIFF-based correction achieves (and can even exceed) the unbiased Cramér-Rao lower bound. We expect the SPIFF approach to be useful in a wide range of localization applications, including single-molecule imaging and particle tracking, in fields ranging from biology to materials science to astronomy.
Li, Z.; Pan, Y.K.; Tao, F.M.
1996-01-15
Bond function basis sets combined with the counterpoise procedure are used to calculate the molecular dissociation energies D{sub e} of 24 diatomic molecules and ions. The calculated values of D{sub e} are compared to those without bond functions and/or counterpoise corrections. The equilibrium bond lengths r{sub e}, and harmonic frequencies w{sub e} are also calculated for a few selected molecules. The calculations at the fourth-order-Moller-Plesset approximation (MP4) have consistently recovered about 95-99% of the experimental values for D{sub e}, compared to as low as 75% without use of bond functions. The calculated values of r{sub 3} are typically 0.01 {Angstrom} larger than the experimental values, and the calculated values of w{sub e} are over 95% of the experimental values. 37 refs., 2 tabs.
A Cavity Corrected 3D-RISM Functional for Accurate Solvation Free Energies
2014-01-01
We show that an Ng bridge function modified version of the three-dimensional reference interaction site model (3D-RISM-NgB) solvation free energy method can accurately predict the hydration free energy (HFE) of a set of 504 organic molecules. To achieve this, a single unique constant parameter was adjusted to the computed HFE of single atom Lennard-Jones solutes. It is shown that 3D-RISM is relatively accurate at predicting the electrostatic component of the HFE without correction but requires a modification of the nonpolar contribution that originates in the formation of the cavity created by the solute in water. We use a free energy functional with the Ng scaling of the direct correlation function [Ng, K. C. J. Chem. Phys.1974, 61, 2680]. This produces a rapid, reliable small molecule HFE calculation for applications in drug design. PMID:24634616
Comparing long-range corrected functionals in the cis-trans isomerisation of the retinal chromophore
NASA Astrophysics Data System (ADS)
Rostov, Ivan V.; Kobayashi, Rika; Amos, Roger D.
2012-10-01
Earlier results for the 11-cis to all-trans isomerisation of the retinal chromophore after photoexcitation, studied using time-dependent density functional theory with the hybrid CAM-B3LYP functional, are compared with new results using other long-range corrected DFT functionals. The TDDFT S0 and S1 minimum energy paths have been compared with the approximate coupled-cluster method RI-CC2. All calculations were consistent in producing an additional avoided crossing minimum on the S 1 minimum energy path lying approximately halfway between the 11-cis and all-trans S1 minima. In this minimum on the S1 potential energy surface, the retinal chromophore has inverted bond order in its carbon chain and lower energy than it has in both the 11-cis and all-trans S1 minima.
Jones, L; Nellist, P D
2014-05-01
In the scanning transmission electron microscope, hardware aberration correctors can now correct for the positive spherical aberration of round electron lenses. These correctors make use of nonround optics such as hexapoles or octupoles, leading to the limiting aberrations often being of a nonround type. Here we explore the effect of a number of potential limiting aberrations on the imaging performance of the scanning transmission electron microscope through their resulting optical transfer functions. In particular, the response of the optical transfer function to changes in defocus are examined, given that this is the final aberration to be tuned just before image acquisition. The resulting three-dimensional optical transfer functions also allow an assessment of the performance of a system for focal-series experiments or optical sectioning applications. © 2014 The Authors Journal of Microscopy © 2014 Royal Microscopical Society.
Combining MRI With PET for Partial Volume Correction Improves Image-Derived Input Functions in Mice
NASA Astrophysics Data System (ADS)
Evans, Eleanor; Buonincontri, Guido; Izquierdo, David; Methner, Carmen; Hawkes, Rob C.; Ansorge, Richard E.; Krieg, Thomas; Carpenter, T. Adrian; Sawiak, Stephen J.
2015-06-01
Accurate kinetic modelling using dynamic PET requires knowledge of the tracer concentration in plasma, known as the arterial input function (AIF). AIFs are usually determined by invasive blood sampling, but this is prohibitive in murine studies due to low total blood volumes. As a result of the low spatial resolution of PET, image-derived input functions (IDIFs) must be extracted from left ventricular blood pool (LVBP) ROIs of the mouse heart. This is challenging because of partial volume and spillover effects between the LVBP and myocardium, contaminating IDIFs with tissue signal. We have applied the geometric transfer matrix (GTM) method of partial volume correction (PVC) to 12 mice injected with 18F - FDG affected by a Myocardial Infarction (MI), of which 6 were treated with a drug which reduced infarction size [1]. We utilised high resolution MRI to assist in segmenting mouse hearts into 5 classes: LVBP, infarcted myocardium, healthy myocardium, lungs/body and background. The signal contribution from these 5 classes was convolved with the point spread function (PSF) of the Cambridge split magnet PET scanner and a non-linear fit was performed on the 5 measured signal components. The corrected IDIF was taken as the fitted LVBP component. It was found that the GTM PVC method could recover an IDIF with less contamination from spillover than an IDIF extracted from PET data alone. More realistic values of Ki were achieved using GTM IDIFs, which were shown to be significantly different (p <; 0.05) between the treated and untreated groups.
Importance of renal depth correction for quantitation of differential renal function
Choi, H.; Kirchner, P.T.
1985-05-01
To assess the frequency and magnitude of errors caused by asymmetries in renal depth, when estimates of differential function are based only posterior projections (as in DTPA studies). The authors compared ratios of right-to-left (R/L) DMSA localization derived from posterior camera images with R/L ratios based on geometric mean of posterior and anterior counts of each kidney. The factor (X) required to convert the ratio of R/L posterior counts to the more accurate R/L geometric counts (Rp/Lp.X = Rg/Lg) was determined in 55 randomly selected patients referred for DMSA studies. Frequency distributions for X and l/X reveal that the use of posterior counts alone is likely to produce differential flow/function estimates with errors greater than 30% in 5% of patients, greater than 20% in 16 of patients. Lack of depth correction also widens the normal range derived from normal controls, thus reducing sensitivity and specificity of quantitative renal studies by two different mechanisms. The authors recommend routine application of depth correction by conjugate counting or ultrasound techniques for all quantitations of renal function.
NASA Astrophysics Data System (ADS)
Hu, Xiao-Su; Arredondo, Maria M.; Gomba, Megan; Confer, Nicole; DaSilva, Alexandre F.; Johnson, Timothy D.; Shalinsky, Mark; Kovelman, Ioulia
2015-12-01
Motion artifacts are the most significant sources of noise in the context of pediatric brain imaging designs and data analyses, especially in applications of functional near-infrared spectroscopy (fNIRS), in which it can completely affect the quality of the data acquired. Different methods have been developed to correct motion artifacts in fNIRS data, but the relative effectiveness of these methods for data from child and infant subjects (which is often found to be significantly noisier than adult data) remains largely unexplored. The issue is further complicated by the heterogeneity of fNIRS data artifacts. We compared the efficacy of the six most prevalent motion artifact correction techniques with fNIRS data acquired from children participating in a language acquisition task, including wavelet, spline interpolation, principal component analysis, moving average (MA), correlation-based signal improvement, and combination of wavelet and MA. The evaluation of five predefined metrics suggests that the MA and wavelet methods yield the best outcomes. These findings elucidate the varied nature of fNIRS data artifacts and the efficacy of artifact correction methods with pediatric populations, as well as help inform both the theory and practice of optical brain imaging analysis.
Mora, Maria F; Nejadnik, M Reza; Baylon-Cardiel, Javier L; Giacomelli, Carla E; Garcia, Carlos D
2010-06-01
This paper is the first report on the characterization of the hydrodynamic conditions in a flow cell designed to study adsorption processes by spectroscopic ellipsometry. The resulting cell enables combining the advantages of in situ spectroscopic ellipsometry with stagnation point flow conditions. An additional advantage is that the proposed cell features a fixed position of the "inlet tube" with respect to the substrate, thus facilitating the alignment of multiple substrates. Theoretical calculations were performed by computational fluid dynamics and compared with experimental data (adsorption kinetics) obtained for the adsorption of polyethylene glycol to silica under a variety of experimental conditions. Additionally, a simple methodology to correct experimental data for errors associated with the size of the measured spot and for variations of mass transfer in the vicinity of the stagnation point is herein introduced. The proposed correction method would allow researchers to reasonably estimate the adsorption kinetics at the stagnation point and quantitatively compare their results, even when using different experimental setups. The applicability of the proposed correction function was verified by evaluating the kinetics of protein adsorption under different experimental conditions.
van de Streek, Jacco; Neumann, Marcus A.
2010-01-01
This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 Å either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect. PMID:20841921
Hollingworth, Andrew; Richard, Ashleigh M.; Luck, Steven J.
2009-01-01
Visual short-term memory (VSTM) has received intensive study over the past decade, with research focused on VSTM capacity and representational format. Yet, the function of VSTM in human cognition is not well understood. Here we demonstrate that VSTM plays an important role in the control of saccadic eye movements. Intelligent human behavior depends on directing the eyes to goal-relevant objects in the world, yet saccades are very often inaccurate and require correction. We hypothesized that VSTM is used to remember the features of the current saccade target so that it can be rapidly reacquired after an errant saccade, a fundamental task faced by the visual system thousands of times each day. In four experiments, memory-based gaze correction was found to be accurate, fast, automatic, and largely unconscious. In addition, a concurrent VSTM load was found to interfere with memory-based gaze correction, but a verbal short-term memory load did not. These findings demonstrate VSTM plays a direct role in a fundamentally important aspect of visually guided behavior, and they suggest the existence of previously unknown links between VSTM representations and the occulomotor system. PMID:18248135
Mora, Maria F.; Nejadnik, M. Reza; Baylon-Cardiel, Javier L.; Giacomelli, Carla E.; Garcia, Carlos D.
2010-01-01
This paper is the first report on the characterization of the hydrodynamic conditions in a flow cell designed to study adsorption processes by spectroscopic ellipsometry. The resulting cell enables combining the advantages of in-situ spectroscopic ellipsometry with stagnation point flow conditions. An additional advantage is that the proposed cell features a fixed position of the “inlet tube” with respect to the substrate, thus facilitating the alignment of multiple substrates. Theoretical calculations were performed by computational fluid dynamics and compared with experimental data (adsorption kinetics) obtained for the adsorption of polyethylene glycol to silica under a variety of experimental conditions. Additionally, a simple methodology to correct experimental data for errors associated with the size of the measured spot and for variations of mass transfer in the vicinity of the stagnation point is herein introduced. The proposed correction method would allow researchers to reasonably estimate the adsorption kinetics at the stagnation point and quantitatively compare their results, even when using different experimental setups. The applicability of the proposed correction function was verified by evaluating the kinetics of protein adsorption under different experimental conditions. PMID:20219204
van de Streek, Jacco; Neumann, Marcus A
2010-10-01
This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 A either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect.
Wave function continuity and the diagonal Born-Oppenheimer correction at conical intersections.
Meek, Garrett A; Levine, Benjamin G
2016-05-14
We demonstrate that though exact in principle, the expansion of the total molecular wave function as a sum over adiabatic Born-Oppenheimer (BO) vibronic states makes inclusion of the second-derivative nonadiabatic energy term near conical intersections practically problematic. In order to construct a well-behaved molecular wave function that has density at a conical intersection, the individual BO vibronic states in the summation must be discontinuous. When the second-derivative nonadiabatic terms are added to the Hamiltonian, singularities in the diagonal BO corrections (DBOCs) of the individual BO states arise from these discontinuities. In contrast to the well-known singularities in the first-derivative couplings at conical intersections, these singularities are non-integrable, resulting in undefined DBOC matrix elements. Though these singularities suggest that the exact molecular wave function may not have density at the conical intersection point, there is no physical basis for this constraint. Instead, the singularities are artifacts of the chosen basis of discontinuous functions. We also demonstrate that continuity of the total molecular wave function does not require continuity of the individual adiabatic nuclear wave functions. We classify nonadiabatic molecular dynamics methods according to the constraints placed on wave function continuity and analyze their formal properties. Based on our analysis, it is recommended that the DBOC be neglected when employing mixed quantum-classical methods and certain approximate quantum dynamical methods in the adiabatic representation.
Adsorption of imidazole on Au(111) surface: Dispersion corrected density functional study
NASA Astrophysics Data System (ADS)
Izzaouihda, Safia; Mahjoubi, Khaled; Abou El Makarim, Hassna; Komiha, Najia; Benoit, David M.
2016-10-01
We use density functional theory in the generalized gradient approximation to study the adsorption of imidazole on the Au(111) surface and account for dispersion effect using Grimme's empirical dispersion correction technique. Our results show that the adsorption energy of imidazole depends on the slab size and on the adsorption site. In agreement with other studies, we find the largest adsorption energy for imidazole on a top site of Au(111). However, we also note that the adsorption energy at other sites is substantial.
Convergent conductivity corrections to the Casimir force via exponential basis functions
Cui, Song; Soh, Yeng Chai
2010-12-15
A closed-form finite conductivity correction factor for the ideal Casimir force is proposed, based on exponential basis functions. Our method can facilitate experimental verifications of theories in the study of the Casimir force. A theoretical analysis is given to explain why our method is accurate at both large and small separation gaps. Numerical computations have been performed to confirm that our method is accurate in various experimental configurations. Our approach is widely applicable to various Casimir force interactions between metals and dielectrics. Our study can be extended to the study of the repulsive Casimir force as well.
Fedotchev, A I; Bondar, A T; Bakhchina, A V; Parin, S B; Polevaya, S A; Radchenko, G S
2016-01-01
Literature review and the results of own studies on the development and experimental testing of musical EEG neurofeedback technology are presented. The technology is based on exposure of subjects to music or music-like signals that are organized in strict accordance with the current values of brain potentials of the patient. The main attention is paid to the analysis of the effectiveness of several versions of the technology, using specific and meaningful for the individual narrow-frequency EEG oscillators during the correction of unfavorable changes of the functional state.
Nakano, K; Swindle, M M; Spinale, F; Ishihara, K; Kanazawa, S; Smith, A; Biederman, R W; Clamp, L; Hamada, Y; Zile, M R
1991-01-01
It is known that long-standing volume overload on the left ventricle due to mitral regurgitation eventually leads to contractile dysfunction. However, it is unknown whether or not correction of the volume overload can lead to recovery of contractility. In this study we tested the hypothesis that depressed contractile function due to volume overload in mitral regurgitation could return toward normal after mitral valve replacement. Using a canine model of mitral regurgitation which is known to produce contractile dysfunction, we examined contractile function longitudinally in seven dogs at baseline, after 3 mo of mitral regurgitation, 1 mo after mitral valve replacement, and 3 mo after mitral valve replacement. After 3 mo of mitral regurgitation (regurgitant fraction 0.62 +/- 0.04), end-diastolic volume had nearly doubled from 68 +/- 6.8 to 123 +/- 12.1 ml (P less than 0.05). All five indices of contractile function which we examined were depressed. For instance, maximum fiber elastance (EmaxF) obtained by assessment of time-varying elastance decreased from 5.95 +/- 0.71 to 2.25 +/- 0.18 (P less than 0.05). The end-systolic stiffness constant (k) was also depressed from 4.2 +/- 0.4 to 2.1 +/- 0.3. 3 mo after mitral valve replacement all indexes of contractile function had returned to or toward normal (e.g., EmaxF 3.65 +/- 0.21 and k 4.2 +/- 0.3). We conclude that previously depressed contractile function due to volume overload can improve after correction of the overload. PMID:1828252
Is the physical decay correction of the (18)F-FDG input function in dynamic PET imaging justified?
Laffon, Eric; Barret, Olivier; Marthan, Roger; Ducassou, Dominique
2009-06-01
In this theoretic note, the rationale for the physical decay correction of the (18)F-FDG input function in dynamic PET is investigated, using the Patlak equation as an example. The Patlak equation conventionally obtained when correcting the (18)F-FDG input function and correcting the tissue activity measurement for (18)F physical decay can also be derived from a 2-compartment analysis that does not conceptually involve any physical decay correction of the (18)F-FDG input function but accounts only for the physical decay of the trapped tracer. We demonstrate that exactly the same equation can be derived from the 2 conceptual approaches, and hence each approach yields the correct uptake rate of the tracer. No advantage in (18)F-FDG dynamic PET can be expected from using the concept of uncorrected data rather than that of decay-corrected data. Nevertheless, conceptually, we show that correcting the (18)F-FDG input function for radioactive decay cannot be justified and that this correction is not compatible with the calculation of patient radiation dose.
In, Myung-Ho; Cho, Shinho; Shu, Yunhong; Min, Hoon-Ki; Bernstein, Matt A; Speck, Oliver; Lee, Kendall H; Jo, Hang Joon
2017-09-01
Functional magnetic resonance imaging (fMRI) is an emerging tool for investigating brain activation associated with, or modulated by, deep brain stimulation (DBS). However, DBS-fMRI generally suffers from severe susceptibility to artifacts in regions near the metallic stimulation electrodes, as well as near tissue/air boundaries of the brain. These result in strong intensity and geometric distortions along the phase-encoding (PE) (i.e., blipped) direction in gradient-echo echo-planar imaging (GE-EPI). Distortion presents a major challenge to conducting reliable data analysis and in interpreting the findings. A recent study showed that the point spread function (PSF) mapping-based reverse gradient approach has a potential to correct for distortions not only in spin-echo EPI, but also in GE-EPI acquired in both the forward and reverse PE directions. In this study, we adapted that approach in order to minimize severe metal-induced susceptibility artifacts for DBS-fMRI, and to evaluate the performance of the approach in a phantom study and a large animal DBS-fMRI study. The method combines the distortion-corrected GE-EPI pair with geometrically different intensity distortions due to the opposing encoding directions. The results demonstrate that the approach can minimize susceptibility artifacts that appear around the metallic electrodes, as well as in the regions near the tissue/air boundaries in the brain. We also demonstrated that an accurate geometric correction is important in improving BOLD contrast in the group dataset, especially in regions where strong susceptibility artifacts appear. Copyright © 2017 Elsevier Inc. All rights reserved.
Kinetic corrections from analytic non-Maxwellian distribution functions in magnetized plasmas
Izacard, Olivier
2016-08-02
In magnetized plasma physics, almost all developed analytic theories assume a Maxwellian distribution function (MDF) and in some cases small deviations are described using the perturbation theory. The deviations with respect to the Maxwellian equilibrium, called kinetic effects, are required to be taken into account especially for fusion reactor plasmas. Generally, because the perturbation theory is not consistent with observed steady-state non-Maxwellians, these kinetic effects are numerically evaluated by very central processing unit (CPU)-expensive codes, avoiding the analytic complexity of velocity phase space integrals. We develop here a new method based on analytic non-Maxwellian distribution functions constructed from non-orthogonal basis sets in order to (i) use as few parameters as possible, (ii) increase the efficiency to model numerical and experimental non-Maxwellians, (iii) help to understand unsolved problems such as diagnostics discrepancies from the physical interpretation of the parameters, and (iv) obtain analytic corrections due to kinetic effects given by a small number of terms and removing the numerical error of the evaluation of velocity phase space integrals. This work does not attempt to derive new physical effects even if it could be possible to discover one from the better understandings of some unsolved problems, but here we focus on the analytic prediction of kinetic corrections from analytic non-Maxwellians. As applications, examples of analytic kinetic corrections are shown for the secondary electron emission, the Langmuir probe characteristic curve, and the entropy. This is done by using three analytic representations of the distribution function: the Kappa distribution function, the bi-modal or a new interpreted non-Maxwellian distribution function (INMDF). The existence of INMDFs is proved by new understandings of the experimental discrepancy of the measured electron temperature between two diagnostics in JET. As main results, it
Kinetic corrections from analytic non-Maxwellian distribution functions in magnetized plasmas
Izacard, Olivier
2016-08-02
In magnetized plasma physics, almost all developed analytic theories assume a Maxwellian distribution function (MDF) and in some cases small deviations are described using the perturbation theory. The deviations with respect to the Maxwellian equilibrium, called kinetic effects, are required to be taken into account especially for fusion reactor plasmas. Generally, because the perturbation theory is not consistent with observed steady-state non-Maxwellians, these kinetic effects are numerically evaluated by very central processing unit (CPU)-expensive codes, avoiding the analytic complexity of velocity phase space integrals. We develop here a new method based on analytic non-Maxwellian distribution functions constructed from non-orthogonal basismore » sets in order to (i) use as few parameters as possible, (ii) increase the efficiency to model numerical and experimental non-Maxwellians, (iii) help to understand unsolved problems such as diagnostics discrepancies from the physical interpretation of the parameters, and (iv) obtain analytic corrections due to kinetic effects given by a small number of terms and removing the numerical error of the evaluation of velocity phase space integrals. This work does not attempt to derive new physical effects even if it could be possible to discover one from the better understandings of some unsolved problems, but here we focus on the analytic prediction of kinetic corrections from analytic non-Maxwellians. As applications, examples of analytic kinetic corrections are shown for the secondary electron emission, the Langmuir probe characteristic curve, and the entropy. This is done by using three analytic representations of the distribution function: the Kappa distribution function, the bi-modal or a new interpreted non-Maxwellian distribution function (INMDF). The existence of INMDFs is proved by new understandings of the experimental discrepancy of the measured electron temperature between two diagnostics in JET. As main
Kinetic corrections from analytic non-Maxwellian distribution functions in magnetized plasmas
Izacard, Olivier
2016-08-02
In magnetized plasma physics, almost all developed analytic theories assume a Maxwellian distribution function (MDF) and in some cases small deviations are described using the perturbation theory. The deviations with respect to the Maxwellian equilibrium, called kinetic effects, are required to be taken into account especially for fusion reactor plasmas. Generally, because the perturbation theory is not consistent with observed steady-state non-Maxwellians, these kinetic effects are numerically evaluated by very central processing unit (CPU)-expensive codes, avoiding the analytic complexity of velocity phase space integrals. We develop here a new method based on analytic non-Maxwellian distribution functions constructed from non-orthogonal basis sets in order to (i) use as few parameters as possible, (ii) increase the efficiency to model numerical and experimental non-Maxwellians, (iii) help to understand unsolved problems such as diagnostics discrepancies from the physical interpretation of the parameters, and (iv) obtain analytic corrections due to kinetic effects given by a small number of terms and removing the numerical error of the evaluation of velocity phase space integrals. This work does not attempt to derive new physical effects even if it could be possible to discover one from the better understandings of some unsolved problems, but here we focus on the analytic prediction of kinetic corrections from analytic non-Maxwellians. As applications, examples of analytic kinetic corrections are shown for the secondary electron emission, the Langmuir probe characteristic curve, and the entropy. This is done by using three analytic representations of the distribution function: the Kappa distribution function, the bi-modal or a new interpreted non-Maxwellian distribution function (INMDF). The existence of INMDFs is proved by new understandings of the experimental discrepancy of the measured electron temperature between two diagnostics in JET. As main results, it
Kinetic corrections from analytic non-Maxwellian distribution functions in magnetized plasmas
Izacard, Olivier
2016-08-15
In magnetized plasma physics, almost all developed analytic theories assume a Maxwellian distribution function (MDF) and in some cases small deviations are described using the perturbation theory. The deviations with respect to the Maxwellian equilibrium, called kinetic effects, are required to be taken into account especially for fusion reactor plasmas. Generally, because the perturbation theory is not consistent with observed steady-state non-Maxwellians, these kinetic effects are numerically evaluated by very central processing unit (CPU)-expensive codes, avoiding the analytic complexity of velocity phase space integrals. We develop here a new method based on analytic non-Maxwellian distribution functions constructed from non-orthogonal basis sets in order to (i) use as few parameters as possible, (ii) increase the efficiency to model numerical and experimental non-Maxwellians, (iii) help to understand unsolved problems such as diagnostics discrepancies from the physical interpretation of the parameters, and (iv) obtain analytic corrections due to kinetic effects given by a small number of terms and removing the numerical error of the evaluation of velocity phase space integrals. This work does not attempt to derive new physical effects even if it could be possible to discover one from the better understandings of some unsolved problems, but here we focus on the analytic prediction of kinetic corrections from analytic non-Maxwellians. As applications, examples of analytic kinetic corrections are shown for the secondary electron emission, the Langmuir probe characteristic curve, and the entropy. This is done by using three analytic representations of the distribution function: the Kappa distribution function, the bi-modal or a new interpreted non-Maxwellian distribution function (INMDF). The existence of INMDFs is proved by new understandings of the experimental discrepancy of the measured electron temperature between two diagnostics in JET. As main results, it
Kinetic corrections from analytic non-Maxwellian distribution functions in magnetized plasmas
NASA Astrophysics Data System (ADS)
Izacard, Olivier
2016-08-01
In magnetized plasma physics, almost all developed analytic theories assume a Maxwellian distribution function (MDF) and in some cases small deviations are described using the perturbation theory. The deviations with respect to the Maxwellian equilibrium, called kinetic effects, are required to be taken into account especially for fusion reactor plasmas. Generally, because the perturbation theory is not consistent with observed steady-state non-Maxwellians, these kinetic effects are numerically evaluated by very central processing unit (CPU)-expensive codes, avoiding the analytic complexity of velocity phase space integrals. We develop here a new method based on analytic non-Maxwellian distribution functions constructed from non-orthogonal basis sets in order to (i) use as few parameters as possible, (ii) increase the efficiency to model numerical and experimental non-Maxwellians, (iii) help to understand unsolved problems such as diagnostics discrepancies from the physical interpretation of the parameters, and (iv) obtain analytic corrections due to kinetic effects given by a small number of terms and removing the numerical error of the evaluation of velocity phase space integrals. This work does not attempt to derive new physical effects even if it could be possible to discover one from the better understandings of some unsolved problems, but here we focus on the analytic prediction of kinetic corrections from analytic non-Maxwellians. As applications, examples of analytic kinetic corrections are shown for the secondary electron emission, the Langmuir probe characteristic curve, and the entropy. This is done by using three analytic representations of the distribution function: the Kappa distribution function, the bi-modal or a new interpreted non-Maxwellian distribution function (INMDF). The existence of INMDFs is proved by new understandings of the experimental discrepancy of the measured electron temperature between two diagnostics in JET. As main results, it
Filatov, Michael; Huix-Rotllant, Miquel; Burghardt, Irene
2015-05-14
State-averaged (SA) variants of the spin-restricted ensemble-referenced Kohn-Sham (REKS) method, SA-REKS and state-interaction (SI)-SA-REKS, implement ensemble density functional theory for variationally obtaining excitation energies of molecular systems. In this work, the currently existing version of the SA-REKS method, which included only one excited state into the ensemble averaging, is extended by adding more excited states to the averaged energy functional. A general strategy for extension of the REKS-type methods to larger ensembles of ground and excited states is outlined and implemented in extended versions of the SA-REKS and SI-SA-REKS methods. The newly developed methods are tested in the calculation of several excited states of ground-state multi-reference systems, such as dissociating hydrogen molecule, and excited states of donor–acceptor molecular systems. For hydrogen molecule, the new method correctly reproduces the distance dependence of the lowest excited state energies and describes an avoided crossing between the doubly excited and singly excited states. For bithiophene–perylenediimide stacked complex, the SI-SA-REKS method correctly describes crossing between the locally excited state and the charge transfer excited state and yields vertical excitation energies in good agreement with the ab initio wavefunction methods.
NASA Astrophysics Data System (ADS)
Landerville, Aaron C.; Oleynik, Ivan I.
2017-01-01
Dispersion Corrected Density Functional Theory (DFT+vdW) calculations are performed to predict vibrational and thermal properties of the bulk energetic materials (EMs) β-octahydrocyclotetramethylene-tetranitramine (β-HMX) and triaminotrinitrobenzene (TATB). DFT+vdW calculations of pressure-dependent crystal structure and the hydrostatic equation of state are followed by frozen-phonon calculations of their respective vibration spectra at each pressure. These are then used under the quasi-harmonic approximation to obtain zero-point and thermal free energy contributions to the pressure, resulting in pressure-volume-temperature (PVT) EOS for each material that are in excellent agreement with experiment. Heat capacities, and coefficients of thermal expansion as functions of temperature are also calculated and compared with experiment.
NASA Astrophysics Data System (ADS)
Kaya, Ali; Kutluk, Emine Seyma
2015-12-01
We express the in-in functional determinant giving the one-loop effective potential for a scalar field propagating in a cosmological spacetime in terms of the mode functions specifying the vacuum of the theory and then apply adiabatic regularization to make this bare potential finite. In this setup, the adiabatic regularization offers a particular renormalization prescription that isolates the effects of the cosmic expansion. We apply our findings to determine the radiative corrections to the classical inflaton potentials in scalar field inflationary models and also we derive an effective potential for the superhorizon curvature perturbation ζ encoding its scatterings with the subhorizon modes. Although the resulting modifications to the cosmological observables like non-Gaussianity turn out to be small, they distinctively appear after horizon crossing.
NASA Astrophysics Data System (ADS)
Landerville, Aaron; Oleynik, Ivan
2015-06-01
Dispersion Corrected Density Functional Theory (DFT+vdW) calculations are performed to predict vibrational and thermal properties of the bulk energetic materials (EMs) β-octahydrocyclotetramethylene-tetranitramine (β-HMX) and triaminotrinitrobenzene (TATB). DFT+vdW calculations of optimized unit cells along the hydrostatic equation of state are followed by frozen-phonon calculations of their respective vibration spectra. These are then used under the quasi-harmonic approximation to obtain zero-point and thermal free energy contributions to the pressure, resulting in PVT equations of state for each material that is in excellent agreement with experiment. Further, heat capacities, thermal expansion coefficients, and Gruneissen parameters as functions of temperature are calculated and compared with experiment. The vibrational properties, including phonon densities of states and pressure dependencies of individual modes, are also analyzed and compared with experiment.
Selected configuration interaction method using sampled first-order corrections to wave functions
NASA Astrophysics Data System (ADS)
Ohtsuka, Yuhki; Hasegawa, Jun-ya
2017-07-01
A new selected configuration interaction (CI) method was proposed for the potential energy surfaces of quasi-degenerate and excited states. Slater determinants are generated by sampling the first-order corrections to the target-state wave functions using the quantum Monte Carlo method in determinant space. As in the Monte Carlo (MC) CI method, the wave function is improved at each iteration by generating new determinants and applying a pruning step. Compared to the random generation in the MCCI calculations, the number of iterations before convergence is significantly reduced. Regarding the potential energy curves of the ground and excited states of C2, the non-parallelity errors were sufficiently small, thus indicating the method's applicability to the calculations of potential energy surfaces.
Water cluster anions studied by the long-range corrected density functional theory.
Yagi, Kiyoshi; Okano, Yuko; Sato, Takeshi; Kawashima, Yukio; Tsuneda, Takao; Hirao, Kimihiko
2008-10-09
Long-range corrected density functional theory (LC-DFT) is applied to a series of small water cluster anions(n= 2-6) to compute their vertical detachment energies (VDEs). The LC scheme is shown to eliminate an unphysical overestimation of the electron-water attraction in the hybrid functional by properly accounting for the long-range exchange repulsions. It is shown that a correct correlation energy behavior for a rapidly varying density is also important for describing a spatially extent, excess electron. The one-parameter progressive (OP) correlation functional, which satisfies this condition, leads to a remarkable improvement in the calculated VDE over the conventional one. The LC-BOP method produces highly accurate VDEs with a mean absolute deviation of 13.8 meV from the reference CCSD(T) results, reducing the error of B3LYP by more than 15 times. LC-BOP is found to be more accurate than MP2 which yields an excess electron underbound by 43.6 meV. The effect of basis sets on the calculated VDE is also examined. The aug-cc-pVDZ basis set with an extra diffuse function is found to be more accurate and reliable than the extended Pople-type basis sets used in the previous works. The extrapolation of the calculated VDE of different electron binding motifs is compared with the VDEs of experimentally observed three isomers (Verlet, J. R. R.; Bragg,A. E.; Kammrath, A.; Cheshnovsky, O.; Neumark, D. M. Science 2005, 307, 93).
Odabasi, Mustafa; Cetin, Banu; Sofuoglu, Aysun
2006-02-01
The Henry's law constant for carbazole was experimentally determined between 5 and 35 degrees C using a gas-stripping technique. The following equation was obtained for dimensionless Henry's law constant (H') versus temperature (T, K): ln H' = -3982(T,K)(-1) + 1.01. Temperature-dependent octanol-air partition coefficients (KOA) and supercooled liquid vapor pressures (PL,Pa) of carbazole were also determined using the GC retention time method. The temperature dependence of KOA and PL were explained by the following: log KOA = 4076/(T,K) - 5.65, log PL(Pa) = -3948(T,K)(- 1) + 11.48. The gas and particle-phase carbazole concentrations measured previously in Chicago, IL in 1995 was used for gas/particle partitioning modeling. Octanol based absorptive partitioning model consistently underpredicted the gas/particle partition coefficients (Kp) for all sampling periods. However, overall there was a good agreement between the measured Kp and soot-based model predictions.
Predictors of emotional functioning in youth after surgical correction of idiopathic scoliosis.
Zebracki, Kathy; Thawrani, Dinesh; Oswald, Timothy S; Anadio, Jennifer M; Sturm, Peter F
2013-09-01
Patients with idiopathic scoliosis, although otherwise healthy, often have significant concerns about their self-image and appearance. In a group of juveniles and adolescents, this can impact adjustment in school, functioning in peer groups, and general sense of well-being. There are limited data to help physicians reliably and precisely identify those who are at higher risk of poor emotional adjustment even after spine deformity correction. The purpose of this study was to determine the predictors of emotional maladjustment in juvenile and adolescent patients after surgical correction of idiopathic scoliosis. A total of 233 juveniles, mean age 11.26 ± 1.02 (range, 8 to 12) years and 909 adolescents, mean age 14.91 ± 1.61 (range, 13 to 21) years, who underwent surgical correction for idiopathic scoliosis and who were participating in a prospective longitudinal multicenter database, were enrolled in the study. Participants completed the Scoliosis Research Society-22 (SRS-22) questionnaire before surgery and 2 years postoperatively. Radiographs were used to measure Cobb angle and surface measurements were used to determine decompensation and trunk shift. Adolescents reported poorer mental health preoperatively (P<0.05) and 2 years postoperatively (P<0.001) than juveniles; however, both groups reported improved mental health (P<0.001) and self-image (P<0.01) postoperatively. Mental health 2 years postoperatively was predicted by preoperative self-image (P<0.05), mental health (P<0.001), and main thoracic Cobb angle (P<0.05) in the juvenile group. Within the adolescent group, mental health 2 years postoperatively was predicted by preoperative mental health (P<0.001); self-image 2 years postoperatively was predicted by preoperative mental health (P<0.01) and self-image (P<0.001). Self-image and mental health are significantly improved after spine deformity correction in juveniles and adolescents with idiopathic scoliosis. However, consistent with normative development
Hao, Feng Mattsson, Ann E.; Armiento, Rickard
2014-05-14
We have previously proposed that further improved functionals for density functional theory can be constructed based on the Armiento-Mattsson subsystem functional scheme if, in addition to the uniform electron gas and surface models used in the Armiento-Mattsson 2005 functional, a model for the strongly confined electron gas is also added. However, of central importance for this scheme is an index that identifies regions in space where the correction provided by the confined electron gas should be applied. The electron localization function (ELF) is a well-known indicator of strongly localized electrons. We use a model of a confined electron gas based on the harmonic oscillator to show that regions with high ELF directly coincide with regions where common exchange energy functionals have large errors. This suggests that the harmonic oscillator model together with an index based on the ELF provides the crucial ingredients for future improved semi-local functionals. For a practical illustration of how the proposed scheme is intended to work for a physical system we discuss monoclinic cupric oxide, CuO. A thorough discussion of this system leads us to promote the cell geometry of CuO as a useful benchmark for future semi-local functionals. Very high ELF values are found in a shell around the O ions, and take its maximum value along the Cu–O directions. An estimate of the exchange functional error from the effect of electron confinement in these regions suggests a magnitude and sign that could account for the error in cell geometry.
Hao, Feng; Armiento, Rickard; Mattsson, Ann E
2014-05-14
We have previously proposed that further improved functionals for density functional theory can be constructed based on the Armiento-Mattsson subsystem functional scheme if, in addition to the uniform electron gas and surface models used in the Armiento-Mattsson 2005 functional, a model for the strongly confined electron gas is also added. However, of central importance for this scheme is an index that identifies regions in space where the correction provided by the confined electron gas should be applied. The electron localization function (ELF) is a well-known indicator of strongly localized electrons. We use a model of a confined electron gas based on the harmonic oscillator to show that regions with high ELF directly coincide with regions where common exchange energy functionals have large errors. This suggests that the harmonic oscillator model together with an index based on the ELF provides the crucial ingredients for future improved semi-local functionals. For a practical illustration of how the proposed scheme is intended to work for a physical system we discuss monoclinic cupric oxide, CuO. A thorough discussion of this system leads us to promote the cell geometry of CuO as a useful benchmark for future semi-local functionals. Very high ELF values are found in a shell around the O ions, and take its maximum value along the Cu-O directions. An estimate of the exchange functional error from the effect of electron confinement in these regions suggests a magnitude and sign that could account for the error in cell geometry.
NASA Astrophysics Data System (ADS)
Siudem, Grzegorz; Fronczak, Agata; Fronczak, Piotr
2016-10-01
In this paper, we provide the exact expression for the coefficients in the low-temperature series expansion of the partition function of the two-dimensional Ising model on the infinite square lattice. This is equivalent to exact determination of the number of spin configurations at a given energy. With these coefficients, we show that the ferromagnetic–to–paramagnetic phase transition in the square lattice Ising model can be explained through equivalence between the model and the perfect gas of energy clusters model, in which the passage through the critical point is related to the complete change in the thermodynamic preferences on the size of clusters. The combinatorial approach reported in this article is very general and can be easily applied to other lattice models.
Siudem, Grzegorz; Fronczak, Agata; Fronczak, Piotr
2016-01-01
In this paper, we provide the exact expression for the coefficients in the low-temperature series expansion of the partition function of the two-dimensional Ising model on the infinite square lattice. This is equivalent to exact determination of the number of spin configurations at a given energy. With these coefficients, we show that the ferromagnetic–to–paramagnetic phase transition in the square lattice Ising model can be explained through equivalence between the model and the perfect gas of energy clusters model, in which the passage through the critical point is related to the complete change in the thermodynamic preferences on the size of clusters. The combinatorial approach reported in this article is very general and can be easily applied to other lattice models. PMID:27721435
Siudem, Grzegorz; Fronczak, Agata; Fronczak, Piotr
2016-10-10
In this paper, we provide the exact expression for the coefficients in the low-temperature series expansion of the partition function of the two-dimensional Ising model on the infinite square lattice. This is equivalent to exact determination of the number of spin configurations at a given energy. With these coefficients, we show that the ferromagnetic-to-paramagnetic phase transition in the square lattice Ising model can be explained through equivalence between the model and the perfect gas of energy clusters model, in which the passage through the critical point is related to the complete change in the thermodynamic preferences on the size of clusters. The combinatorial approach reported in this article is very general and can be easily applied to other lattice models.
NASA Astrophysics Data System (ADS)
Reeve, Samuel Temple; Strachan, Alejandro
2017-04-01
We use functional, Fréchet, derivatives to quantify how thermodynamic outputs of a molecular dynamics (MD) simulation depend on the potential used to compute atomic interactions. Our approach quantifies the sensitivity of the quantities of interest with respect to the input functions as opposed to its parameters as is done in typical uncertainty quantification methods. We show that the functional sensitivity of the average potential energy and pressure in isothermal, isochoric MD simulations using Lennard-Jones two-body interactions can be used to accurately predict those properties for other interatomic potentials (with different functional forms) without re-running the simulations. This is demonstrated under three different thermodynamic conditions, namely a crystal at room temperature, a liquid at ambient pressure, and a high pressure liquid. The method provides accurate predictions as long as the change in potential can be reasonably described to first order and does not significantly affect the region in phase space explored by the simulation. The functional uncertainty quantification approach can be used to estimate the uncertainties associated with constitutive models used in the simulation and to correct predictions if a more accurate representation becomes available.
Software with partial functions: Automating correctness proofs via nonstrict explicit domains
Yakhnis, A.; Yakhnis, V.; Winter, V.
1996-07-30
As our society becomes technologically more complex, computers are being used in greater and greater numbers of high consequence systems. Giving a machine control over the lives of humans can be disturbing, especially if the software that is run on such a machine has bugs. Formal reasoning is one of the most powerful techniques available to demonstrate the correctness of a piece of software. When reasoning about software and its development, one frequently encounters expressions that contain partial functions. As might be expected, the presence of partial functions introduces an additional dimension of difficulty to the reasoning framework. This difficulty produces an especially strong impact in the case of high consequence systems. An ability to use formal methods for constructing software is essential if we want to obtain greater confidence in such systems through formal reasoning. This is only reasonable under automation of software development and verification. However, the ubiquitous presence of partial functions prevents a uniform application to software of any tools not specifically accounting for partial functions. In this paper we will describe a framework for reasoning about software, based on the nonstrict explicit domain approach, that is applicable to a large class of software/hardware systems. In this framework the Hoare triples containing partial functions can be reasoned about automatically in a well-defined and uniform manner.
Prefrontal neuromodulation using rTMS improves error monitoring and correction function in autism.
Sokhadze, Estate M; Baruth, Joshua M; Sears, Lonnie; Sokhadze, Guela E; El-Baz, Ayman S; Casanova, Manuel F
2012-06-01
One important executive function known to be compromised in autism spectrum disorder (ASD) is related to response error monitoring and post-error response correction. Several reports indicate that children with ASD show reduced error processing and deficient behavioral correction after an error is committed. Error sensitivity can be readily examined by measuring event-related potentials (ERP) associated with responses to errors, the fronto-central error-related negativity (ERN), and the error-related positivity (Pe). The goal of our study was to investigate whether reaction time (RT), error rate, post-error RT change, ERN, and Pe will show positive changes following 12-week long slow frequency repetitive TMS (rTMS) over dorsolateral prefrontal cortex (DLPFC) in high functioning children with ASD. We hypothesized that 12 sessions of 1 Hz rTMS bilaterally applied over the DLPFC will result in improvements reflected in both behavioral and ERP measures. Participants were randomly assigned to either active rTMS treatment or wait-list (WTL) groups. Baseline and post-TMS/or WTL EEG was collected using 128 channel EEG system. The task involved the recognition of a specific illusory shape, in this case a square or triangle, created by three or four inducer disks. ERN in TMS treatment group became significantly more negative. The number of omission errors decreased post-TMS. The RT did not change, but post-error RT became slower. There were no changes in RT, error rate, post-error RT slowing, nor in ERN/Pe measures in the wait-list group. Our results show significant post-TMS differences in the response-locked ERP such as ERN, as well as behavioral response monitoring measures indicative of improved error monitoring and correction function. The ERN and Pe, along with behavioral performance measures, can be used as functional outcome measures to assess the effectiveness of neuromodulation (e.g., rTMS) in children with autism and thus may have important practical implications.
NASA Astrophysics Data System (ADS)
Derrida, Bernard; Retaux, Martin
2013-09-01
The symmetric simple exclusion process is one of the simplest out-of-equilibrium systems for which the steady state is known. Its large deviation functional of the density has been computed in the past both by microscopic and macroscopic approaches. Here we obtain the leading finite size correction to this large deviation functional. The result is compared to the similar corrections for equilibrium systems.
Heiberg, Johan
2016-01-01
Patients with pectus excavatum (PE) often describe improvements in exercise stamina following corrective surgery. Studies have investigated the surgical effect on physiological parameters; still, no consensus has yet been reached. Therefore, the aim of this literature review was to describe the cardiac outcome after surgical correction, both at rest and during exercise. In February 2016, a detailed search of the databases PubMed, Medline, and EMBASE was performed. We assessed clinical studies that described cardiac outcomes both before and after surgical correction of PE. We only included studies reporting either pre-defined echocardiographic or exercise test parameters. No exclusion criteria or statistical analyses were applied. Twenty-one full-text articles, published between 1972 and 2016, were selected, with cohort-ranges of 3–168 patients, mean age-ranges of 5–33 years, and mean follow-up-ranges from immediately to 4 years after surgery. Twelve studies described resting cardiac parameters. Four studies measured cardiac output, where one described 36% immediate increase after surgery, one reported 15% increase after Nuss-bar removal and two found no difference. Three studies demonstrated improvement in mean stroke volume ranges of 22–34% and two studies found no difference. Fifteen studies investigated exercise capacity, with 11 considering peak O2 pr. kg, where five studies demonstrated improvements with the mean ranging from 8% to 15% after surgery, five studies demonstrated no difference, and one saw a decrease of 19% 3 months after Nuss-bar implantation. A measurable increase in exercise capacity exists following surgery, which may be caused by multiple factors. This may be owed to the relief of compressed cardiac chambers with the increased anterior-posterior thoracic dimensions, which could facilitate an improved filling of the heart. With these results, the positive physiological impact of the surgery is emphasized and the potential gain in cardiac
Maagaard, Marie; Heiberg, Johan
2016-09-01
Patients with pectus excavatum (PE) often describe improvements in exercise stamina following corrective surgery. Studies have investigated the surgical effect on physiological parameters; still, no consensus has yet been reached. Therefore, the aim of this literature review was to describe the cardiac outcome after surgical correction, both at rest and during exercise. In February 2016, a detailed search of the databases PubMed, Medline, and EMBASE was performed. We assessed clinical studies that described cardiac outcomes both before and after surgical correction of PE. We only included studies reporting either pre-defined echocardiographic or exercise test parameters. No exclusion criteria or statistical analyses were applied. Twenty-one full-text articles, published between 1972 and 2016, were selected, with cohort-ranges of 3-168 patients, mean age-ranges of 5-33 years, and mean follow-up-ranges from immediately to 4 years after surgery. Twelve studies described resting cardiac parameters. Four studies measured cardiac output, where one described 36% immediate increase after surgery, one reported 15% increase after Nuss-bar removal and two found no difference. Three studies demonstrated improvement in mean stroke volume ranges of 22-34% and two studies found no difference. Fifteen studies investigated exercise capacity, with 11 considering peak O2 pr. kg, where five studies demonstrated improvements with the mean ranging from 8% to 15% after surgery, five studies demonstrated no difference, and one saw a decrease of 19% 3 months after Nuss-bar implantation. A measurable increase in exercise capacity exists following surgery, which may be caused by multiple factors. This may be owed to the relief of compressed cardiac chambers with the increased anterior-posterior thoracic dimensions, which could facilitate an improved filling of the heart. With these results, the positive physiological impact of the surgery is emphasized and the potential gain in cardiac
Goyenvalle, Aurélie; Griffith, Graziella; Babbs, Arran; El Andaloussi, Samir; Ezzat, Kariem; Avril, Aurélie; Dugovic, Branislav; Chaussenot, Rémi; Ferry, Arnaud; Voit, Thomas; Amthor, Helge; Bühr, Claudia; Schürch, Stefan; Wood, Matthew J A; Davies, Kay E; Vaillend, Cyrille; Leumann, Christian; Garcia, Luis
2015-03-01
Antisense oligonucleotides (AONs) hold promise for therapeutic correction of many genetic diseases via exon skipping, and the first AON-based drugs have entered clinical trials for neuromuscular disorders. However, despite advances in AON chemistry and design, systemic use of AONs is limited because of poor tissue uptake, and recent clinical reports confirm that sufficient therapeutic efficacy has not yet been achieved. Here we present a new class of AONs made of tricyclo-DNA (tcDNA), which displays unique pharmacological properties and unprecedented uptake by many tissues after systemic administration. We demonstrate these properties in two mouse models of Duchenne muscular dystrophy (DMD), a neurogenetic disease typically caused by frame-shifting deletions or nonsense mutations in the gene encoding dystrophin and characterized by progressive muscle weakness, cardiomyopathy, respiratory failure and neurocognitive impairment. Although current naked AONs do not enter the heart or cross the blood-brain barrier to any substantial extent, we show that systemic delivery of tcDNA-AONs promotes a high degree of rescue of dystrophin expression in skeletal muscles, the heart and, to a lesser extent, the brain. Our results demonstrate for the first time a physiological improvement of cardio-respiratory functions and a correction of behavioral features in DMD model mice. This makes tcDNA-AON chemistry particularly attractive as a potential future therapy for patients with DMD and other neuromuscular disorders or with other diseases that are eligible for exon-skipping approaches requiring whole-body treatment.
Irwig, L; Groeneveld, H; Becklake, M
1988-01-01
The regression of lung function change on the initial lung function level is biased when the initial level is measured with random error. Several methods have been proposed to obtain unbiased estimates of regression coefficients in such circumstances. We apply these methods to examine the relationship between lung function loss over 11 years and its initial level in 433 men aged about 20 when first seen. On theoretical and practical grounds the best method is the correction of the regression coefficient using the reliability coefficient. This is defined as the ratio of the error free variance to the variance of the variable measured with error, and is easily estimated as the correlation between repeat measurements of the underlying level. In young men the loss of some lung functions (forced vital capacity [FVC], forced expiratory volume in one second [FEV1], forced expiratory flow in the middle half of expiration, and the ratio FEV1/FVC) do not appear to be related to initial level. PMID:3256581
Toyoda, Kenji; Hamada, Ikutaro; Yanagisawa, Susumu; Morikawa, Yoshitada
2011-04-01
We have studied the atomic geometries and the electronic properties of benzene/metal interfaces by using density functional theoretical (DFT) calculations with van der Waals corrections. Adsorption energies of benzene on Cu(111), Ag(111), and Au(111) surfaces calculated by van der Waals density functional proposed by Dion and co-workers agree reasonably well with experimentally reported values, while those calculated by a semi-empirical van der Waals correction proposed by Grimme are overestimated slightly. The work function change induced by benzene adsorption on the three surfaces are quite well reproduced by the semi-empirical correction, suggesting that weak adsorption geometries can be quite well reproduced by DFT with a semi-empirical dispersion correction scheme.
2017-07-01
Reports an error in "Default mode functional connectivity is associated with social functioning in schizophrenia" by Jaclyn M. Fox, Samantha V. Abram, James L. Reilly, Shaun Eack, Morris B. Goldman, John G. Csernansky, Lei Wang and Matthew J. Smith (Journal of Abnormal Psychology, 2017[May], Vol 126[4], 392-405). In the article, the email address of corresponding author Matthew J. Smith was set as matthewsmith@northwestern.edu. It should have been mattjsmi@umich.edu. The online version of this article has been corrected. (The following abstract of the original article appeared in record 2017-14073-001.) Individuals with schizophrenia display notable deficits in social functioning. Research indicates that neural connectivity within the default mode network (DMN) is related to social cognition and social functioning in healthy and clinical populations. However, the association between DMN connectivity, social cognition, and social functioning has not been studied in schizophrenia. For the present study, the authors used resting-state neuroimaging data to evaluate connectivity between the main DMN hubs (i.e., the medial prefrontal cortex [mPFC] and the posterior cingulate cortex-anterior precuneus [PPC]) in individuals with schizophrenia (n = 28) and controls (n = 32). The authors also examined whether DMN connectivity was associated with social functioning via social attainment (measured by the Specific Levels of Functioning Scale) and social competence (measured by the Social Skills Performance Assessment), and if social cognition mediates the association between DMN connectivity and these measures of social functioning. Results revealed that DMN connectivity did not differ between individuals with schizophrenia and controls. However, connectivity between the mPFC and PCC hubs was significantly associated with social competence and social attainment in individuals with schizophrenia but not in controls as reflected by a significant group-by-connectivity interaction
Green{close_quote}s function approach to infrared factorization and finite eikonal corrections
Gellas, G.C.; Karanikas, A.I.; Ktorides, C.N. |
1997-04-01
The infrared sector of a generic gauge theory with spin-1/2 matter fields and, for simplicity, only one mass scale, is factored out via a procedure which relies on a path integral (worldline) casting of the field system. The basic idea is to employ a velocity expansion which imposes the spin-1/2 particle{close_quote}s mass as a cutoff for the factorized sector. Anomalous dimensions characterizing the infrared regime are derived in connection with two- and three-point Green{close_quote}s functions. Finally, an off mass shell expansion of the propagator is achieved which contains genuine corrections to the eikonal approximation. {copyright} 1997 Academic Press, Inc.
STEM Image Post-processing for Instability and Aberration Correction for Transfer Function Extension
NASA Astrophysics Data System (ADS)
Jones, Lewys; Nellist, Peter D.
2012-07-01
Scanning transmission electron microscopy (STEM) images can be limited by either aberrations or, because of the technique's serial acquisition, by the effects of environmental instabilities. MatLab image-processing code was written which performs a two stage process to restore degraded high-resolution high-angle annular dark-field (HAADF) STEM images. Firstly, individual images were analysed to identify and correct for high-frequency scan noise; image resolution and signal-noise ratio (SNR) are used as performance metrics and were improved by up to 11.8% and 49% respectively. Secondly, a focal series was used to identify variations in information transfer as a function of defocus (aberrations) whereafter a single image was reconstructed yielding an increase in resolution and SNR of 9.88% and 205% respectively.
Kronik, Leeor; Tkatchenko, Alexandre
2014-11-18
CONSPECTUS: Molecular crystals are ubiquitous in many areas of science and engineering, including biology and medicine. Until recently, our ability to understand and predict their structure and properties using density functional theory was severely limited by the lack of approximate exchange-correlation functionals able to achieve sufficient accuracy. Here we show that there are many cases where the simple, minimally empirical pairwise correction scheme of Tkatchenko and Scheffler provides a useful prediction of the structure and properties of molecular crystals. After a brief introduction of the approach, we demonstrate its strength through some examples taken from our recent work. First, we show the accuracy of the approach using benchmark data sets of molecular complexes. Then we show its efficacy for structural determination using the hemozoin crystal, a challenging system possessing a wide range of strong and weak binding scenarios. Next, we show that it is equally useful for response properties by considering the elastic constants exhibited by the supramolecular diphenylalanine peptide solid and the infrared signature of water libration movements in brushite. Throughout, we emphasize lessons learned not only for the methodology but also for the chemistry and physics of the crystals in question. We further show that in many other scenarios where the simple pairwise correction scheme is not sufficiently accurate, one can go beyond it by employing a computationally inexpensive many-body dispersive approach that results in useful, quantitative accuracy, even in the presence of significant screening and/or multibody contributions to the dispersive energy. We explain the principles of the many-body approach and demonstrate its accuracy for benchmark data sets of small and large molecular complexes and molecular solids.
Quantum principles and free particles. [evaluation of partitions
NASA Technical Reports Server (NTRS)
1976-01-01
The quantum principles that establish the energy levels and degeneracies needed to evaluate the partition functions are explored. The uncertainty principle is associated with the dual wave-particle nature of the model used to describe quantized gas particles. The Schroedinger wave equation is presented as a generalization of Maxwell's wave equation; the former applies to all particles while the Maxwell equation applies to the special case of photon particles. The size of the quantum cell in phase space and the representation of momentum as a space derivative operator follow from the uncertainty principle. A consequence of this is that steady-state problems that are space-time dependent for the classical model become only space dependent for the quantum model and are often easier to solve. The partition function is derived for quantized free particles and, at normal conditions, the result is the same as that given by the classical phase integral. The quantum corrections that occur at very low temperatures or high densities are derived. These corrections for the Einstein-Bose gas qualitatively describe the condensation effects that occur in liquid helium, but are unimportant for most practical purposes otherwise. However, the corrections for the Fermi-Dirac gas are important because they quantitatively describe the behavior of high-density conduction electron gases in metals and explain the zero point energy and low specific heat exhibited in this case.
Li, Shaohong L; Marenich, Aleksandr V; Xu, Xuefei; Truhlar, Donald G
2014-01-16
Linear response (LR) Kohn-Sham (KS) time-dependent density functional theory (TDDFT), or KS-LR, has been widely used to study electronically excited states of molecules and is the method of choice for large and complex systems. The Tamm-Dancoff approximation to TDDFT (TDDFT-TDA or KS-TDA) gives results similar to KS-LR and alleviates the instability problem of TDDFT near state intersections. However, KS-LR and KS-TDA share a debilitating feature; conical intersections of the reference state and a response state occur in F - 1 instead of the correct F - 2 dimensions, where F is the number of internal degrees of freedom. Here, we propose a new method, named the configuration interaction-corrected Tamm-Dancoff approximation (CIC-TDA), that eliminates this problem. It calculates the coupling between the reference state and an intersecting response state by interpreting the KS reference-state Slater determinant and linear response as if they were wave functions. Both formal analysis and test results show that CIC-TDA gives similar results to KS-TDA far from a conical intersection, but the intersection occurs with the correct dimensionality. We anticipate that this will allow more realistic application of TDDFT to photochemistry.
Self-interaction corrected density functional calculations of molecular Rydberg states
Gudmundsdóttir, Hildur; Zhang, Yao; Weber, Peter M.; Jónsson, Hannes
2013-11-21
A method is presented for calculating the wave function and energy of Rydberg excited states of molecules. A good estimate of the Rydberg state orbital is obtained using ground state density functional theory including Perdew-Zunger self-interaction correction and an optimized effective potential. The total energy of the excited molecule is obtained using the Delta Self-Consistent Field method where an electron is removed from the highest occupied orbital and placed in the Rydberg orbital. Results are presented for the first few Rydberg states of NH{sub 3}, H{sub 2}O, H{sub 2}CO, C{sub 2}H{sub 4}, and N(CH{sub 3}){sub 3}. The mean absolute error in the energy of the 33 molecular Rydberg states presented here is 0.18 eV. The orbitals are represented on a real space grid, avoiding the dependence on diffuse atomic basis sets. As in standard density functional theory calculations, the computational effort scales as NM{sup 2} where N is the number of orbitals and M is the number of grid points included in the calculation. Due to the slow scaling of the computational effort with system size and the high level of parallelism in the real space grid approach, the method presented here makes it possible to estimate Rydberg electron binding energy in large molecules.
Ribosomal Stalk Protein Silencing Partially Corrects the ΔF508-CFTR Functional Expression Defect
Veit, Guido; Oliver, Kathryn; Apaja, Pirjo M.; Perdomo, Doranda; Bidaud-Meynard, Aurélien; Guo, Jingyu; Icyuz, Mert; Sorscher, Eric J.; Hartman, John L.; Lukacs, Gergely L.
2016-01-01
The most common cystic fibrosis (CF) causing mutation, deletion of phenylalanine 508 (ΔF508 or Phe508del), results in functional expression defect of the CF transmembrane conductance regulator (CFTR) at the apical plasma membrane (PM) of secretory epithelia, which is attributed to the degradation of the misfolded channel at the endoplasmic reticulum (ER). Deletion of phenylalanine 670 (ΔF670) in the yeast oligomycin resistance 1 gene (YOR1, an ABC transporter) of Saccharomyces cerevisiae phenocopies the ΔF508-CFTR folding and trafficking defects. Genome-wide phenotypic (phenomic) analysis of the Yor1-ΔF670 biogenesis identified several modifier genes of mRNA processing and translation, which conferred oligomycin resistance to yeast. Silencing of orthologues of these candidate genes enhanced the ΔF508-CFTR functional expression at the apical PM in human CF bronchial epithelia. Although knockdown of RPL12, a component of the ribosomal stalk, attenuated the translational elongation rate, it increased the folding efficiency as well as the conformational stability of the ΔF508-CFTR, manifesting in 3-fold augmented PM density and function of the mutant. Combination of RPL12 knockdown with the corrector drug, VX-809 (lumacaftor) restored the mutant function to ~50% of the wild-type channel in primary CFTRΔF508/ΔF508 human bronchial epithelia. These results and the observation that silencing of other ribosomal stalk proteins partially rescue the loss-of-function phenotype of ΔF508-CFTR suggest that the ribosomal stalk modulates the folding efficiency of the mutant and is a potential therapeutic target for correction of the ΔF508-CFTR folding defect. PMID:27168400
Normalization of off-shell boundary state, g-function and zeta function regularization
NASA Astrophysics Data System (ADS)
Itoyama, H.; Oota, T.
2002-11-01
We consider the model in two dimensions with boundary quadratic deformation (BQD), which has been discussed in tachyon condensation. The partition function of this model (BQD) on a cylinder is determined using the method of zeta function regularization. We show that, for closed channel partition function, a subtraction procedure must be introduced in order to reproduce the correct results at conformal points. The boundary entropy (g-function) is determined from the partition function and the off-shell boundary state. We propose and consider a supersymmetric generalization of the BQD model, which includes a boundary fermion mass term, and check the validity of the subtraction procedure.
NASA Astrophysics Data System (ADS)
Wehr, R. A.; Munger, J. W.; McManus, J. B.; Nelson, D. D.; Zahniser, M. S.; Saleska, S. R.
2013-12-01
Conventional methods for partitioning the net ecosystem-atmosphere exchange (NEE) of CO2 into gross primary production (GPP) and ecosystem respiration (R) work by extrapolating GPP or R using an empirical function fit to a week or a month of data. Accordingly, these methods do not allow investigation of short-term (e.g. diel) deviations of GPP or R from their monthly average behaviors. Moreover, these methods assume that daytime R is either constant or a smoothly varying function of temperature. Isotopic partitioning is an alternative that involves no assumptions about the behavior of R or GPP (though it requires knowledge or assumptions about the isotopic fractionations occurring in and around the leaves) and which allows for the investigation of diel variations because each flux measurement is partitioned separately. A novel isotopic flux partitioning approach using our unique long-term isotopic CO2 eddy flux record at the Harvard Forest reveals significant differences in both the diel and the seasonally averaged behavior of GPP as compared to conventional partitioning. At the diel timescale, large (~10 μmol m-2 s-1), rapid (~2 hours) variations in the respiratory component of measured NEE associated with subtle changes in wind direction (due to the breakdown of the basic EC assumption of horizontal landscape homogeneity) are misattributed to GPP by conventional partitioning, leading to inconsistency in the response of GPP to photosynthetically active radiation (PAR). Isotopically partitioned GPP responds much more consistently to PAR, and the seasonally averaged light response curve of isotopically partitioned GPP is much more linear than that of conventionally partitioned GPP (after controlling for the leaf-air water vapor gradient), suggesting that unsaturated (steeply inclined) leaves perform most of the canopy photosynthesis (Figure 1). The behavior of isotopically partitioned GPP follows largely from the observed behavior of the canopy-integrated stomatal
Exact finite-size corrections for the spanning-tree model under different boundary conditions
NASA Astrophysics Data System (ADS)
Izmailian, N. Sh.; Kenna, R.
2015-02-01
We express the partition functions of the spanning tree on finite square lattices under five different sets of boundary conditions in terms of a principal partition function with twisted-boundary conditions. Based on these expressions, we derive the exact asymptotic expansions of the logarithm of the partition function for each case. We have also established several groups of identities relating spanning-tree partition functions for the different boundary conditions. We also explain an apparent discrepancy between logarithmic correction terms in the free energy for a two-dimensional spanning-tree model with periodic and free-boundary conditions and conformal field theory predictions. We have obtained corner free energy for the spanning tree under free-boundary conditions in full agreement with conformal field theory predictions.
NASA Astrophysics Data System (ADS)
Hervo, Maxime; Poltera, Yann; Haefele, Alexander
2016-07-01
Imperfections in a lidar's overlap function lead to artefacts in the background, range and overlap-corrected lidar signals. These artefacts can erroneously be interpreted as an aerosol gradient or, in extreme cases, as a cloud base leading to false cloud detection. A correct specification of the overlap function is hence crucial in the use of automatic elastic lidars (ceilometers) for the detection of the planetary boundary layer or of low cloud. In this study, an algorithm is presented to correct such artefacts. It is based on the assumption of a homogeneous boundary layer and a correct specification of the overlap function down to a minimum range, which must be situated within the boundary layer. The strength of the algorithm lies in a sophisticated quality-check scheme which allows the reliable identification of favourable atmospheric conditions. The algorithm was applied to 2 years of data from a CHM15k ceilometer from the company Lufft. Backscatter signals corrected for background, range and overlap were compared using the overlap function provided by the manufacturer and the one corrected with the presented algorithm. Differences between corrected and uncorrected signals reached up to 45 % in the first 300 m above ground. The amplitude of the correction turned out to be temperature dependent and was larger for higher temperatures. A linear model of the correction as a function of the instrument's internal temperature was derived from the experimental data. Case studies and a statistical analysis of the strongest gradient derived from corrected signals reveal that the temperature model is capable of a high-quality correction of overlap artefacts, in particular those due to diurnal variations. The presented correction method has the potential to significantly improve the detection of the boundary layer with gradient-based methods because it removes false candidates and hence simplifies the attribution of the detected gradients to the planetary boundary layer. A
Baxter, Jamie C; Funnell, Barbara E
2014-12-01
The stable maintenance of low-copy-number plasmids in bacteria is actively driven by partition mechanisms that are responsible for the positioning of plasmids inside the cell. Partition systems are ubiquitous in the microbial world and are encoded by many bacterial chromosomes as well as plasmids. These systems, although different in sequence and mechanism, typically consist of two proteins and a DNA partition site, or prokaryotic centromere, on the plasmid or chromosome. One protein binds site-specifically to the centromere to form a partition complex, and the other protein uses the energy of nucleotide binding and hydrolysis to transport the plasmid, via interactions with this partition complex inside the cell. For plasmids, this minimal cassette is sufficient to direct proper segregation in bacterial cells. There has been significant progress in the last several years in our understanding of partition mechanisms. Two general areas that have developed are (i) the structural biology of partition proteins and their interactions with DNA and (ii) the action and dynamics of the partition ATPases that drive the process. In addition, systems that use tubulin-like GTPases to partition plasmids have recently been identified. In this chapter, we concentrate on these recent developments and the molecular details of plasmid partition mechanisms.
Otero-de-la-Roza, A; Johnson, Erin R
2013-05-28
The exchange-hole dipole-moment model (XDM) for dispersion is combined with a collection of semilocal, hybrid, and range-separated hybrid functionals. The resulting XDM-corrected functionals are tested against standard benchmarks for non-covalent interactions at and away from equilibrium, conformer ranking in water clusters, thermochemistry, and kinetics. We show that functionals with the correct -1∕r tail of the exchange potential yield superior accuracy for weak interactions. Thus, balancing long-range exchange with dispersion interactions in XDM is essential in the correct description of dimers with significant non-dispersion contributions to binding. With the exception of the noble gases, the performance of PW86PBE-XDM is improved upon at the semilocal (BLYP), hybrid (B3LYP), and range-separated hybrid (LC-ωPBE) levels. Based on its excellent performance, we propose LC-ωPBE-XDM as an accurate functional for hard and soft matter.
NASA Astrophysics Data System (ADS)
Otero-de-la-Roza, A.; Johnson, Erin R.
2013-05-01
The exchange-hole dipole-moment model (XDM) for dispersion is combined with a collection of semilocal, hybrid, and range-separated hybrid functionals. The resulting XDM-corrected functionals are tested against standard benchmarks for non-covalent interactions at and away from equilibrium, conformer ranking in water clusters, thermochemistry, and kinetics. We show that functionals with the correct -1/r tail of the exchange potential yield superior accuracy for weak interactions. Thus, balancing long-range exchange with dispersion interactions in XDM is essential in the correct description of dimers with significant non-dispersion contributions to binding. With the exception of the noble gases, the performance of PW86PBE-XDM is improved upon at the semilocal (BLYP), hybrid (B3LYP), and range-separated hybrid (LC-ωPBE) levels. Based on its excellent performance, we propose LC-ωPBE-XDM as an accurate functional for hard and soft matter.
Red wine polyphenols correct vascular function injured by chronic carbon tetrachloride intoxication.
Cačányiová, Soňa; Pecháňová, Oľga; Babál, Pavel; Cerná, Andrea; Janega, Pavol; Andriantsitohaina, Ramaroson
2011-06-01
The aim of the study was to evaluate the effect of red wine polyphenols extract Provinols™ on the development of cardiovascular injury in the model of carbon tetrachloride (CCl4) intoxication. We followed the thoracic aorta vasoactivity and left ventricle nitric oxide (NO) synthase activity in male Wistar rats. In the preventive experiment lasting for 12 weeks the control group, the group receiving CCl4 (0.5 ml/kg) two times a week subcutaneously, the group receiving Provinols™ (30 mg/kg/day) in drinking water and the group receiving CCl4+Provinols™ was used. In the recovery experiment, the initial 12 weeks of CCl4 treatment were followed by 3 weeks of spontaneous recovery or recovery with Provinols™. CCl4-intoxication resulted in the injury of vasoactivity which was demonstrated by the inhibition of acetylcholine-induced relaxation as well as noradrenaline-induced contraction. In the preventive as well as recovery experiment administration of polyphenols refreshed endothelium-dependent relaxant response and normalized inhibited contraction to adrenergic stimuli. Provinols™ treatment significantly increased NO-synthase activity in all groups. The results revealed beneficial effects of red wine polyphenols on vascular function injured by chronic CCl4 intoxication. The correction of endothelial function seems to be attributed to the activation of NO pathway by polyphenols.
Screened van der Waals correction to density functional theory for solids
NASA Astrophysics Data System (ADS)
Tao, Jianmin; Zheng, Fan; Gebhardt, Julian; Perdew, John P.; Rappe, Andrew M.
2017-07-01
Lattice constant and cohesive energy are basic properties in the design of materials and devices. However, due to neglect of long-range van der Waals (vdW) interactions, density functional approximations (DFAs) often yield unusually large errors for ionic solids and heavy metals. Here, we propose a model for the dynamically screened vdW correction, including the leading order as well as higher-order contributions. The striking feature of this model is that important screening effects and higher-order contributions are properly considered and that its contribution to the short-range part is removed by a novel damping function for the avoidance of double counting. As a result, the model dramatically reduces the error of the DFA-GGA in lattice constant and cohesive energy. We also find that the three-body interactions are small, due to the screening effects. These observations greatly improve our fundamental understanding of vdW interactions and enhance the applicability of efficient semilocal DFAs.
Kim, Hyungjun; Choi, Jeong-Mo; Goddard, William A
2012-02-02
Conventional density functional theory (DFT) fails to describe accurately the London dispersion essential for describing molecular interactions in soft matter (biological systems, polymers, nucleic acids) and molecular crystals. This has led to several methods in which atom-dependent potentials are added into the Kohn-Sham DFT energy. Some of these corrections were fitted to accurate quantum mechanical results, but it will be tedious to determine the appropriate parameters to describe all of the atoms of the periodic table. We propose an alternative approach in which a single parameter in the low-gradient (lg) functional form is combined with the rule-based UFF (universal force-field) nonbond parameters developed for the entire periodic table (up to Lr, Z = 103), named as a DFT-ulg method. We show that DFT-ulg method leads to a very accurate description of the properties for molecular complexes and molecular crystals, providing the means for predicting more accurate weak interactions across the periodic table.
NASA Technical Reports Server (NTRS)
Lan, C. E.; Lamar, J. E.
1977-01-01
A logarithmic-singularity correction factor is derived for use in kernel function methods associated with Multhopp's subsonic lifting-surface theory. Because of the form of the factor, a relation was formulated between the numbers of chordwise and spanwise control points needed for good accuracy. This formulation is developed and discussed. Numerical results are given to show the improvement of the computation with the new correction factor.
Huang, Chen; Muñoz-García, Ana Belén; Pavone, Michele
2016-12-28
Density-functional embedding theory provides a general way to perform multi-physics quantum mechanics simulations of large-scale materials by dividing the total system's electron density into a cluster's density and its environment's density. It is then possible to compute the accurate local electronic structures and energetics of the embedded cluster with high-level methods, meanwhile retaining a low-level description of the environment. The prerequisite step in the density-functional embedding theory is the cluster definition. In covalent systems, cutting across the covalent bonds that connect the cluster and its environment leads to dangling bonds (unpaired electrons). These represent a major obstacle for the application of density-functional embedding theory to study extended covalent systems. In this work, we developed a simple scheme to define the cluster in covalent systems. Instead of cutting covalent bonds, we directly split the boundary atoms for maintaining the valency of the cluster. With this new covalent embedding scheme, we compute the dehydrogenation energies of several different molecules, as well as the binding energy of a cobalt atom on graphene. Well localized cluster densities are observed, which can facilitate the use of localized basis sets in high-level calculations. The results are found to converge faster with the embedding method than the other multi-physics approach ONIOM. This work paves the way to perform the density-functional embedding simulations of heterogeneous systems in which different types of chemical bonds are present.
NASA Astrophysics Data System (ADS)
Huang, Chen; Muñoz-García, Ana Belén; Pavone, Michele
2016-12-01
Density-functional embedding theory provides a general way to perform multi-physics quantum mechanics simulations of large-scale materials by dividing the total system's electron density into a cluster's density and its environment's density. It is then possible to compute the accurate local electronic structures and energetics of the embedded cluster with high-level methods, meanwhile retaining a low-level description of the environment. The prerequisite step in the density-functional embedding theory is the cluster definition. In covalent systems, cutting across the covalent bonds that connect the cluster and its environment leads to dangling bonds (unpaired electrons). These represent a major obstacle for the application of density-functional embedding theory to study extended covalent systems. In this work, we developed a simple scheme to define the cluster in covalent systems. Instead of cutting covalent bonds, we directly split the boundary atoms for maintaining the valency of the cluster. With this new covalent embedding scheme, we compute the dehydrogenation energies of several different molecules, as well as the binding energy of a cobalt atom on graphene. Well localized cluster densities are observed, which can facilitate the use of localized basis sets in high-level calculations. The results are found to converge faster with the embedding method than the other multi-physics approach ONIOM. This work paves the way to perform the density-functional embedding simulations of heterogeneous systems in which different types of chemical bonds are present.
NASA Astrophysics Data System (ADS)
Itoyama, H.; Oota, T.; Yoshioka, R.
2013-12-01
We propose and demonstrate a limiting procedure in which, starting from the q-lifted version (or K-theoretic five-dimensional version) of the (W)AGT conjecture to be assumed in this paper, the Virasoro/W block is generated in the r-th root of unity limit in q in the 2d side, while the same limit automatically generates the projection of the five-dimensional instanton partition function onto that on the ALE space R4/Zr. This circumvents case-by-case conjectures to be made in a wealth of examples found so far. In the 2d side, we successfully generate the super-Virasoro algebra and the proper screening charge in the q→-1, t→-1 limit, from the defining relation of the q-Virasoro algebra and the q-deformed Heisenberg algebra. The central charge obtained coincides with that of the minimal series carrying odd integers of the N=1 superconformal algebra. In the r-th root of unity limit in q in the 2d side, we give some evidence of the appearance of the parafermion-like currents. Exploiting the q-analysis literatures, q-deformed su(n) block is readily generated both at generic q,t and the r-th root of unity limit. In the 4d side, we derive the proper normalization function for general (n,r) that accomplishes the automatic projection through the limit.
Risser, Laurent; Vincent, Thomas; Ciuciu, Philippe; Idier, Jérôme
2009-01-01
In this paper, we present a fast numerical scheme to estimate Partition Functions (PF) of 3D Ising fields. Our strategy is applied to the context of the joint detection-estimation of brain activity from functional Magnetic Resonance Imaging (fMRI) data, where the goal is to automatically recover activated regions and estimate region-dependent hemodynamic filters. For any region, a specific binary Markov random field may embody spatial correlation over the hidden states of the voxels by modeling whether they are activated or not. To make this spatial regularization fully adaptive, our approach is first based upon a classical path-sampling method to approximate a small subset of reference PFs corresponding to prespecified regions. Then, the proposed extrapolation method allows us to approximate the PFs associated with the Ising fields defined over the remaining brain regions. In comparison with preexisting approaches, our method is robust to topological inhomogeneities in the definition of the reference regions. As a result, it strongly alleviates the computational burden and makes spatially adaptive regularization of whole brain fMRI datasets feasible.
NASA Astrophysics Data System (ADS)
Sheehy, Christopher D.; McCrady, Nate; Graham, James R.
2006-08-01
The point-spread function (PSF) of an adaptive optics (AO) system is often poorly known. This ignorance can lead to significant systematic errors. Since the degree of AO correction is sensitive to the observing conditions (seeing, wind speed, brightness of the wave front reference, etc.), it would be desirable to estimate the PSF from the data themselves rather than from observations of a PSF star at another time. We have developed a method to estimate the PSF delivered by an AO system in the case where the scene consists of a crowded star field. We model the modulation transfer function (MTF) of several key components of the imaging system (atmosphere filtered by an AO system, telescope pupil, and pixel array). The power spectrum of the image, even a dense star field, can be used to constrain our model, which in turn can be used to reconstruct the PSF. In the case of circularly symmetric PSFs, we demonstrate that the power spectrum of the source distribution function can be successfully removed from the measured MTF and that our fit successfully recovers input parameters from a model data set constructed from these parameters. We also show that the method yields reasonable fit parameters and a useful approximation to the PSF when applied to data from the laser guide star (LGS) AO system at the Keck Observatory. Comparison of Keck LGS AO data and Hubble Space Telescope observations with NICMOS show that photometric accuracy of a few percent can be achieved for data with Strehl ratios as low as 4%. Based on observations obtained at the W. M. Keck Observatory.
NASA Astrophysics Data System (ADS)
Fox, R. J.; Bellwood, D. R.
2013-03-01
Niche theory predicts that coexisting species minimise competition by evolving morphological or behavioural specialisations that allow them to spread out along resource axes such as space, diet and temporal activity. These specialisations define how a species interacts with its environment and, by extension, determine its functional role. Here, we examine the feeding niche of three species of coral reef-dwelling rabbitfishes (Siganidae, Siganus). By comparing aspects of their feeding behaviour (bite location, bite rate, foraging distance) with that of representative species from two other abundant herbivorous fish families, the parrotfishes (Labridae, Scarus) and surgeonfishes (Acanthuridae, Acanthurus), we examine whether rabbitfishes have a feeding niche distinct from other members of the herbivore guild. Measurements of the penetration of the fishes' snouts and bodies into reef concavities when feeding revealed that rabbitfish fed to a greater degree from reef crevices and interstices than other herbivores. There was just a 40 % overlap in the penetration-depth niche between rabbitfish and surgeonfish and a 45 % overlap between rabbitfish and parrotfish, compared with the almost complete niche overlap (95 %) recorded for parrotfish and surgeonfish along this spatial niche axis. Aspects of the morphology of rabbitfish which may contribute to this niche segregation include a comparatively longer, narrower snout and narrower head. Our results suggest that sympatric coexistence of rabbitfish and other reef herbivores is facilitated by segregation along a spatial (and potentially dietary) axis. This segregation results in a unique functional role for rabbitfishes among roving herbivores that of "crevice-browser": a group that specifically feeds on crevice-dwelling algal or benthic organisms. This functional trait may have implications for reef ecosystem processes in terms of controlling the successional development of crevice-based algal communities, reducing their
Jiménez-Garduño, Aura M; Mitkovski, Miso; Alexopoulos, Ioannis K; Sánchez, Araceli; Stühmer, Walter; Pardo, Luis A; Ortega, Alicia
2014-03-01
KV10.1 potassium channels are implicated in a variety of cellular processes including cell proliferation and tumour progression. Their expression in over 70% of human tumours makes them an attractive diagnostic and therapeutic target. Although their physiological role in the central nervous system is not yet fully understood, advances in their precise cell localization will contribute to the understanding of their interactions and function. We have determined the plasma membrane (PM) distribution of the KV10.1 protein in an enriched mouse brain PM fraction and its association with cholesterol- and sphingolipid-rich domains. We show that the KV10.1 channel has two different populations in a 3:2 ratio, one associated to and another excluded from Detergent Resistant Membranes (DRMs). This distribution of KV10.1 in isolated PM is cholesterol- and cytoskeleton-dependent since alteration of those factors changes the relationship to 1:4. In transfected HEK-293 cells with a mutant unable to bind Ca(2+)/CaM to KV10.1 protein, Kv10.1 distribution in DRM/non-DRM is 1:4. Mean current density was doubled in the cholesterol-depleted cells, without any noticeable effects on other parameters. These results demonstrate that recruitment of the KV10.1 channel to the DRM fractions involves its functional regulation.
Evaluating the Influence of Spatial Resampling for Motion Correction in Resting-State Functional MRI
Yuan, Lisha; He, Hongjian; Zhang, Han; Zhong, Jianhui
2016-01-01
Head motion is one of major concerns in current resting-state functional MRI studies. Image realignment including motion estimation and spatial resampling is often applied to achieve rigid-body motion correction. While the accurate estimation of motion parameters has been addressed in most studies, spatial resampling could also produce spurious variance, and lead to unexpected errors on the amplitude of BOLD signal. In this study, two simulation experiments were designed to characterize these variance related with spatial resampling. The fluctuation amplitude of spurious variance was first investigated using a set of simulated images with estimated motion parameters from a real dataset, and regions more likely to be affected by spatial resampling were found around the peripheral regions of the cortex. The other simulation was designed with three typical types of motion parameters to represent different extents of motion. It was found that areas with significant correlation between spurious variance and head motion scattered all over the brain and varied greatly from one motion type to another. In the last part of this study, four popular motion regression approaches were applied respectively and their performance in reducing spurious variance was compared. Among them, Friston 24 and Voxel-specific 12 model (Friston et al., 1996), were found to have the best outcomes. By separating related effects during fMRI analysis, this study provides a better understanding of the characteristics of spatial resampling and the interpretation of motion-BOLD relationship. PMID:28082860
Mehler, Michaela; Eckert, Carl Elias; Busche, Alena; Kulhei, Jennifer; Michaelis, Jonas; Becker-Baldus, Johanna; Wachtveitl, Josef; Dötsch, Volker; Glaubitz, Clemens
2015-01-01
Protein trans-splicing using split inteins is well established as a useful tool for protein engineering. Here we show, for the first time, that this method can be applied to a membrane protein under native conditions. We provide compelling evidence that the heptahelical proteorhodopsin can be assembled from two separate fragments consisting of helical bundles A and B and C, D, E, F, and G via a splicing site located in the BC loop. The procedure presented here is on the basis of dual expression and ligation in vivo. Global fold, stability, and photodynamics were analyzed in detergent by CD, stationary, as well as time-resolved optical spectroscopy. The fold within lipid bilayers has been probed by high field and dynamic nuclear polarization-enhanced solid-state NMR utilizing a 13C-labeled retinal cofactor and extensively 13C-15N-labeled protein. Our data show unambiguously that the ligation product is identical to its non-ligated counterpart. Furthermore, our data highlight the effects of BC loop modifications onto the photocycle kinetics of proteorhodopsin. Our data demonstrate that a correctly folded and functionally intact protein can be produced in this artificial way. Our findings are of high relevance for a general understanding of the assembly of membrane proteins for elucidating intramolecular interactions, and they offer the possibility of developing novel labeling schemes for spectroscopic applications. PMID:26405032
Chan, Poh Yin; Tong, Chi Ming; Durrant, Marcus C
2011-09-01
An empirical method for estimation of the boiling points of organic molecules based on density functional theory (DFT) calculations with polarized continuum model (PCM) solvent corrections has been developed. The boiling points are calculated as the sum of three contributions. The first term is calculated directly from the structural formula of the molecule, and is related to its effective surface area. The second is a measure of the electronic interactions between molecules, based on the DFT-PCM solvation energy, and the third is employed only for planar aromatic molecules. The method is applicable to a very diverse range of organic molecules, with normal boiling points in the range of -50 to 500 °C, and includes ten different elements (C, H, Br, Cl, F, N, O, P, S and Si). Plots of observed versus calculated boiling points gave R²=0.980 for a training set of 317 molecules, and R²=0.979 for a test set of 74 molecules. The role of intramolecular hydrogen bonding in lowering the boiling points of certain molecules is quantitatively discussed.
NASA Technical Reports Server (NTRS)
Delaney, J. S.; Sutton, S. R.; Newville, M.; Jones, J. H.; Hanson, B.; Dyar, M. D.; Schreiber, H.
2000-01-01
Oxidation state microanalyses for V in glass have been made by calibrating XANES spectral features with optical spectroscopic measurements. The oxidation state change with fugacity of O2 will strongly influence partitioning results.
Reckien, Werner; Janetzko, Florian; Peintinger, Michael F; Bredow, Thomas
2012-09-30
A recently developed empirical dispersion correction (Grimme et al., J. Chem. Phys. 2010, 132, 154104) to standard density functional theory (DFT-D3) is implemented in the plane-wave program package VASP. The DFT-D3 implementation is compared with an implementation of the earlier DFT-D2 version (Grimme, J. Comput. Chem. 2004, 25, 1463; Grimme, J. Comput. Chem. 2006, 27, 1787). Summation of empirical pair potential terms is performed over all atom pairs in the reference cell and over atoms in shells of neighboring cells until convergence of the dispersion energy is obtained. For DFT-D3, the definition of coordination numbers has to be modified with respect to the molecular version to ensure convergence. The effect of three-center terms as implemented in the original molecular DFT-D3 version is investigated. The empirical parameters are taken from the original DFT-D3 version where they had been optimized for a reference set of small molecules. As the coordination numbers of atoms in bulk and surfaces are much larger than in the reference compounds, this effect has to be discussed. The results of test calculations for bulk properties of metals, metal oxides, benzene, and graphite indicate that the original parameters are also suitable for solid-state systems. In particular, the interlayer distance in bulk graphite and lattice constants of molecular crystals is considerably improved over standard functionals. With the molecular standard parameters (Grimme et al., J. Chem. Phys. 2010, 132, 154104; Grimme, J. Comput. Chem. 2006, 27, 1787) a slight overbinding is observed for ionic oxides where dispersion should not contribute to the bond. For simple adsorbate systems, such as Xe atoms and benzene on Ag(111), the DFT-D implementations reproduce experimental results with a similar accuracy as more sophisticated approaches based on perturbation theory (Rohlfing and Bredow, Phys. Rev. Lett. 2008, 101, 266106). Copyright © 2012 Wiley Periodicals, Inc.
Lai, Chung-Sheng; Chang, Kao-Ping; Lee, Su-Shin; Hsieh, Tung-Ying; Lai, Hsin-Ti; Huang, Yu-Hao; Lai, Ya-Wei
2013-12-01
On the basis of the close anatomical interdigitation between the longitudinal-oriented frontalis muscle and the horizontal-oriented orbicularis oculi muscle (OOM), frontalis OOM (FOOM) flap was developed to treat blepharoptosis. Retrospective study during an 11-year period, 66 patients with 81 poor levator function ptotic eyelids accepted FOOM flap shortening (65 lids; 80.2%) or double-breasted FOOM flap advancement (16 lids; 19.8%) to correct blepharoptosis. There were 51 (77.3%) patients with unilateral ptosis and 15 (22.7%) patients with bilateral ptosis. Severity of blepharoptosis included severe type in 72 (88.9%) lids, moderate type in 5 (6.2%) lids, and mild type in 4 (4.9%) lids. The underlying etiology included congenital origin in 43 (65.1%) patients, involutional change in 19 (28.8%) patients, and neurologic origin in 4 (6.1%) patients. Marginal reflex distance 1 and lid slit distance improved from -1.6 (2.0) to 3.3 (1.2) and 3.2 (2.0) to 7.2 (1.4) mm, respectively, after operation. The postoperative outcome includes good results in 54 (81.8%) patients, fair results in 10 (15.2%) patients, and poor results in 2 (3.0%) patients. The undercorrection or recurrence rate is 14.8%, and secondary revision rate is 11.1%. Positive Hering law is 17.6% among patients with unilateral ptosis. Overall patients' satisfaction rate is 95.1%. Both FOOM flap shortening and double-breasted FOOM flap advancement are effective to treat poor levator function blepharoptosis. Double-breasted FOOM flap advancement is highly recommended because of the more natural contour and minimal lagophthalmos postoperatively, because of the maximal preservation of OOM.
Desgranges, Caroline; Delhommelle, Jerome
2014-03-14
Combining rules, such as the Lorentz-Berthelot rules, are routinely used to calculate the thermodynamic properties of mixtures using molecular simulations. Here we extend the expanded Wang-Landau simulation approach to determine the impact of the combining rules on the value of the partition function of binary systems, and, in turn, on the phase coexistence and thermodynamics of these mixtures. We study various types of mixtures, ranging from systems of rare gases to biologically and technologically relevant mixtures, such as water-urea and water-carbon dioxide. Comparing the simulation results to the experimental data on mixtures of rare gases allows us to rank the performance of combining rules. We find that the widely used Lorentz-Berthelot rules exhibit the largest deviations from the experimental data, both for the bulk and at coexistence, while the Kong and Waldman-Hagler provide much better alternatives. In particular, in the case of aqueous solutions of urea, we show that the use of the Lorentz-Berthelot rules has a strong impact on the Gibbs free energy of the solute, overshooting the value predicted by the Waldman-Hagler rules by 7%. This result emphasizes the importance of the combining rule for the determination of hydration free energies using molecular simulations.
Francisco, Ana Paula; Harner, Tom; Eng, Anita
2017-05-01
Polyurethane foam - air partition coefficients (KPUF-air) for 9 polycyclic aromatic hydrocarbons (PAHs), 10 alkyl-substituted PAHs, 4 organochlorine pesticides (OCPs) and dibenzothiophene were measured as a function of temperature over the range 5 °C-35 °C, using a generator column approach. Enthalpies of PUF-to-air transfer (ΔHPUF-air, kJ/mol) were determined from the slopes of log KPUF-air versus 1000/T (K), and have an average value of 81.2 ± 7.03 kJ/mol. The log KPUF-air values at 22 °C ranged from 4.99 to 7.25. A relationship for log KPUF-air versus log KOA was shown to agree with a previous relationship based on only polychlorinated biphenyls (PCBs) and derived from long-term indoor uptake study experiments. The results also confirm that the existing KOA-based model for predicting log KPUF-air values is accurate. This new information is important in the derivation of uptake profiles and effective air sampling volumes for PUF disk samplers so that results can be reported in units of concentration in air. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.
Desgranges, Caroline; Delhommelle, Jerome
2012-05-14
We propose to apply expanded Wang-Landau simulations to study the adsorption of atomic and molecular fluids in porous materials. This approach relies on a uniform sampling of the number of atoms and molecules adsorbed. The method consists in determining a high-accuracy estimate of the grand-canonical partition function for the adsorbed fluids. Then, using the formalism of statistical mechanics, we calculate absolute and excess thermodynamic properties relevant to adsorption processes. In this paper, we examine the adsorption of argon and carbon dioxide in the isoreticular metal-organic framework (IRMOF-1). We assess the reliability of the method by showing that the predicted adsorption isotherms and isosteric heats are in excellent agreement with simulation results obtained from grand-canonical Monte Carlo simulations. We also show that the proposed method is very efficient since a single expanded Wang-Landau simulation run at a given temperature provides the whole adsorption isotherm. Moreover, this approach provides a direct access to a wide range of thermodynamic properties, such as, e.g., the excess Gibbs free energy and the excess entropy of adsorption.
NASA Astrophysics Data System (ADS)
Szarecka, Agnieszka; White, Ronald P.; Meirovitch, Hagai
2003-12-01
The hypothetical scanning (HS) method provides the absolute entropy and free energy from a Boltzmann sample generated by Monte Carlo, molecular dynamics or any other exact simulation procedure. Thus far HS has been applied successfully to magnetic and polymer chain models; in this paper and the following one it is extended to fluid systems by treating a Lennard-Jones model of argon. With HS a probability Pi approximating the Boltzmann probability of system configuration i is calculated with a stepwise reconstruction procedure, based on adding atoms gradually layer-by-layer to an initially empty volume, where they are replaced in their positions at i. At each step a transition probability (TP) is obtained from local grand canonical partition functions calculated over a limited space of the still unvisited (future) volume, the larger this space the better the approximation. Pi is the product of the step TPs, where ln Pi is an upper bound of the absolute entropy, which leads to upper and lower bounds for the free energy. We demonstrate that very good results for the entropy and the free energy can be obtained for a wide range of densities of the argon system by calculating TPs that are based on only a very limited future volume.
Kishi, Ryohei; Bonness, Sean; Yoneda, Kyohei; Takahashi, Hideaki; Nakano, Masayoshi; Botek, Edith; Champagne, Benoît; Kubo, Takashi; Kamada, Kenji; Ohta, Koji; Tsuneda, Takao
2010-03-07
Within the spin-unrestricted density functional theory (DFT) the long-range correction (LC) scheme combined with the Becke-Lee-Yang-Parr exchange-correlation functional, referred to as LC-UBLYP method, has been applied to the calculation of the second hyperpolarizability (gamma) of open-shell singlet diradical systems of increasing complexity and has demonstrated good performance: (i) for the simplest H(2) dissociation model, the gamma values calculated by the LC-UBLYP method significantly overshoot the full configuration interaction result but reproduce qualitatively the evolution of gamma as a function of the diradical character, (ii) for small singlet diradical 1,3-dipole systems, the diradical character dependence of gamma determined by the UCCSD and UCCSD(T) reference methods is reproduced semiquantitatively by the LC-UBLYP method except in the small diradical character region, where the spin-unrestricted solutions coincide with spin-restricted solutions, (iii) the LC-UBLYP method also closely reproduces the UCCSD(T) results on the diradical character dependence of gamma of the p-quinodimethane model system, particularly in the intermediate and large diradical character regions, whereas it shows an abrupt change for a diradical character (y) close to 0.2 originating from the triplet instability, (iv) the reliability of LC-UBLYP to reproduce reference coupled cluster results on open-shell singlet systems with intermediate and large diradical characters has also been substantiated in the case of gamma of 1,4-bis-(imidazol-2-ylidene)-cyclohexa-2,5-diene (BI2Y), then (v), for real systems built from a pair of phenalenyl radicals separated by a conjugated linker, the LC-UBLYP results have been found to closely match the UBHandHLYP values-which, for small systems are in good agreement with those obtained using correlated molecular orbital methods-whereas the UB3LYP results can be much different. These results are not only important from the viewpoint of an efficient
Correction for collimator-detector response in SPECT using point spread function template.
Chun, Se Young; Fessler, Jeffrey A; Dewaraja, Yuni K
2013-02-01
Compensating for the collimator-detector response (CDR) in SPECT is important for accurate quantification. The CDR consists of both a geometric response and a septal penetration and collimator scatter response. The geometric response can be modeled analytically and is often used for modeling the whole CDR if the geometric response dominates. However, for radionuclides that emit medium or high-energy photons such as I-131, the septal penetration and collimator scatter response is significant and its modeling in the CDR correction is important for accurate quantification. There are two main methods for modeling the depth-dependent CDR so as to include both the geometric response and the septal penetration and collimator scatter response. One is to fit a Gaussian plus exponential function that is rotationally invariant to the measured point source response at several source-detector distances. However, a rotationally-invariant exponential function cannot represent the star-shaped septal penetration tails in detail. Another is to perform Monte-Carlo (MC) simulations to generate the depth-dependent point spread functions (PSFs) for all necessary distances. However, MC simulations, which require careful modeling of the SPECT detector components, can be challenging and accurate results may not be available for all of the different SPECT scanners in clinics. In this paper, we propose an alternative approach to CDR modeling. We use a Gaussian function plus a 2-D B-spline PSF template and fit the model to measurements of an I-131 point source at several distances. The proposed PSF-template-based approach is nearly non-parametric, captures the characteristics of the septal penetration tails, and minimizes the difference between the fitted and measured CDR at the distances of interest. The new model is applied to I-131 SPECT reconstructions of experimental phantom measurements, a patient study, and a MC patient simulation study employing the XCAT phantom. The proposed model
Harr, Jeffrey N; Moore, Ernest E; Ghasabyan, Arsen; Chin, Theresa L; Sauaia, Angela; Banerjee, Anirban; Silliman, Christopher C
2013-01-01
Thromboelastography (TEG) is emerging as the standard in the management of acute coagulopathies in injured patients. Although TEG is sensitive in detecting abnormalities in clot strength, one shortcoming is differentiating between fibrinogen and platelet contributions to clot integrity. Current American algorithms suggest platelet transfusion, whereas European guidelines suggest fibrinogen concentrates for correcting low clot strength. Therefore, we hypothesized that a TEG-based functional fibrinogen (FF) assay would assess the contribution of fibrinogen and platelets to clot strength and provide insight to transfusion priorities. Blood samples were obtained from trauma patients on arrival to the emergency department or who were admitted to the surgical intensive care unit (n = 68). Citrated kaolin TEG, FF, and von Clauss fibrinogen levels (plasma-based clinical standard) were measured. Correlations were assessed using linear regression models. In vitro studies were also performed with adding fibrinogen concentrates to blood collected from healthy volunteers (n = 10). Functional fibrinogen and citrated kaolin TEG parameters were measured. Functional fibrinogen strongly correlated with von Clauss fibrinogen levels (R = 0.87) and clot strength (R = 0.80). The mean fibrinogen contribution to clot strength was 30%; however, there was a direct linear relationship with fibrinogen level and percent fibrinogen contribution to clot strength (R = 0.83). Traditional TEG parameters associated with fibrinogen activity (α angle and kinetic time) had significantly lower correlations with FF (R = 0.70 and 0.35). Furthermore, platelet count had only a moderate correlation to clot strength (R = 0.51). The addition of fibrinogen concentrate in in vitro studies increased clot strength (MA) (60.44 ± 1.48 to 68.12 ± 1.39) and percent fibrinogen contribution to clot strength (23.8% ± 1.8% to 37.7% ± 2.5%). Functional fibrinogen can be performed rapidly with TEG and correlates well
Cerdá, Xim; Retana, Javier
2015-01-01
We analyze the relative contribution of environmental and spatial variables to the alpha and beta components of taxonomic (TD), phylogenetic (PD), and functional (FD) diversity in ant communities found along different climate and anthropogenic disturbance gradients across western and central Europe, in order to assess the mechanisms structuring ant biodiversity. To this aim we calculated alpha and beta TD, PD, and FD for 349 ant communities, which included a total of 155 ant species; we examined 10 functional traits and phylogenetic relatedness. Variation partitioning was used to examine how much variation in ant diversity was explained by environmental and spatial variables. Autocorrelation in diversity measures and each trait’s phylogenetic signal were also analyzed. We found strong autocorrelation in diversity measures. Both environmental and spatial variables significantly contributed to variation in TD, PD, and FD at both alpha and beta scales; spatial structure had the larger influence. The different facets of diversity showed similar patterns along environmental gradients. Environment explained a much larger percentage of variation in FD than in TD or PD. All traits demonstrated strong phylogenetic signals. Our results indicate that environmental filtering and dispersal limitations structure all types of diversity in ant communities. Strong dispersal limitations appear to have led to clustering of TD, PD, and FD in western and central Europe, probably because different historical and evolutionary processes generated different pools of species. Remarkably, these three facets of diversity showed parallel patterns along environmental gradients. Trait-mediated species sorting and niche conservatism appear to structure ant diversity, as evidenced by the fact that more variation was explained for FD and that all traits had strong phylogenetic signals. Since environmental variables explained much more variation in FD than in PD, functional diversity should be a
Arnan, Xavier; Cerdá, Xim; Retana, Javier
2015-01-01
We analyze the relative contribution of environmental and spatial variables to the alpha and beta components of taxonomic (TD), phylogenetic (PD), and functional (FD) diversity in ant communities found along different climate and anthropogenic disturbance gradients across western and central Europe, in order to assess the mechanisms structuring ant biodiversity. To this aim we calculated alpha and beta TD, PD, and FD for 349 ant communities, which included a total of 155 ant species; we examined 10 functional traits and phylogenetic relatedness. Variation partitioning was used to examine how much variation in ant diversity was explained by environmental and spatial variables. Autocorrelation in diversity measures and each trait's phylogenetic signal were also analyzed. We found strong autocorrelation in diversity measures. Both environmental and spatial variables significantly contributed to variation in TD, PD, and FD at both alpha and beta scales; spatial structure had the larger influence. The different facets of diversity showed similar patterns along environmental gradients. Environment explained a much larger percentage of variation in FD than in TD or PD. All traits demonstrated strong phylogenetic signals. Our results indicate that environmental filtering and dispersal limitations structure all types of diversity in ant communities. Strong dispersal limitations appear to have led to clustering of TD, PD, and FD in western and central Europe, probably because different historical and evolutionary processes generated different pools of species. Remarkably, these three facets of diversity showed parallel patterns along environmental gradients. Trait-mediated species sorting and niche conservatism appear to structure ant diversity, as evidenced by the fact that more variation was explained for FD and that all traits had strong phylogenetic signals. Since environmental variables explained much more variation in FD than in PD, functional diversity should be a
Prediction of d^0 magnetism in self-interaction corrected density functional theory
NASA Astrophysics Data System (ADS)
Das Pemmaraju, Chaitanya
2010-03-01
Over the past couple of years, the phenomenon of ``d^0 magnetism'' has greatly intrigued the magnetism community [1]. Unlike conventional magnetic materials, ``d^0 magnets'' lack any magnetic ions with open d or f shells but surprisingly, exhibit signatures of ferromagnetism often with a Curie temperature exceeding 300 K. Current research in the field is geared towards trying to understand the mechanism underlying this observed ferromagnetism which is difficult to explain within the conventional m-J paradigm [1]. The most widely studied class of d^0 materials are un-doped and light element doped wide gap Oxides such as HfO2, MgO, ZnO, TiO2 all of which have been put forward as possible d0 ferromagnets. General experimental trends suggest that the magnetism is a feature of highly defective samples leading to the expectation that the phenomenon must be defect related. In particular, based on density functional theory (DFT) calculations acceptor defects formed from the O-2p states in these Oxides have been proposed as being responsible for the ferromagnetism [2,3]. However. predicting magnetism originating from 2p orbitals is a delicate problem, which depends on the subtle interplay between covalency and Hund's coupling. DFT calculations based on semi-local functionals such as the local spin-density approximation (LSDA) can lead to qualitative failures on several fronts. On one hand the excessive delocalization of spin-polarized holes leads to half-metallic ground states and the expectation of room-temperature ferromagnetism. On the other hand, in some cases a magnetic ground state may not be predicted at all as the Hund's coupling might be under estimated. Furthermore, polaronic distortions which are often a feature of acceptor defects in Oxides are not predicted [4,5]. In this presentation, we argue that the self interaction error (SIE) inherent to semi-local functionals is responsible for the failures of LSDA and demonstrate through various examples that beyond
Zhang, Zengcui; Belcram, Harry; Gornicki, Piotr; Charles, Mathieu; Just, Jérémy; Huneau, Cécile; Magdelenat, Ghislaine; Couloux, Arnaud; Samain, Sylvie; Gill, Bikram S.; Rasmussen, Jack B.; Barbe, Valérie; Faris, Justin D.; Chalhoub, Boulos
2011-01-01
The Q gene encodes an AP2-like transcription factor that played an important role in domestication of polyploid wheat. The chromosome 5A Q alleles (5AQ and 5Aq) have been well studied, but much less is known about the q alleles on wheat homoeologous chromosomes 5B (5Bq) and 5D (5Dq). We investigated the organization, evolution, and function of the Q/q homoeoalleles in hexaploid wheat (Triticum aestivum L.). Q/q gene sequences are highly conserved within and among the A, B, and D genomes of hexaploid wheat, the A and B genomes of tetraploid wheat, and the A, S, and D genomes of the diploid progenitors, but the intergenic regions of the Q/q locus are highly divergent among homoeologous genomes. Duplication of the q gene 5.8 Mya was likely followed by selective loss of one of the copies from the A genome progenitor and the other copy from the B, D, and S genomes. A recent V329-to-I mutation in the A lineage is correlated with the Q phenotype. The 5Bq homoeoalleles became a pseudogene after allotetraploidization. Expression analysis indicated that the homoeoalleles are coregulated in a complex manner. Combined phenotypic and expression analysis indicated that, whereas 5AQ plays a major role in conferring domestication-related traits, 5Dq contributes directly and 5Bq indirectly to suppression of the speltoid phenotype. The evolution of the Q/q loci in polyploid wheat resulted in the hyperfunctionalization of 5AQ, pseudogenization of 5Bq, and subfunctionalization of 5Dq, all contributing to the domestication traits. PMID:22042872
NASA Astrophysics Data System (ADS)
Nasser, Jamil A.; Chassagne, Luc; Topçu, Suat; Linares, Jorge; Alayli, Yasser
2014-03-01
In spin-conversion (SC) compounds containing molecules organized around an iron (II) ion the fundamental level of the ion is low spin (LS), S = 0, and its first excited one is high spin (HS), S = 2. This energy diagram is due to the ligands field interaction on 3d electrons and to the spin pairing energy. Heating the compound increases the magnetic susceptibility which corresponds to a change of populations of both levels and consequently a change of spin value of the molecules. This mechanism, called spin conversion (SC), can be accompagnied by thermal hysteresis observed by studying magnetic susceptibility or high spin fraction. In that case one considers that the (SC) takes place through a first-order phase transition due to intermolecular interactions. In the atom-phonon coupling model the molecules are considered as two-level systems, or two-level atoms, and it is assumed that the elastic force constant value of the spring which links two atoms first neighbours is depending on the electronic states of both atoms. In this study we calculate the partition function of a linear chain of N atoms (N ≤ 16) and we describe the role of phonons and that of the parameter Δ which corresponds to the distance in energy between both levels. The chain free-energy function is Fatph. We introduce for the chain a free-energy function defined by the set (FHS, FLS, Fbarr) and we show that Fatph tends towards the previous set when N → ∞. The previous set allows to describe a first order phase transition between a (LS) phase and a (HS) one. At the crossing point between the function FLS and FHS, and around this point, there is an intermediate free-energy barrier which prevents the chain to change phase which can lead to thermal hysteresis. The energy gap between the free-energy function Fatph and that defined by the set (FHS, FLS, Fbarr) is small. So we can expect that a nanoparticule takes for free-energy function that defined by the set and then displays a thermal
Brigadoi, Sabrina; Ceccherini, Lisa; Cutini, Simone; Scarpa, Fabio; Scatturin, Pietro; Selb, Juliette; Gagnon, Louis; Boas, David A.; Cooper, Robert J.
2013-01-01
Motion artifacts are a significant source of noise in many functional near-infrared spectroscopy (fNIRS) experiments. Despite this, there is no well-established method for their removal. Instead, functional trials of fNIRS data containing a motion artifact are often rejected completely. However, in most experimental circumstances the number of trials is limited, and multiple motion artifacts are common, particularly in challenging populations. Many methods have been proposed recently to correct for motion artifacts, including principle component analysis, spline interpolation, Kalman filtering, wavelet filtering and correlation-based signal improvement. The performance of different techniques has been often compared in simulations, but only rarely has it been assessed on real functional data. Here, we compare the performance of these motion correction techniques on real functional data acquired during a cognitive task, which required the participant to speak aloud, leading to a low-frequency, low-amplitude motion artifact that is correlated with the hemodynamic response. To compare the efficacy of these methods, objective metrics related to the physiology of the hemodynamic response have been derived. Our results show that it is always better to correct for motion artifacts than reject trials, and that wavelet filtering is the most effective approach to correcting this type of artifact, reducing the area under the curve where the artifact is present in 93% of the cases. Our results therefore support previous studies that have shown wavelet filtering to be the most promising and powerful technique for the correction of motion artifacts in fNIRS data. The analyses performed here can serve as a guide for others to objectively test the impact of different motion correction algorithms and therefore select the most appropriate for the analysis of their own fNIRS experiment. PMID:23639260
Brigadoi, Sabrina; Ceccherini, Lisa; Cutini, Simone; Scarpa, Fabio; Scatturin, Pietro; Selb, Juliette; Gagnon, Louis; Boas, David A; Cooper, Robert J
2014-01-15
Motion artifacts are a significant source of noise in many functional near-infrared spectroscopy (fNIRS) experiments. Despite this, there is no well-established method for their removal. Instead, functional trials of fNIRS data containing a motion artifact are often rejected completely. However, in most experimental circumstances the number of trials is limited, and multiple motion artifacts are common, particularly in challenging populations. Many methods have been proposed recently to correct for motion artifacts, including principle component analysis, spline interpolation, Kalman filtering, wavelet filtering and correlation-based signal improvement. The performance of different techniques has been often compared in simulations, but only rarely has it been assessed on real functional data. Here, we compare the performance of these motion correction techniques on real functional data acquired during a cognitive task, which required the participant to speak aloud, leading to a low-frequency, low-amplitude motion artifact that is correlated with the hemodynamic response. To compare the efficacy of these methods, objective metrics related to the physiology of the hemodynamic response have been derived. Our results show that it is always better to correct for motion artifacts than reject trials, and that wavelet filtering is the most effective approach to correcting this type of artifact, reducing the area under the curve where the artifact is present in 93% of the cases. Our results therefore support previous studies that have shown wavelet filtering to be the most promising and powerful technique for the correction of motion artifacts in fNIRS data. The analyses performed here can serve as a guide for others to objectively test the impact of different motion correction algorithms and therefore select the most appropriate for the analysis of their own fNIRS experiment.
NASA Astrophysics Data System (ADS)
Song, Jong-Won; Watson, Mark A.; Sekino, Hideo; Hirao, Kimihiko
2008-07-01
Polarizabilities (α), second-hyperpolarizabilities (γ), and the γ scaling factors (c) of polyynes [H -(C≡C)n-H, n =1-8] were evaluated using the long-range corrected (LC) density functional theory (DFT) and LC-DFT with a short-range Gaussian attenuation (LCgau), as well as high quality wavefunction methods. We show that the c values obtained from LC- and LCgau-DFT are consistent with those from CCSD(T ) calculations. Furthermore, the polyyne c values we obtained are seen to be smaller than the c values derived from previously calculated polyene γ values [Sekino et al., J. Chem. Phys. 126, 014107 (2007)] in all the methods we consider. We compare our results with those obtained experimentally [Shepkov et al., J. Chem. Phys. 120, 6807 (2004).] from end-capped polyynes [i-Pr3Si—(C≡C)n—Sii-Pr3], which show larger c values for polyynes than polyenes. Our α and γ calculations with i-Pr3Si—(C ≡C)n—Sii-Pr3 (n =4,5,6, and 8) show that i-Pr3Si— may participate in π molecular orbital delocalization, which can unexpectedly affect the c value. We also confirm the importance of molecular geometry in these nonlinear optical calculations. We find that while LC- and LCgau-DFT excellently reproduce experimental geometries and bond length alternation (BLA), MP2 optimized geometries have a BLA that is too short to be used for accurate α and γ calculations.
NASA Astrophysics Data System (ADS)
Eom, J.; Seo, K. W.
2015-12-01
Since its launch in March 2002, the Gravity Recovery And Climate Experiment (GRACE) has provided monthly geopotential fields represented by Stokes coefficients of spherical harmonics (SH). Nominally, GRACE gravity solutions exclude effects from tides, ocean dynamics and barometric pressure by incorporating geophysical models for them. However, those models are imperfect, and thus GRACE solutions include the residual gravity effects. Particularly, unmodeled gravity variations of sub-monthly or shorter time scale cause aliasing error, which produces peculiar longitudinal stripes. Those north-south patterns are removed by spatial filtering, but caution is necessary for the aliasing correction because signals with longitudinal patterns are possibly removed during the procedure. This would be particularly problematic for studies associated with Greenland ice mass balance since large ice mass variations are expected in the West and South-West coast of Greenland that are elongated along the longitudinal direction. In this study, we develop a novel method to remove the correlation error using extended Empirical Orthogonal Function (extended EOF). The extended EOF is useful to separate spatially and temporally coherent signal from high frequency variations. Since temporal variability of the correlation error is high, the error is possibly removed via the extended EOF. Ice mass variations reduced by the extended EOF show more detail patterns of ice mass loss/gain than those from the conventional spatial filtering. Large amount of ice loss has occurred along the West, South-West and East coastal area during summer. The extended EOF is potentially useful to enhance signal to noise ratio and increase spatial resolution of GRACE data.
Ribera, Albert; Haurigot, Virginia; Garcia, Miguel; Marcó, Sara; Motas, Sandra; Villacampa, Pilar; Maggioni, Luca; León, Xavier; Molas, Maria; Sánchez, Víctor; Muñoz, Sergio; Leborgne, Christian; Moll, Xavier; Pumarola, Martí; Mingozzi, Federico; Ruberte, Jesús; Añor, Sònia; Bosch, Fatima
2015-04-01
Gene therapy is an attractive tool for the treatment of monogenic disorders, in particular for lysosomal storage diseases (LSD) caused by deficiencies in secretable lysosomal enzymes in which neither full restoration of normal enzymatic activity nor transduction of all affected cells are necessary. However, some LSD such as Mucopolysaccharidosis Type IIIB (MPSIIIB) are challenging because the disease's main target organ is the brain and enzymes do not efficiently cross the blood-brain barrier even if present at very high concentration in circulation. To overcome these limitations, we delivered AAV9 vectors encoding for α-N-acetylglucosaminidase (NAGLU) to the Cerebrospinal Fluid (CSF) of MPSIIIB mice with the disease already detectable at biochemical, histological and functional level. Restoration of enzymatic activity in Central Nervous System (CNS) resulted in normalization of glycosaminoglycan content and lysosomal physiology, resolved neuroinflammation and restored the pattern of gene expression in brain similar to that of healthy animals. Additionally, transduction of the liver due to passage of vectors to the circulation led to whole-body disease correction. Treated animals also showed reversal of behavioural deficits and extended lifespan. Importantly, when the levels of enzymatic activity were monitored in the CSF of dogs following administration of canine NAGLU-coding vectors to animals that were either naïve or had pre-existing immunity against AAV9, similar levels of activity were achieved, suggesting that CNS efficacy would not be compromised in patients seropositive for AAV9. Our studies provide a strong rationale for the clinical development of this novel therapeutic approach as the treatment for MPSIIIB.
Garza, Jorge; Nichols, Jeffrey A.; Dixon, David A.
2000-05-08
The Krieger, Li, and Iafrate approximation to the optimized effective potential including the self-interaction correction for density functional theory has been implemented in a molecular code, NWChem, that uses Gaussian functions to represent the Kohn and Sham spin-orbitals. The differences between the implementation of the self-interaction correction in codes where planewaves are used with an optimized effective potential are discussed. The importance of the localization of the spin-orbitals to maximize the exchange-correlation of the self-interaction correction is discussed. We carried out exchange-only calculations to compare the results obtained with these approximations, and those obtained with the local spin density approximation, the generalized gradient approximation and Hartree-Fock theory. Interesting results for the energy difference (GAP) between the highest occupied molecular orbital, HOMO, and the lowest unoccupied molecular orbital, LUMO, (spin-orbital energies of closed shell atoms and molecules) using the optimized effective potential and the self-interaction correction have been obtained. The effect of the diffuse character of the basis set on the HOMO and LUMO eigenvalues at the various levels is discussed. Total energies obtained with the optimized effective potential and the self-interaction correction show that the exchange energy with these approximations is overestimated and this will be an important topic for future work. (c) 2000 American Institute of Physics.
NASA Technical Reports Server (NTRS)
Langhoff, S. R.; Scott, W. R.; Suzuki, N.; Chong, D. P.
1979-01-01
Ordinary Rayleigh-Schroudinger perturbation theory with Moller-Plesset (RSMP) partitioning is used to calculate second- and third-order correlation corrections to the CHF polarizability and dipole moment of the water molecule by a finite-field procedure. Pade approximants are found to be useful in accelerating the convergence of the property perturbation expansions. Field-induced polarization functions suitable for polarizability calculations are determined. The average polarizability calculated, neglecting vibrational averaging, with Dunning's (9s5p/4s-4s2p/2s) contracted GTO basis set augmented by field-induced lslp2d/lp polarization functions is within 3 per cent of the experimental result. Correlation corrections to the dipole moment and polarizability of the water molecule calculated by the finite-field RSMP and single + double excitation CI(SDCI) methods for the same basis set are found to be in close agreement. The RSMP approach has the advantages of being size-consistent and of being capable of greater efficiency than the SCDI method. Comparative calculations carried out using Epstein-Nesbet partitioning show that through third order RSEN correlation perturbation expansions for the dipole moment and polarizability are less rapidly convergent than RSMP expansions. However, reasonable accord with RSMP results can be achieved by using Pade approximants to accelerate the convergence of RSEN energy perturbation expansions. The convergence of RSMP property correlation expansions based on the zeroth-order uncoupled-Hartree-Fock (UCHF) and coupled-Hartree-Fock (CHF) approximations are compared through third order. Whereas the CHF + RSMP expansions are for practical purposes fully converged, the UCHF + RSMP expansions are not adequately converged.
Jeong, Yoonah; Schäffer, Andreas; Smith, Kilian
2017-05-01
Oasis hydrophilic lipophilic balance(®) (Oasis HLB) is commonly employed in solid phase extraction (SPE) of environmental contaminants and within polar organic chemical integrative passive samplers (POCIS). In this study batch experiments were carried out to evaluate the relative affinity of a range of relevant organic pollutants to Oasis HLB in aqueous systems. The influence of sorbate concentration, temperature, pH, and salinity on the equilibrium sorption was investigated. Equilibrium partition ratios (KD) of 28 compounds were determined, ranging over three orders of magnitude from 1.16 × 10(3) L/kg (atenolol) to 1.07 × 10(6) L/kg (isoproturon). The Freundlich model was able to describe the equilibrium partitioning to Oasis HLB, and an analysis of the thermodynamic parameters revealed the spontaneous and exothermic nature of the partitioning process. Ionic strength had only a minor effect on the partitioning, whereas pH had a considerable effect but only for ionizable compounds. The results show that apolar interactions between the Oasis HLB and analyte mainly determine the equilibrium partitioning. These research findings can be used to optimize the application of SPE and POCIS for analyses of environmental contaminants even in complex mixtures.
Kushner, Adam M.; Brent, Jensen L.; Schoenfeld, Brad J.; Hugentobler, Jason; Lloyd, Rhodri S.; Vermeil, Al; Chu, Donald A.; Harbin, Jason; McGill, Stuart M.; Myer, Gregory D.
2015-01-01
The back squat is a well-researched and widely used exercise to enhance fundamental movement competency that creates a foundation for optimal mechanical strategies during a broad range of activities. The primary commentary introduced the Back Squat Assessment (BSA): a criterion based assessment of the back squat that delineates 30 potentially observable functional deficits. This follow-up commentary provides a targeted system of training cues and exercises to supplement the BSA to guide corrective intervention. We propose a criterion driven approach to corrective exercise that can support practitioners in their goal to help individuals achieve movement competency in the back squat. PMID:26823657
Kushner, Adam M; Brent, Jensen L; Schoenfeld, Brad J; Hugentobler, Jason; Lloyd, Rhodri S; Vermeil, Al; Chu, Donald A; Harbin, Jason; McGill, Stuart M; Myer, Gregory D
2015-04-01
The back squat is a well-researched and widely used exercise to enhance fundamental movement competency that creates a foundation for optimal mechanical strategies during a broad range of activities. The primary commentary introduced the Back Squat Assessment (BSA): a criterion based assessment of the back squat that delineates 30 potentially observable functional deficits. This follow-up commentary provides a targeted system of training cues and exercises to supplement the BSA to guide corrective intervention. We propose a criterion driven approach to corrective exercise that can support practitioners in their goal to help individuals achieve movement competency in the back squat.
Pavlov, F. F.
2012-06-15
The relativistic deuteron has been considered in the light-cone formalism as a system of two strongly interacting nucleons (two-nucleon approximation). The technique for the calculation of the average helicity of the proton in the deuteron has been considered in the light-cone variables. A receipt has been pro-posed for the consistent calculation of relativistic nuclear corrections to the average helicity of the proton in the deuteron and to the spin structure function of the deuteron g{sub 1}{sup D}. Relativistic-correction-induced change in the Bjorken sum rule has been discussed.
Arensman, F W; Radley-Smith, R; Grieve, L; Gibson, D G; Yacoub, M H
1986-01-01
Left ventricular function before and after anatomical correction of transposition of the great arteries was assessed by computer assisted analysis of 78 echocardiographs from 27 patients obtained one year before to five years after operation. Sixteen patients had simple transposition, and 11 had complex transposition with additional large ventricular septal defect. Immediately after correction mean shortening fraction fell from 46(9)% to 33(8)%. There was a corresponding drop in normalised peak shortening rate from 5.4(3.7) to 3.3(1.1) s-1 and normal septal motion was usually absent. Systolic shortening fraction increased with time after correction and left ventricular end diastolic diameter increased appropriately for age. The preoperative rate of free wall thickening was significantly higher in simple (5.6(2.8) s-1) and complex transposition (4.5(1.8) s-1) than in controls (2.9(0.8) s-1). After operation these values remained high in both the short and long term. Thus, computer assisted analysis of left ventricular dimensions and their rates of change before and after anatomical correction showed only slight postoperative changes which tended to become normal with time. Septal motion was commonly absent after operation. This was associated with an increase in the rate of posterior wall thickening that suggested normal ventricular function associated with an altered contraction pattern. Computer assisted echocardiographic analysis may be helpful in the long term assessment of ventricular function after operation for various heart abnormalities. PMID:3942650
Zaghloul, Mofreh R.
2010-12-15
The problem of the calculation of equilibrium thermodynamic properties and the establishment of statistical-thermodynamically consistent finite bound-state partition functions in nonideal multicomponent plasma systems is revised within the chemical picture. The present exploration accompanied by the introduction of a generalized consistent formulation, in terms of the solution of the inverse problem, clears ambiguities and gives a better understanding of the problem on top of pointing out weaknesses and inaccuracies/inconsistencies buried in widely used models in literature.
A table of integrals of the error function. II - Additions and corrections.
NASA Technical Reports Server (NTRS)
Geller, M.; Ng, E. W.
1971-01-01
Integrals of products of error functions with other functions are presented, taking into account a combination of the error function with powers, a combination of the error function with exponentials and powers, a combination of the error function with exponentials of more complicated arguments, definite integrals from Laplace transforms, and a combination of the error function with trigonometric functions. Other integrals considered include a combination of the error function with logarithms and powers, a combination of two error functions, and a combination of the error function with other special functions.
A table of integrals of the error function. II - Additions and corrections.
NASA Technical Reports Server (NTRS)
Geller, M.; Ng, E. W.
1971-01-01
Integrals of products of error functions with other functions are presented, taking into account a combination of the error function with powers, a combination of the error function with exponentials and powers, a combination of the error function with exponentials of more complicated arguments, definite integrals from Laplace transforms, and a combination of the error function with trigonometric functions. Other integrals considered include a combination of the error function with logarithms and powers, a combination of two error functions, and a combination of the error function with other special functions.
Peña, Javier; Ojeda, Natalia; Segarra, Rafael; Eguiluz, Jose Ignacio; García, Jon; Gutiérrez, Miguel
2011-03-01
Few studies have analysed factors that predict the ultimate clinical diagnosis in first-episode psychosis (FEP), and none has included cognitive factors. Eighty-six FEP patients and 34 healthy controls were recruited and followed up for two years. Positive and negative symptoms, depression, mania, duration of untreated psychosis (DUP), premorbid functioning, functional outcome and neurocognition were assessed over 2 years. Logistic regression models revealed that Wisconsin Card Sorting Test correctly distinguished the patients ultimately diagnosed with schizophrenia (87%) from those with bipolar disorder (80%) and those with other psychoses (85%), for an overall correct-diagnosis rate of 84.4%. The prediction was stable despite the inclusion of clinical and affective symptoms, DUP, clinical impression, and functional outcome scores. Results highlight the importance of reconsidering neurocognition as a diagnostic criterion for psychosis and schizophrenia.
Nandi, Prithwish Kumar; Valsakumar, M C; Chandra, Sharat; Sahu, H K; Sundar, C S
2010-09-01
We calculate properties like equilibrium lattice parameter, bulk modulus and monovacancy formation energy for nickel (Ni), iron (Fe) and chromium (Cr) using Kohn-Sham density functional theory (DFT). We compare the relative performance of local density approximation (LDA) and generalized gradient approximation (GGA) for predicting such physical properties for these metals. We also make a relative study between two different flavors of GGA exchange correlation functional, namely PW91 and PBE. These calculations show that there is a discrepancy between DFT calculations and experimental data. In order to understand this discrepancy in the calculation of vacancy formation energy, we introduce a correction for the surface intrinsic error corresponding to an exchange correlation functional using the scheme implemented by Mattsson et al (2006 Phys. Rev. B 73 195123) and compare the effectiveness of the correction scheme for Al and the 3d transition metals.
Carbon partitioning in photosynthesis.
Melis, Anastasios
2013-06-01
The work seeks to raise awareness of a fundamental problem that impacts the renewable generation of fuels and chemicals via (photo)synthetic biology. At issue is regulation of the endogenous cellular carbon partitioning between different biosynthetic pathways, over which the living cell exerts stringent control. The regulation of carbon partitioning in photosynthesis is not understood. In plants, microalgae and cyanobacteria, methods need be devised to alter photosynthetic carbon partitioning between the sugar, terpenoid, and fatty acid biosynthetic pathways, to lower the prevalence of sugar biosynthesis and correspondingly upregulate terpenoid and fatty acid hydrocarbons production in the cell. Insight from unusual but naturally occurring carbon-partitioning processes can help in the design of blueprints for improved photosynthetic fuels and chemicals production. Copyright © 2013 Elsevier Ltd. All rights reserved.
Dynamical Correction to Linear Kohn-Sham Conductances from Static Density Functional Theory
NASA Astrophysics Data System (ADS)
Kurth, S.; Stefanucci, G.
2013-07-01
For molecules weakly coupled to leads the exact linear Kohn-Sham (KS) conductance can be orders of magnitude larger than the true linear conductance due to the lack of dynamical exchange-correlation (xc) corrections. In this work we show how to incorporate dynamical effects in KS transport calculations. The only quantity needed is the static xc potential in the molecular junction. Our scheme provides a comprehensive description of Coulomb blockade without breaking the spin symmetry. This is explicitly demonstrated in single-wall nanotubes where the corrected conductance is in good agreement with experimental data whereas the KS conductance fails dramatically.
NASA Astrophysics Data System (ADS)
Oprea, Corneliu I.; Rinkevicius, Zilvinas; Vahtras, Olav; Ågren, Hans; Ruud, Kenneth
2005-07-01
This work outlines the calculation of indirect nuclear spin-spin coupling constants with spin-orbit corrections using density functional response theory. The nonrelativistic indirect nuclear spin-spin couplings are evaluated using the linear response method, whereas the relativistic spin-orbit corrections are computed using quadratic response theory. The formalism is applied to the homologous systems H2X (X=O,S,Se,Te) and XH4 (X =C,Si,Ge,Sn,Pb) to calculate the indirect nuclear spin-spin coupling constants between the protons. The results confirm that spin-orbit corrections are important for compounds of the H2X series, for which the electronic structure allows for an efficient coupling between the nuclei mediated by the spin-orbit interaction, whereas in the case of the XH4 series the opposite situation is encountered and the spin-orbit corrections are negligible for all compounds of this series. In addition we analyze the performance of the density functional theory in the calculations of nonrelativistic indirect nuclear spin-spin coupling constants.
The Benefits of Adaptive Partitioning for Parallel AMR Applications
Steensland, Johan
2008-07-01
Parallel adaptive mesh refinement methods potentially lead to realistic modeling of complex three-dimensional physical phenomena. However, the dynamics inherent in these methods present significant challenges in data partitioning and load balancing. Significant human resources, including time, effort, experience, and knowledge, are required for determining the optimal partitioning technique for each new simulation. In reality, scientists resort to using the on-board partitioner of the computational framework, or to using the partitioning industry standard, ParMetis. Adaptive partitioning refers to repeatedly selecting, configuring and invoking the optimal partitioning technique at run-time, based on the current state of the computer and application. In theory, adaptive partitioning automatically delivers superior performance and eliminates the need for repeatedly spending valuable human resources for determining the optimal static partitioning technique. In practice, however, enabling frameworks are non-existent due to the inherent significant inter-disciplinary research challenges. This paper presents a study of a simple implementation of adaptive partitioning and discusses implied potential benefits from the perspective of common groups of users within computational science. The study is based on a large set of data derived from experiments including six real-life, multi-time-step adaptive applications from various scientific domains, five complementing and fundamentally different partitioning techniques, a large set of parameters corresponding to a wide spectrum of computing environments, and a flexible cost function that considers the relative impact of multiple partitioning metrics and diverse partitioning objectives. The results show that even a simple implementation of adaptive partitioning can automatically generate results statistically equivalent to the best static partitioning. Thus, it is possible to effectively eliminate the problem of determining the
NASA Astrophysics Data System (ADS)
Okura, Yuki; Futamase, Toshifumi
2011-03-01
We develop a new method of estimating gravitational shear by adopting an elliptical weight function to measure background galaxy images. In doing so, we introduce the new concept of "zero plane," which is an imaginary source plane where shapes of all sources are perfect circles, and regard the intrinsic shear as the result of an imaginary lensing distortion. This makes the relation between the observed shear, intrinsic shear, and lensing distortion much simpler, and thus higher-order calculations are easier. The elliptical weight function allows us to measure the multipole moments of the shapes of background galaxies more precisely by weighting brighter parts of the image highly, and to reduce systematic error due to insufficient expansion of the weight function in the original approach of Kaiser et al. (KSB). Point-spread function (PSF) correction in the elliptically weighted higher-order lensing image characteristics (E-HOLICs) method becomes more complicated than in the KSB method. In this paper, we study isotropic PSF correction in detail. By adopting the lensing distortion as the ellipticity of the weight function, we are able to show that the shear estimation in the E-HOLICs method reduces to solve a polynomial in the absolute magnitude of the distortion. We compare the systematic errors between our approach and that of KSB using the Shear Testing Programme 2 simulation. It is confirmed that the KSB method overestimates the input shear for images with large ellipticities, and E-HOLICs correctly estimates the input shear even for such images. Anisotropic PSF correction and analysis of real data will be presented in a forthcoming paper.
NASA Astrophysics Data System (ADS)
Göltl, Florian; Hafner, Jürgen
2012-02-01
The structural and energetic properties of purely siliceous, proton-, and Cu- and Co-exchanged chabazite have been studied using periodic density-functional (DFT) calculations with both conventional gradient-corrected exchange-correlation functionals and hybrid functionals mixing exact (i.e., Hartree-Fock) and DFT exchange. Spin-polarized and fixed-moment calculations have been performed to determine the equilibrium and excited spin-configurations of the metal-exchanged chabazites. For the purely siliceous chabazite, hybrid functionals predict a slightly more accurate cell volume and lattice geometry. For isolated Al/Si substitution sites, gradient-corrected functionals predict that the lattice distortion induced by the substitution preserves the local tetrahedral symmetry, whereas hybrid functionals lead to a distorted Al coordination with two short and two long Al-O bonds. Hybrid functionals yield a stronger cation-framework binding that conventional functionals in metal-exchanged zeolites, they favor shorter cation-oxygen bonds and eventually also a higher coordination of the cation. Both types of functionals predict the same spin in the ground-state. The structural optimization of the excited spin-states shows that the formation of a high-spin configuration leads to a strong lattice relaxation and a weaker cation-framework bonding. For both Cu- and Co-exchanged chabazite, the prediction of a preferred location of the cation in a six-membered ring of the zeolite agrees with experiment, but the energy differences between possible cation locations and the lattice distortion induced by the Al/Si substitution and the bonding of the cation depends quite significantly on the choice of the functional. All functionals predict similar energy differences for excited spin states. Spin-excitations are shown to be accompanied by significant changes in the cation coordination, which are more pronounced with hybrid functionals. The consequences of electronic spectra and
Mardirossian, Narbe; Head-Gordon, Martin
2014-05-14
The limit of accuracy for semi-empirical generalized gradient approximation (GGA) density functionals is explored by parameterizing a variety of local, global hybrid, and range-separated hybrid functionals. The training methodology employed differs from conventional approaches in 2 main ways: (1) Instead of uniformly truncating the exchange, same-spin correlation, and opposite-spin correlation functional inhomogeneity correction factors, all possible fits up to fourth order are considered, and (2) Instead of selecting the optimal functionals based solely on their training set performance, the fits are validated on an independent test set and ranked based on their overall performance on the training and test sets. The 3 different methods of accounting for exchange are trained both with and without dispersion corrections (DFT-D2 and VV10), resulting in a total of 491 508 candidate functionals. For each of the 9 functional classes considered, the results illustrate the trade-off between improved training set performance and diminished transferability. Since all 491 508 functionals are uniformly trained and tested, this methodology allows the relative strengths of each type of functional to be consistently compared and contrasted. The range-separated hybrid GGA functional paired with the VV10 nonlocal correlation functional emerges as the most accurate form for the present training and test sets, which span thermochemical energy differences, reaction barriers, and intermolecular interactions involving lighter main group elements.
NASA Astrophysics Data System (ADS)
Mardirossian, Narbe; Head-Gordon, Martin
2014-05-01
The limit of accuracy for semi-empirical generalized gradient approximation (GGA) density functionals is explored by parameterizing a variety of local, global hybrid, and range-separated hybrid functionals. The training methodology employed differs from conventional approaches in 2 main ways: (1) Instead of uniformly truncating the exchange, same-spin correlation, and opposite-spin correlation functional inhomogeneity correction factors, all possible fits up to fourth order are considered, and (2) Instead of selecting the optimal functionals based solely on their training set performance, the fits are validated on an independent test set and ranked based on their overall performance on the training and test sets. The 3 different methods of accounting for exchange are trained both with and without dispersion corrections (DFT-D2 and VV10), resulting in a total of 491 508 candidate functionals. For each of the 9 functional classes considered, the results illustrate the trade-off between improved training set performance and diminished transferability. Since all 491 508 functionals are uniformly trained and tested, this methodology allows the relative strengths of each type of functional to be consistently compared and contrasted. The range-separated hybrid GGA functional paired with the VV10 nonlocal correlation functional emerges as the most accurate form for the present training and test sets, which span thermochemical energy differences, reaction barriers, and intermolecular interactions involving lighter main group elements.
NASA Astrophysics Data System (ADS)
Nozdrenko, D. M.; Zavodovskyi, D. O.; Matvienko, T. Yu.; Zay, S. Yu.; Bogutska, K. I.; Prylutskyy, Yu. I.; Ritter, U.; Scharff, P.
2017-02-01
The therapeutic effect of pristine C60 fullerene aqueous colloid solution (C60FAS) on the functioning of the rat soleus muscle at ischemic injury depending on the time of the general pathogenesis of muscular system and method of administration C60FAS in vivo was investigated. It was found that intravenous administration of C60FAS is the optimal for correction of speed macroparameters of contraction for ischemic muscle damage. At the same time, intramuscular administration of C60FAS shows pronounced protective effect in movements associated with the generation of maximum force responses or prolonged contractions, which increase the muscle fatigue level. Analysis of content concentration of creatine phosphokinase and lactate dehydrogenase enzymes in the blood of experimental animals indicates directly that C60FAS may be a promising therapeutic agent for the prevention and correction of ischemic-damaged skeletal muscle function.
Baer, Marcel D; Mundy, Christopher J; McGrath, Matthew J; Kuo, I-F Will; Siepmann, J Ilja; Tobias, Douglas J
2011-09-28
First-principles molecular dynamics simulations, in which the forces are computed from electronic structure calculations, have great potential to provide unique insight into structure, dynamics, electronic properties, and chemistry of interfacial systems that is not available from empirical force fields. The majority of current first-principles simulations are driven by forces derived from density functional theory with generalized gradient approximations to the exchange-correlation energy, which do not capture dispersion interactions. We have carried out first-principles molecular dynamics simulations of air-water interfaces employing a particular generalized gradient approximation to the exchange-correlation functional (BLYP), with and without empirical dispersion corrections. We assess the utility of the dispersion corrections by comparison of a variety of structural, dynamic, and thermodynamic properties of bulk and interfacial water with experimental data, as well as other first-principles and force field-based simulations.
On bottleneck partitioning k-ary n-cubes
NASA Technical Reports Server (NTRS)
Nicol, David M.; Mao, Weizhen
1994-01-01
Graph partitioning is a topic of extensive interest, with applications to parallel processing. In this context graph nodes typically represent computation, and edges represent communication. One seeks to distribute the workload by partitioning the graph so that every processor has approximately the same workload, and the communication cost (measured as a function of edges exposed by the partition) is minimized. Measures of partition quality vary; in this paper we consider a processor's cost to be the sum of its computation and communication costs, and consider the cost of a partition to be the bottleneck, or maximal processor cost induced by the partition. For a general graph the problem of finding an optimal partitioning is intractable. In this paper we restrict our attention to the class of k-art n-cube graphs with uniformly weighted nodes. Given mild restrictions on the node weight and number of processors, we identify partitions yielding the smallest bottleneck. We also demonstrate by example that some restrictions are necessary for the partitions we identify to be optimal. In particular, there exist cases where partitions that evenly partition nodes need not be optimal.
Romanenko, E G
2014-04-01
Morphological changes in the gingiva under the effect of drugs improving microcirculation were studied in pubertal Wistar rats with experimental gastroduodenitis. Chronic gastroduodenitis was induced by intragastric administration of 50% medical bile (1 ml/100 g body weight daily) for 40 days. The best medical correction was attained with altan and citrarginine. Morphologic studies showed signs of regeneration plastic activity of the epithelium, restructuring of the gingival lamina propria, and enlargement of the vascular bed area. Calcium-D3 Nycomed disordered the regeneration processes in the rat epithelium, because of calcium ion capacity to increase oxygen demand in tissues and cause destructive processes. Hence, pathogenetic drug correction of degenerative processes in the gingiva under conditions of chronic gastroduodenitis should include drugs promoting recovery of the microcirculatory bed, altan and citrarginine.
Brandenburg, Jan Gerit; Alessio, Maristella; Civalleri, Bartolomeo; Peintinger, Michael F; Bredow, Thomas; Grimme, Stefan
2013-09-26
We extend the previously developed geometrical correction for the inter- and intramolecular basis set superposition error (gCP) to periodic density functional theory (DFT) calculations. We report gCP results compared to those from the standard Boys-Bernardi counterpoise correction scheme and large basis set calculations. The applicability of the method to molecular crystals as the main target is tested for the benchmark set X23. It consists of 23 noncovalently bound crystals as introduced by Johnson et al. (J. Chem. Phys. 2012, 137, 054103) and refined by Tkatchenko et al. (J. Chem. Phys. 2013, 139, 024705). In order to accurately describe long-range electron correlation effects, we use the standard atom-pairwise dispersion correction scheme DFT-D3. We show that a combination of DFT energies with small atom-centered basis sets, the D3 dispersion correction, and the gCP correction can accurately describe van der Waals and hydrogen-bonded crystals. Mean absolute deviations of the X23 sublimation energies can be reduced by more than 70% and 80% for the standard functionals PBE and B3LYP, respectively, to small residual mean absolute deviations of about 2 kcal/mol (corresponding to 13% of the average sublimation energy). As a further test, we compute the interlayer interaction of graphite for varying distances and obtain a good equilibrium distance and interaction energy of 6.75 Å and -43.0 meV/atom at the PBE-D3-gCP/SVP level. We fit the gCP scheme for a recently developed pob-TZVP solid-state basis set and obtain reasonable results for the X23 benchmark set and the potential energy curve for water adsorption on a nickel (110) surface.
Talbot, Clifford B; Lagarto, João; Warren, Sean; Neil, Mark A A; French, Paul M W; Dunsby, Chris
2015-09-01
A correction is proposed to the Delta function convolution method (DFCM) for fitting a multiexponential decay model to time-resolved fluorescence decay data using a monoexponential reference fluorophore. A theoretical analysis of the discretised DFCM multiexponential decay function shows the presence an extra exponential decay term with the same lifetime as the reference fluorophore that we denote as the residual reference component. This extra decay component arises as a result of the discretised convolution of one of the two terms in the modified model function required by the DFCM. The effect of the residual reference component becomes more pronounced when the fluorescence lifetime of the reference is longer than all of the individual components of the specimen under inspection and when the temporal sampling interval is not negligible compared to the quantity (τR (-1) - τ(-1))(-1), where τR and τ are the fluorescence lifetimes of the reference and the specimen respectively. It is shown that the unwanted residual reference component results in systematic errors when fitting simulated data and that these errors are not present when the proposed correction is applied. The correction is also verified using real data obtained from experiment.
NASA Astrophysics Data System (ADS)
Nath, N. M.; Sarma, J. K.
2017-05-01
A calculation of the non-singlet part of spin dependent structure function, xg1^{NS}(x,Q2) and associated sum rule, the Bjorken Sum rule up to next-next-to-leading order(NNLO) is presented. We use a unified approach incorporating Regge theory and the theoretical framework of perturbative Quantum Chromodynamics. Using a Regge behaved model with Q 2 dependent intercept as the initial input, we have solved the Dokshitzer-Gribov-Lipatov-Altarelli-Parisi (DGLAP) evolution equation up to NNLO at small- x for xg1^{NS}(x,Q2) and the solutions are utilised to calculate the polarised Bjorken sum rule(BSR). We have also extracted the higher twist contribution to BSR based on a simple parametrisation. These results for both of xg1^{NS}(x,Q2) and BSR, along with higher twist corrections are observed to be consistent with the available data taken from SMC, E143, HERMES, COMPASS and JLab experiments. In addition, our results are also compared with that of other theoretical and phenomenological analysis based on different models and a very good agreement is also observed in this regard. Further a very good consistency between our calculated results and theoretical QCD predictions of BSR is also achieved.
Jensen, Lasse; Govind, Niranjan
2009-09-10
In this work, we present a study of the excitation energies of adenine, cytosine, guanine, thymine, and the adenine-thymine (AT) and guanine-cytosine (GC) base pairs using long-range corrected (LC) density functional theory. We compare three recent LC functionals, BNL, CAM-B3LYP, and LC-PBE0, with B3LYP and coupled cluster results from the literature. We find that the best overall performance is for the BNL functional based on LDA. However, in order to achieve this good agreement, a smaller attenuation parameter is needed, which leads to nonoptimum performance for ground-state properties. B3LYP, on the other hand, severely underestimates the charge-transfer (CT) transitions in the base pairs. Surprisingly, we also find that the CAM-B3LYP functional also underestimates the CT excitation energy for the GC base pair but correctly describes the AT base pair. This illustrates the importance of retaining the full long-range exact exchange even at distances as short as that of the DNA base pairs. The worst overall performance is obtained with the LC-PBE0 functional, which overestimates the excitations for the individual bases as well as the base pairs. It is therefore crucial to strike a good balance between the amount of local and long-range exact exchange. Thus, this work highlights the difficulties in obtained LC functionals, which provides a good description of both ground- and excited-state properties.
Excited States of DNA Base Pairs Using Long-Range Corrected Time-Dependent Density Functional Theory
NASA Astrophysics Data System (ADS)
Jensen, Lasse; Govind, Niranjan
2009-08-01
In this work, we present a study of the excitation energies of adenine, cytosine, guanine, thymine, and the adenine-thymine (AT) and guanine-cytosine (GC) base pairs using long-range corrected (LC) density functional theory. We compare three recent LC functionals, BNL, CAM-B3LYP, and LC-PBE0, with B3LYP and coupled cluster results from the literature. We find that the best overall performance is for the BNL functional based on LDA. However, in order to achieve this good agreement, a smaller attenuation parameter is needed, which leads to nonoptimum performance for ground-state properties. B3LYP, on the other hand, severely underestimates the charge-transfer (CT) transitions in the base pairs. Surprisingly, we also find that the CAM-B3LYP functional also underestimates the CT excitation energy for the GC base pair but correctly describes the AT base pair. This illustrates the importance of retaining the full long-range exact exchange even at distances as short as that of the DNA base pairs. The worst overall performance is obtained with the LC-PBE0 functional, which overestimates the excitations for the individual bases as well as the base pairs. It is therefore crucial to strike a good balance between the amount of local and long-range exact exchange. Thus, this work highlights the difficulties in obtained LC functionals, which provides a good description of both ground- and excited-state properties.
Partitioning in Avionics Architectures: Requirements, Mechanisms, and Assurance
NASA Technical Reports Server (NTRS)
Rushby, John
1999-01-01
Automated aircraft control has traditionally been divided into distinct "functions" that are implemented separately (e.g., autopilot, autothrottle, flight management); each function has its own fault-tolerant computer system, and dependencies among different functions are generally limited to the exchange of sensor and control data. A by-product of this "federated" architecture is that faults are strongly contained within the computer system of the function where they occur and cannot readily propagate to affect the operation of other functions. More modern avionics architectures contemplate supporting multiple functions on a single, shared, fault-tolerant computer system where natural fault containment boundaries are less sharply defined. Partitioning uses appropriate hardware and software mechanisms to restore strong fault containment to such integrated architectures. This report examines the requirements for partitioning, mechanisms for their realization, and issues in providing assurance for partitioning. Because partitioning shares some concerns with computer security, security models are reviewed and compared with the concerns of partitioning.
Partitioning Breaks Communities
NASA Astrophysics Data System (ADS)
Reid, Fergal; McDaid, Aaron; Hurley, Neil
Considering a clique as a conservative definition of community structure, we examine how graph partitioning algorithms interact with cliques. Many popular community-finding algorithms partition the entire graph into non-overlapping communities. We show that on a wide range of empirical networks, from different domains, significant numbers of cliques are split across the separate partitions produced by these algorithms. We then examine the largest connected component of the subgraph formed by retaining only edges in cliques, and apply partitioning strategies that explicitly minimise the number of cliques split. We further examine several modern overlapping community finding algorithms, in terms of the interaction between cliques and the communities they find, and in terms of the global overlap of the sets of communities they find. We conclude that, due to the connectedness of many networks, any community finding algorithm that produces partitions must fail to find at least some significant structures. Moreover, contrary to traditional intuition, in some empirical networks, strong ties and cliques frequently do cross community boundaries; much community structure is fundamentally overlapping and unpartitionable in nature.
NASA Astrophysics Data System (ADS)
Chouhan, Manil D.; Bainbridge, Alan; Atkinson, David; Punwani, Shonit; Mookerjee, Rajeshwar P.; Lythgoe, Mark F.; Taylor, Stuart A.
2017-02-01
Liver dynamic contrast enhanced (DCE) MRI pharmacokinetic modelling could be useful in the assessment of diffuse liver disease and focal liver lesions, but is compromised by errors in arterial input function (AIF) sampling. In this study, we apply cardiac output correction to arterial input functions (AIFs) for liver DCE MRI and investigate the effect on dual-input single compartment hepatic perfusion parameter estimation and reproducibility. Thirteen healthy volunteers (28.7 ± 1.94 years, seven males) underwent liver DCE MRI and cardiac output measurement using aortic root phase contrast MRI (PCMRI), with reproducibility (n = 9) measured at 7 d. Cardiac output AIF correction was undertaken by constraining the first pass AIF enhancement curve using the indicator-dilution principle. Hepatic perfusion parameters with and without cardiac output AIF correction were compared and 7 d reproducibility assessed. Differences between cardiac output corrected and uncorrected liver DCE MRI portal venous (PV) perfusion (p = 0.066), total liver blood flow (TLBF) (p = 0.101), hepatic arterial (HA) fraction (p = 0.895), mean transit time (MTT) (p = 0.646), distribution volume (DV) (p = 0.890) were not significantly different. Seven day corrected HA fraction reproducibility was improved (mean difference 0.3%, Bland-Altman 95% limits-of-agreement (BA95%LoA) ±27.9%, coefficient of variation (CoV) 61.4% versus 9.3%, ±35.5%, 81.7% respectively without correction). Seven day uncorrected PV perfusion was also improved (mean difference 9.3 ml min-1/100 g, BA95%LoA ±506.1 ml min-1/100 g, CoV 64.1% versus 0.9 ml min-1/100 g, ±562.8 ml min-1/100 g, 65.1% respectively with correction) as was uncorrected TLBF (mean difference 43.8 ml min-1/100 g, BA95%LoA ±586.7 ml min-1/ 100 g, CoV 58.3% versus 13.3 ml min-1/100 g, ±661.5 ml min-1/100 g, 60.9% respectively with correction
Laskowski, Tamara J; Van Caeneghem, Yasmine; Pourebrahim, Rasoul; Ma, Chao; Ni, Zhenya; Garate, Zita; Crane, Ana M; Li, Xuan Shirley; Liao, Wei; Gonzalez-Garay, Manuel; Segovia, Jose Carlos; Paschon, David E; Rebar, Edward J; Holmes, Michael C; Kaufman, Dan; Vandekerckhove, Bart; Davis, Brian R
2016-08-09
Wiskott-Aldrich syndrome (WAS) is an X-linked primary immunodeficiency disease caused by mutations in the gene encoding the WAS protein (WASp). Here, induced pluripotent stem cells (iPSCs) were derived from a WAS patient (WAS-iPSC) and the endogenous chromosomal WAS locus was targeted with a wtWAS-2A-eGFP transgene using zinc finger nucleases (ZFNs) to generate corrected WAS-iPSC (cWAS-iPSC). WASp and GFP were first expressed in the earliest CD34(+)CD43(+)CD45(-) hematopoietic precursor cells and later in all hematopoietic lineages examined. Whereas differentiation to non-lymphoid lineages was readily obtained from WAS-iPSCs, in vitro T lymphopoiesis from WAS-iPSC was deficient with few CD4(+)CD8(+) double-positive and mature CD3(+) T cells obtained. T cell differentiation was restored for cWAS-iPSCs. Similarly, defects in natural killer cell differentiation and function were restored on targeted correction of the WAS locus. These results demonstrate that the defects exhibited by WAS-iPSC-derived lymphoid cells were fully corrected and suggests the potential therapeutic use of gene-corrected WAS-iPSCs. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.
Diab, Aliaa A; Moustafa, Ibrahim M
2012-04-01
To investigate the effect of forward head posture correction on pain and nerve root function in cases of cervical spondylotic radiculopathy. A randomized controlled study with six months follow-up. University research laboratory. Ninety-six patients with unilateral lower cervical spondylotic radiculopathy (C5-C6 and C6-C7) and craniovertebral angle measured less than or equal to 50° were randomly assigned to an exercise or a control group. The control group (n = 48) received ultrasound and infrared radiation, whereas the exercise group (n = 48) received a posture corrective exercise programme in addition to ultrasound and infrared radiation. The peak-to-peak amplitude of dermatomal somatosensory evoked potentials, craniovertebral angle, visual analogue scale were measured for all patients at three intervals (before treatment, after 10 weeks of treatment, and at follow-up of six months). There was a significant difference between groups adjusted to baseline value of outcome at 10 weeks post-treatment for craniovertebral angle, pain, C6 and C7 peak-to-peak amplitude of dermatomal somatosensory evoked potentials P = 0.000, 0.01, 0.000, 0.001 respectively and at follow-up for all previous variables (P = 0.000). Forward head posture correction using a posture corrective exercise programme in addition to ultrasound and infrared radiation decreased pain and craniovertebral angle and increased the peak-to-peak amplitude of dermatomal somatosensory evoked potentials for C6 and C7 in cases of lower cervical spondylotic radiculopathy.
Zhong, Min; Kundu, Bijoy K.
2013-01-01
Quantitative evaluation of dynamic Positron Emission Tomography (PET) of mouse heart in vivo is challenging due to the small size of the heart and limited intrinsic spatial resolution of the PET scanner. Here, we optimized a compartment model which can simultaneously correct for spill over and partial volume effects for both blood pool and the myocardium, compute kinetic rate parameters and generate model corrected blood input function (MCBIF) from ordered subset expectation maximization – maximum a posteriori (OSEM-MAP) cardiac and respiratory gated 18F-FDG PET images of mouse heart with attenuation correction in vivo, without any invasive blood sampling. Arterial blood samples were collected from a single mouse to indicate the feasibility of the proposed method. In order to establish statistical significance, venous blood samples from n=6 mice were obtained at 2 late time points, when SP contamination from the tissue to the blood is maximum. We observed that correct bounds and initial guesses for the PV and SP coefficients accurately model the wash-in and wash-out dynamics of the tracer from mouse blood. The residual plot indicated an average difference of about 1.7% between the blood samples and MCBIF. The downstream rate of myocardial FDG influx constant, Ki (0.15±0.03 min−1), compared well with Ki obtained from arterial blood samples (P=0.716). In conclusion, the proposed methodology is not only quantitative but also reproducible. PMID:24741130
NASA Astrophysics Data System (ADS)
Ruud, Kenneth; Åstrand, Per-Olof; Taylor, Peter R.
2000-02-01
We have recently presented a formalism for calculating zero-point vibrational corrections to molecular properties of polyatomic molecules in which the contribution to the zero-point vibrational correction from the anharmonicity of the potential is included in the calculations by performing a perturbation expansion of the vibrational wave function around an effective geometry. In this paper we describe an implementation of this approach, focusing on computational aspects such as the definition of normal coordinates at a nonequilibrium geometry and the use of the Eckart frame in order to obtain accurate nonisotropic molecular properties. The formalism allows for a black-box evaluation of zero-point vibrational corrections, completed in two successive steps, requiring a total of two molecular Hessians, 6K-11 molecular gradients, and 6K-11 property evaluations, K being the number of atoms. We apply the approach to the study of a number of electric and magnetic properties—the dipole and quadrupole moments, the static and frequency-dependent polarizability, the magnetizability, the rotational g tensor and the nuclear shieldings—of the molecules hydrogen fluoride, water, ammonia, and methane. Particular attention is paid to the importance of electron correlation and of the importance of the zero-point vibrational corrections for obtaining accurate estimates of molecular properties for a direct comparison with experiment.
Iron Partitioning in Ferropericlase
NASA Astrophysics Data System (ADS)
Braithwaite, J. W. H.; Stixrude, L. P.; Pinilla, C.; Holmstrom, E.
2015-12-01
Ferropericlase, (Mg,Fe)O, is the second most abundant mineral in the Earth's lower mantle. Whether iron favours the liquid or solid phase of (Mg,Fe)O has important implications for the Earth's mantle, both chemically and dynamically. As iron is much heavier than magnesium, the partitioning of iron between liquid and solid will lead to a contrast in densities. This difference in density will lead one phase to be more buoyant than the other and would help, in part, to explain how the mantle crystallised from the magma ocean of the Hadean eon to its current state. The partitioning of iron between the two phases is characterized by partition coefficients. Using ab-initio methods, thermodynamic integration and adiabatic switching these coefficients have been determined. Results are presented for pressures encompassing the region between the upper mantle and the core-mantle boundary (10-140GPa).
Excited States of DNA Base Pairs Using Long-Range Corrected Time-Dependent Density Functional Theory
Jensen, Lasse; Govind, Niranjan
2009-09-10
In this work we present a study of the excitation energies of adenine, cytosine, guanine, thymine and the adenine-thymine (AT) and guanine-cytosine (GC) base pairs using long-range corrected (LC) density functional theory. We compare three recent LC-functionals, BNL, CAM-B3LYP and LC-PBE0 with B3LYP and coupled cluster results from the literature. We find that the best overall performance is for the BNL functional based on LDA. However, in order to achieve this good agreement a smaller attenuation parameter was needed which leads to non-optimum performance for ground state properties. B3LYP, on the other hand, severely underestimates the charge transfer (CT) transitions in the base pairs. Surprisingly we also find that the CAM-B3LYP functional also underestimates the CT excitation energy for the GC base pair, but correctly describes the AT base pair. This illustrates the importance of retaining the full long-range exact exchange even at distances as short as that of the DNA base pairs. The worst overall performance was obtained with the LC-PBE0 functional which overestimates the excitations for the individual bases as well as the base pairs. It is therefore crucial to strike a good balance between the amount of local and long-range exact exchange.
NASA Technical Reports Server (NTRS)
Vanalstine, James M.
1993-01-01
Project NAS8-36955 D.O. #100 initially involved the following tasks: (1) evaluation of various coatings' ability to control wall wetting and surface zeta potential expression; (2) testing various methods to mix and control the demixing of phase systems; and (3) videomicroscopic investigation of cell partition. Three complementary areas were identified for modification and extension of the original contract. They were: (1) identification of new supports for column cell partition; (2) electrokinetic detection of protein adsorption; and (3) emulsion studies related to bioseparations.
Lehtola, Susi; Jónsson, Elvar Ö; Jónsson, Hannes
2016-09-13
The spurious interaction of an electron with itself-self-interaction error-is one of the biggest problems in modern density-functional theory. Some of its most glaring effects, such as qualitatively incorrect charge separation upon dissociation, can be removed by an approximate self-interaction correction due to Perdew and Zunger (PZ) (Perdew, J.; Zunger, A. Phys. Rev. B 1981, 23, 5048). However, the correction introduces an explicit dependence on the occupied orbital densities, which makes proper minimization of the functional difficult. Previous work (Vydrov et al., J. Chem. Phys. 2006, 124, 094108) has suggested that the application of the PZ correction results in worse atomization energies than those obtained with the uncorrected parent functional. But, it has only recently been found that the correct minimization of the PZ energy functional requires complex-valued orbitals, which have not been used in previous work on atomization energies. Here, we study the effect of the proper use of complex-valued orbitals on the atomization energies of molecules in the W4-11 data set (Karton, A.; Daon, S.; Martin, J. M. Chem. Phys. Lett. 2001, 510, 165). We find that the correction has a tendency to weaken the binding of molecules. The correction using complex-valued orbitals is invariably found to yield better atomization energies than the correction with real-valued orbitals. The correction applied to the PBEsol exchange-correlation functional results in a functional that is more accurate than the (uncorrected) PBE functional.
van de Streek, Jacco; Neumann, Marcus A.
2014-01-01
In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom. PMID:25449625
van de Streek, Jacco; Neumann, Marcus A
2014-12-01
In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX