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Sample records for accurate equilibrium structure

  1. Accurate equilibrium structures of fluoro- and chloroderivatives of methane

    NASA Astrophysics Data System (ADS)

    Vogt, Natalja; Demaison, Jean; Rudolph, Heinz Dieter

    2014-11-01

    This work is a systematic study of molecular structure of fluoro-, chloro-, and fluorochloromethanes. For the first time, the accurate ab initio structure is computed for 10 molecules (CF4, CClF3, CCl2F2, CCl3F, CHClF2, CHCl2F, CH2F2, CH2ClF, CH2Cl2, and CCl4) at the coupled cluster level of electronic structure theory including single and double excitations augmented by a perturbational estimate of the effects of connected triple excitations [CCSD(T)] with all electrons being correlated and Gaussian basis sets of at least quadruple-ζ quality. Furthermore, when possible, namely for the molecules CH2F2, CH2Cl2, CH2ClF, CHClF2, and CCl2F2, accurate semi-experimental equilibrium (rSEe) structure has also been determined. This is achieved through a least-squares structural refinement procedure based on the equilibrium rotational constants of all available isotopomers, determined by correcting the experimental ground-state rotational constants with computed ab initio vibration-rotation interaction constants and electronic g-factors. The computed and semi-experimental equilibrium structures are in excellent agreement with each other, but the rSEe structure is generally more accurate, in particular for the CF and CCl bond lengths. The carbon-halogen bond length is discussed within the framework of the ligand close-packing model as a function of the atomic charges. For this purpose, the accurate equilibrium structures of some other molecules with alternative ligands, such as CH3Li, CF3CCH, and CF3CN, are also computed.

  2. Equilibrium gas flow computations. I - Accurate and efficient calculation of equilibrium gas properties

    NASA Technical Reports Server (NTRS)

    Liu, Yen; Vinokur, Marcel

    1989-01-01

    This paper treats the accurate and efficient calculation of thermodynamic properties of arbitrary gas mixtures for equilibrium flow computations. New improvements in the Stupochenko-Jaffe model for the calculation of thermodynamic properties of diatomic molecules are presented. A unified formulation of equilibrium calculations for gas mixtures in terms of irreversible entropy is given. Using a highly accurate thermo-chemical data base, a new, efficient and vectorizable search algorithm is used to construct piecewise interpolation procedures with generate accurate thermodynamic variable and their derivatives required by modern computational algorithms. Results are presented for equilibrium air, and compared with those given by the Srinivasan program.

  3. Structural design using equilibrium programming

    NASA Technical Reports Server (NTRS)

    Scotti, Stephen J.

    1992-01-01

    Multiple nonlinear programming methods are combined in the method of equilibrium programming. Equilibrium programming theory has been appied to problems in operations research, and in the present study it is investigated as a framework to solve structural design problems. Several existing formal methods for structural optimization are shown to actually be equilibrium programming methods. Additionally, the equilibrium programming framework is utilized to develop a new structural design method. Selected computational results are presented to demonstrate the methods.

  4. Approaching system equilibrium with accurate or not accurate feedback information in a two-route system

    NASA Astrophysics Data System (ADS)

    Zhao, Xiao-mei; Xie, Dong-fan; Li, Qi

    2015-02-01

    With the development of intelligent transport system, advanced information feedback strategies have been developed to reduce traffic congestion and enhance the capacity. However, previous strategies provide accurate information to travelers and our simulation results show that accurate information brings negative effects, especially in delay case. Because travelers prefer to the best condition route with accurate information, and delayed information cannot reflect current traffic condition but past. Then travelers make wrong routing decisions, causing the decrease of the capacity and the increase of oscillations and the system deviating from the equilibrium. To avoid the negative effect, bounded rationality is taken into account by introducing a boundedly rational threshold BR. When difference between two routes is less than the BR, routes have equal probability to be chosen. The bounded rationality is helpful to improve the efficiency in terms of capacity, oscillation and the gap deviating from the system equilibrium.

  5. Equilibrium Macroscopic Structure Revisited from Spatial Constraint

    NASA Astrophysics Data System (ADS)

    Yuge, Koretaka

    2016-02-01

    In classical systems, we reexamine how macroscopic structures in equilibrium state connect with spatial constraint on the systems. For example, volume and density as the constraint for liquids in rigid box, and crystal lattice as the constraint for crystalline solids. We find that in disordered states, equilibrium macroscopic structure, depending on temperature and on multibody interactions in the system, can be well characterized by a single special microscopic structure independent of temperature and of interactions. The special microscopic structure depends only on the spatial constraint. We demonstrate the present findings providing (i) significantly efficient and systematic prediction of macroscopic structures for possible combination of constituents in multicomponent systems using first-principles calculations, and (ii) unique and accurate prediction of multibody interactions in given system from measured macroscopic structure, without performing trial-and-error simulation.

  6. A time-accurate implicit method for chemical non-equilibrium flows at all speeds

    NASA Technical Reports Server (NTRS)

    Shuen, Jian-Shun

    1992-01-01

    A new time accurate coupled solution procedure for solving the chemical non-equilibrium Navier-Stokes equations over a wide range of Mach numbers is described. The scheme is shown to be very efficient and robust for flows with velocities ranging from M less than or equal to 10(exp -10) to supersonic speeds.

  7. A time-accurate algorithm for chemical non-equilibrium viscous flows at all speeds

    NASA Technical Reports Server (NTRS)

    Shuen, J.-S.; Chen, K.-H.; Choi, Y.

    1992-01-01

    A time-accurate, coupled solution procedure is described for the chemical nonequilibrium Navier-Stokes equations over a wide range of Mach numbers. This method employs the strong conservation form of the governing equations, but uses primitive variables as unknowns. Real gas properties and equilibrium chemistry are considered. Numerical tests include steady convergent-divergent nozzle flows with air dissociation/recombination chemistry, dump combustor flows with n-pentane-air chemistry, nonreacting flow in a model double annular combustor, and nonreacting unsteady driven cavity flows. Numerical results for both the steady and unsteady flows demonstrate the efficiency and robustness of the present algorithm for Mach numbers ranging from the incompressible limit to supersonic speeds.

  8. Structural design using equilibrium programming formulations

    NASA Astrophysics Data System (ADS)

    Scotti, Stephen J.

    1995-06-01

    Solutions to increasingly larger structural optimization problems are desired. However, computational resources are strained to meet this need. New methods will be required to solve increasingly larger problems. The present approaches to solving large-scale problems involve approximations for the constraints of structural optimization problems and/or decomposition of the problem into multiple subproblems that can be solved in parallel. An area of game theory, equilibrium programming (also known as noncooperative game theory), can be used to unify these existing approaches from a theoretical point of view (considering the existence and optimality of solutions), and be used as a framework for the development of new methods for solving large-scale optimization problems. Equilibrium programming theory is described, and existing design techniques such as fully stressed design and constraint approximations are shown to fit within its framework. Two new structural design formulations are also derived. The first new formulation is another approximation technique which is a general updating scheme for the sensitivity derivatives of design constraints. The second new formulation uses a substructure-based decomposition of the structure for analysis and sensitivity calculations. Significant computational benefits of the new formulations compared with a conventional method are demonstrated.

  9. Structural design using equilibrium programming formulations

    NASA Technical Reports Server (NTRS)

    Scotti, Stephen J.

    1995-01-01

    Solutions to increasingly larger structural optimization problems are desired. However, computational resources are strained to meet this need. New methods will be required to solve increasingly larger problems. The present approaches to solving large-scale problems involve approximations for the constraints of structural optimization problems and/or decomposition of the problem into multiple subproblems that can be solved in parallel. An area of game theory, equilibrium programming (also known as noncooperative game theory), can be used to unify these existing approaches from a theoretical point of view (considering the existence and optimality of solutions), and be used as a framework for the development of new methods for solving large-scale optimization problems. Equilibrium programming theory is described, and existing design techniques such as fully stressed design and constraint approximations are shown to fit within its framework. Two new structural design formulations are also derived. The first new formulation is another approximation technique which is a general updating scheme for the sensitivity derivatives of design constraints. The second new formulation uses a substructure-based decomposition of the structure for analysis and sensitivity calculations. Significant computational benefits of the new formulations compared with a conventional method are demonstrated.

  10. Accurate Prediction of Docked Protein Structure Similarity.

    PubMed

    Akbal-Delibas, Bahar; Pomplun, Marc; Haspel, Nurit

    2015-09-01

    One of the major challenges for protein-protein docking methods is to accurately discriminate nativelike structures. The protein docking community agrees on the existence of a relationship between various favorable intermolecular interactions (e.g. Van der Waals, electrostatic, desolvation forces, etc.) and the similarity of a conformation to its native structure. Different docking algorithms often formulate this relationship as a weighted sum of selected terms and calibrate their weights against specific training data to evaluate and rank candidate structures. However, the exact form of this relationship is unknown and the accuracy of such methods is impaired by the pervasiveness of false positives. Unlike the conventional scoring functions, we propose a novel machine learning approach that not only ranks the candidate structures relative to each other but also indicates how similar each candidate is to the native conformation. We trained the AccuRMSD neural network with an extensive dataset using the back-propagation learning algorithm. Our method achieved predicting RMSDs of unbound docked complexes with 0.4Å error margin. PMID:26335807

  11. The empirical equilibrium structure of diacetylene

    NASA Astrophysics Data System (ADS)

    Thorwirth, Sven; Harding, Michael E.; Muders, Dirk; Gauss, Jürgen

    2008-09-01

    High-level quantum-chemical calculations are reported at the MP2 and CCSD(T) levels of theory for the equilibrium structure and the harmonic and anharmonic force fields of diacetylene, H sbnd C tbnd C sbnd C tbnd C sbnd H. The calculations were performed employing Dunning's hierarchy of correlation-consistent basis sets cc-pV XZ, cc-pCV XZ, and cc-pwCV XZ, as well as the ANO2 basis set of Almlöf and Taylor. An empirical equilibrium structure based on experimental rotational constants for 13 isotopic species of diacetylene and computed zero-point vibrational corrections is determined (reemp:r=1.0615 Å,r=1.2085 Å,r=1.3727 Å) and in good agreement with the best theoretical structure (CCSD(T)/cc-pCV5Z: r=1.0617 Å, r=1.2083 Å, r=1.3737 Å). In addition, the computed fundamental vibrational frequencies are compared with the available experimental data and found in satisfactory agreement.

  12. Isomerism of Cyanomethanimine: Accurate Structural, Energetic, and Spectroscopic Characterization.

    PubMed

    Puzzarini, Cristina

    2015-11-25

    The structures, relative stabilities, and rotational and vibrational parameters of the Z-C-, E-C-, and N-cyanomethanimine isomers have been evaluated using state-of-the-art quantum-chemical approaches. Equilibrium geometries have been calculated by means of a composite scheme based on coupled-cluster calculations that accounts for the extrapolation to the complete basis set limit and core-correlation effects. The latter approach is proved to provide molecular structures with an accuracy of 0.001-0.002 Å and 0.05-0.1° for bond lengths and angles, respectively. Systematically extrapolated ab initio energies, accounting for electron correlation through coupled-cluster theory, including up to single, double, triple, and quadruple excitations, and corrected for core-electron correlation and anharmonic zero-point vibrational energy, have been used to accurately determine relative energies and the Z-E isomerization barrier with an accuracy of about 1 kJ/mol. Vibrational and rotational spectroscopic parameters have been investigated by means of hybrid schemes that allow us to obtain rotational constants accurate to about a few megahertz and vibrational frequencies with a mean absolute error of ∼1%. Where available, for all properties considered, a very good agreement with experimental data has been observed. PMID:26529434

  13. Structure of Non-Equilibrium Adsorbed Polymer Layers

    NASA Astrophysics Data System (ADS)

    O'Shaughnessy, Ben; Vavylonis, Dimitrios

    2004-03-01

    Equilibrium polymer adsorption has been widely studied theoretically. Many experiments however implicate strong non-equilibrium effects for monomer sticking energies somewhat larger than kT, the most common case. The structure and slow dynamics in these layers is not understood. We analyze theoretically non-equilibrium layers from dilute solutions in the limit of irreversible monomer adsorption. We find the density profile ˜ z-4/3 and loop distribution ˜ s-11/5 of the resulting layer are no different to equilibrium. However, single chain statistics are radically different: the layer consists of a flat inner portion of fully collapsed chains plus an outer part whose chains make only fN surface contacts where N is chain length. The contact fractions f follow a broad distribution, P(f) ˜ f-4/5, consistent with experiment [H. M. Schneider et al, Langmuir 12, 994 (1996)], and the lateral size R of adsorbed chains is of order the bulk coil size, R ˜ N^3/5. For equilibrium layers, by contrast, P has a unique peak at a value of f of order unity, while R ˜ N^1/2 is significantly less. The relaxation of a non-equilibrium layer towards equilibrium thus entails chain shrinkage and tighter binding. We speculate that the observed decrease of bulk-layer chain exchange rates with increasing aging reflects these internal layer dynamics.

  14. Equilibrium structures in partially ionized rotating plasmas within Hall magnetohydrodynamics

    NASA Astrophysics Data System (ADS)

    Krishan, V.; Yoshida, Z.

    2006-09-01

    The formation of equilibrium structures in partially ionized rotating plasmas, consisting of electrons, ions, and neutral molecules, including the Hall effect, is studied in order to diagnose the possible velocity and the magnetic field configurations in a self-consistent manner. A few simple examples show that the linear and the nonlinear force-free magnetic configurations along with essentially nonlinear Beltrami flow field seem to be the general features of plasmas in the special case of the Keplerian rotation relevant for astrophysical plasmas. Thus rotation along with axial bipolar flows emerges as a natural pattern in gravitationally controlled magnetohydrodynamic systems. However, the equilibrium conditions permit more general flow and the magnetic field profiles that can perhaps be fully explored numerically. A special class of equilibria with unit magnetic Prandtl number and equal values of the fractional ion mass density α =ρi/ρn and the Hall parameter ɛ =λi/L exists where ρ's are the uniform mass densities, λi is the ion inertial scale, and L is the scale of the equilibrium structure. An approximate scaling law between the ionization fraction and the scale of the structure is found. Further by expressing the not so well known ionization fraction in terms of the temperature of the system, assuming thermal equilibrium, relationships among the extensive parameters such as the scale, the neutral particle density, the flow velocity, the temperature, and the magnetic field of the equilibrium structure can be determined. There seems to be a good overlap between the Hall and the thermal equilibria. The validity of the neglect of the ion dynamics is discussed.

  15. Experimental rovibrational constants and equilibrium structure of phosphorus trifluoride

    NASA Astrophysics Data System (ADS)

    Najib, Hamid

    2014-11-01

    Thanks to recent high-resolution Fourier transform infrared (FTIR) and pure rotational (RF/CM/MMW) measurements, several experimental values of the rotation-vibration parameters of the oblate molecule PF3 have been extracted, contributing thus to the knowledge of the molecular potential of phosphorus trifluoride. The data used are those of the fundamental, overtone and combination bands studied in the 300-1500 cm-1 range. The new values are in good agreement with ones determined at low resolution, but significantly more accurate. The agreement is excellent with the available values determined by ab initio HF-SCF calculations employing the TZP/TZ2P triple-zeta basis. From the recent experimental rovibrational interaction constants αC and αB, new accurate equilibrium rotational constants Ce and Be have been derived for the symmetric top molecule PF3, which were used to derive the equilibrium geometry of this molecule: re(F-P) = 1.560986 (43) Å; θe(FPF) = 97.566657 (64)°.

  16. Accurate and efficient reconstruction of deep phylogenies from structured RNAs

    PubMed Central

    Stocsits, Roman R.; Letsch, Harald; Hertel, Jana; Misof, Bernhard; Stadler, Peter F.

    2009-01-01

    Ribosomal RNA (rRNA) genes are probably the most frequently used data source in phylogenetic reconstruction. Individual columns of rRNA alignments are not independent as a consequence of their highly conserved secondary structures. Unless explicitly taken into account, these correlation can distort the phylogenetic signal and/or lead to gross overestimates of tree stability. Maximum likelihood and Bayesian approaches are of course amenable to using RNA-specific substitution models that treat conserved base pairs appropriately, but require accurate secondary structure models as input. So far, however, no accurate and easy-to-use tool has been available for computing structure-aware alignments and consensus structures that can deal with the large rRNAs. The RNAsalsa approach is designed to fill this gap. Capitalizing on the improved accuracy of pairwise consensus structures and informed by a priori knowledge of group-specific structural constraints, the tool provides both alignments and consensus structures that are of sufficient accuracy for routine phylogenetic analysis based on RNA-specific substitution models. The power of the approach is demonstrated using two rRNA data sets: a mitochondrial rRNA set of 26 Mammalia, and a collection of 28S nuclear rRNAs representative of the five major echinoderm groups. PMID:19723687

  17. Accurate and efficient reconstruction of deep phylogenies from structured RNAs.

    PubMed

    Stocsits, Roman R; Letsch, Harald; Hertel, Jana; Misof, Bernhard; Stadler, Peter F

    2009-10-01

    Ribosomal RNA (rRNA) genes are probably the most frequently used data source in phylogenetic reconstruction. Individual columns of rRNA alignments are not independent as a consequence of their highly conserved secondary structures. Unless explicitly taken into account, these correlation can distort the phylogenetic signal and/or lead to gross overestimates of tree stability. Maximum likelihood and Bayesian approaches are of course amenable to using RNA-specific substitution models that treat conserved base pairs appropriately, but require accurate secondary structure models as input. So far, however, no accurate and easy-to-use tool has been available for computing structure-aware alignments and consensus structures that can deal with the large rRNAs. The RNAsalsa approach is designed to fill this gap. Capitalizing on the improved accuracy of pairwise consensus structures and informed by a priori knowledge of group-specific structural constraints, the tool provides both alignments and consensus structures that are of sufficient accuracy for routine phylogenetic analysis based on RNA-specific substitution models. The power of the approach is demonstrated using two rRNA data sets: a mitochondrial rRNA set of 26 Mammalia, and a collection of 28S nuclear rRNAs representative of the five major echinoderm groups. PMID:19723687

  18. The Equilibrium Structure of Charged Rotating Relativistic Stars

    NASA Astrophysics Data System (ADS)

    Mirza, Babur M.

    General relativistic equilibrium conditions imply that an electrically charged compact star, in a spherically symmetric configuration, can sustain a huge amount of electric charge (up to 1020 C). The equilibrium, however, is reached under very critical conditions such that a perturbation to the stellar structure can cause these systems to collapse. We study the effects of rotation in charged compact stars and obtain conditions, the modified Tolman-Oppenheimer-Volkoff (TOV) equations, under which such stars form a stable gravitational system against Coulomb repulsion. We assume the star to be rotating slowly. We also assume that the charge density is proportional to the mass density everywhere inside the star. The modified TOV equations for hydrostatic equilibrium are integrated numerically for the general equation of state for a polytrope. The detailed numerical study shows that the centrifugal force adds to the Coulomb pressure in the star. In the stable equilibrium configurations, therefore, a loss in stellar mass (energy) density occurs for higher values of the angular frequency. The additional energy is radiated in the form of electrical energy. The stellar radius is also decreased so that the star does not necessarily becomes more compact.

  19. EFFECT OF SOLAR CHROMOSPHERIC NEUTRALS ON EQUILIBRIUM FIELD STRUCTURES

    SciTech Connect

    Arber, T. D.; Botha, G. J. J.; Brady, C. S. E-mail: G.J.J.Botha@warwick.ac.u

    2009-11-10

    Solar coronal equilibrium fields are often constructed by nonlinear force-free field (NLFFF) extrapolation from photospheric magnetograms. It is well known that the photospheric field is not force-free and the correct lower boundary for NLFFF construction ought to be the top of the chromosphere. To compensate for this, pre-filtering algorithms are often applied to the photospheric data to remove the non-force-free components. Such pre-filtering models, while physically constrained, do not address the mechanisms that may be responsible for the field becoming force-free. The chromospheric field can change through, for example, field expansion due to gravitational stratification, reconnection, or flux emergence. In this paper, we study and quantify the effect of the chromospheric neutrals on equilibrium field structures. It is shown that, depending on the degree to which the photospheric field is not force-free, the chromosphere will change the structure of the equilibrium field. This is quantified to give an estimate of the change in alpha profiles one might expect due to neutrals in the chromosphere. Simple scaling of the decay time of non-force-free components of the magnetic field due to chromospheric neutrals is also derived. This is used to quantify the rate at which, or equivalent at which height, the chromosphere is expected to become force-free.

  20. The equilibrium structure of thin magnetic flux tubes. I

    NASA Technical Reports Server (NTRS)

    Ferrari, A.; Massaglia, S.; Kalkofen, W.; Rosner, R.; Bodo, G.

    1985-01-01

    A model atmosphere within a thin magnetic flux tube that is embedded in an arbitrarily stratified medium is presently constructed by solving the radiative transfer equation in the two-stream approximation for gray opacity, under the assumption that the magnetic field is sufficiently strong to warrant the neglect of both thermal conduction and convective diffusion; energy inside the flux tube therefore being transported solely by radiation. The structure of the internal atmosphere is determined on the basis of the hydrostatic and radiative equilibrium conditions of the tube embedded in an external atmosphere. The gas temperature along the axis of the tube is computed, and the geometry of the flux tube is determined on the basis of magnetic flux conservation and total pressure equilibrium.

  1. Experimental values of the rotational and vibrational constants and equilibrium structure of nitrogen trifluoride

    NASA Astrophysics Data System (ADS)

    Najib, Hamid

    2015-06-01

    Several accurate experimental values of the rovibrational interaction constants αC and αB, the harmonic wave-number parameters ωij, and the anharmonicity xij and gij constants have been extracted from the most recent high-resolution Fourier transform infrared (FTIR), centimeter-wave (CMW) and millimeter-wave (MMW) measurements in the spectra of the oblate symmetric top molecule 14NF3. The data used are those of the four fundamental, the overtone, the combination and the hot bands identified and analyzed in the range between 400 cm-1 and 2000 cm-1. Combining the recent experimental values of the constants αC and αB, with the accurate experimental ground state rotational constants C0 and B0, new equilibrium rotational constants have been evaluated: Ce = 0.1968006 (26) cm-1 and Be = 0.358981442 (43) cm-1 for the pyramidal molecule NF3, from which the following equilibrium structure is obtained: re(F-N) = 1.36757 (58) Å; θe(FNF) = 101.8513 (10)°. This experimental equilibrium geometry is in excellent agreement with the recent structure determined by ab initio calculations at the CCSD(T)/aug-cc-pVQZ level of theory.

  2. Equilibrium structures of heterocyclic molecules with large principal axis rotations upon isotopic substitution.

    PubMed

    Demaison, Jean; Császár, Attila G; Margulès, Laurent D; Rudolph, Heinz Dieter

    2011-12-01

    Equilibrium structures, r(e), of the heterocyclic molecules oxirane, furazan, furan, ethylene ozonide, and 1,3,4-oxadiazole have been determined using three different, somewhat complementary techniques: a completely experimental technique (r(m)), a semiexperimental technique (r(e)(SE), whereby equilibrium rotational constants are derived from experimental effective ground-state rotational constants and corrections based principally on an ab initio cubic force field), and an ab initio technique (r(e)(BO), whereby geometry optimizations are usually performed at the coupled cluster level of theory including single and double excitations augmented by a perturbational estimate of the effects of connected triple excitations [CCSD(T)] using quadruple-ζ Gaussian basis sets). All these molecules are asymmetric tops with the moment of inertia I(c) much larger than the other two moments of inertia, I(a) and I(b). Molecules of this shape experience a large rotation of the principal axis system upon certain isotopic substitutions. For such isotopologues it is difficult to obtain a good structural fit to the semiexperimental moments of inertia I(a) and I(b), which may significantly reduce the accuracy of the r(e)(SE) structural parameters. The origin of this difficulty is explained. For the heavy-atom skeleton of these molecules it was possible to determine a rather accurate empirical mass-dependent structure without a priori knowledge of the equilibrium structure. PMID:22032750

  3. Torsional barrier and equilibrium structure of ethyl cyanide

    NASA Astrophysics Data System (ADS)

    Demaison, J.; Margulès, L.; Mäder, H.; Sheng, M.; Rudolph, H. D.

    2008-12-01

    The quadratic, cubic and semi-diagonal quartic force field of ethyl cyanide has been calculated at the B3LYP level of theory employing a basis set of triple-ζ quality. A semi-experimental equilibrium structure has been derived from experimental ground state rotational constants and rovibrational interaction parameters calculated from the ab initio force field. This structure is in excellent agreement with the ab initio structure calculated at the CCSD(T) level of theory using a basis set of quadruple-ζ quality and a core correlation correction. The empirical structures are also determined and their accuracy is discussed. The potential barrier V3 hindering internal rotation of the methyl group has been calculated from 23 rotational transitions of CH 3CH 2C 15N which were found split into doublets, giving V3 = 3074(27) cal mol -1.

  4. Equilibrium Structures of Differentially Rotating Primary Components of Binary Stars

    NASA Astrophysics Data System (ADS)

    Mohan, C.; Lal, A. K.; Singh, V. P.

    1997-11-01

    In this paper a method is proposed for computing the equilibrium structures and various other observable physical parameters of the primary components of stars in binary systems assuming that the primary is more massive than the secondary and is rotating differentially about its axis. Kippenhahn and Thomas averaging approach (1970) is used in a manner earlier used by Mohan, Saxena and Agarwal (1990) to incorporate the rotational and tidal effects in the equations of stellar structure. Explicit expressions for the distortional terms appearing in the stellar structure equations have been obtained by assuming a general law of differential rotation of the typeω2 = b 0+b 1 s 2+b 2 s 4, where ω is the angular velocity of rotation of a fluid element in the star at a distance s from the axis of rotation, and b 0, b 1, b 2 are suitably chosen numerical constants. The expressions incorporate the effects of differential rotation and tidal distortions up to second order terms. The use of the proposed method has been illustrated by applying it to obtain the structures and observable parameters of certain differentially rotating primary components of the binary stars assuming the primary components to have polytropic structures.

  5. A benchmark study of molecular structure by experimental and theoretical methods: Equilibrium structure of uracil from gas-phase electron diffraction data and coupled-cluster calculations

    NASA Astrophysics Data System (ADS)

    Vogt, Natalja; Khaikin, Leonid S.; Grikina, Olga E.; Rykov, Anatolii N.

    2013-10-01

    The equilibrium structure of uracil, one of the nucleobases, which build nucleic acids, has been determined for the first time by the gas-phase electron diffraction (GED) method. The necessary rovibrational corrections to the experimental internuclear distances have been calculated with quadratic and cubic force constants in the MP2(all)/cc-pVTZ approximation. For the first time, the equilibrium structure has been optimized by the very time-consuming coupled-cluster method with single and double excitations and perturbative treatment of connected triples using the correlation-consistent polarized weighted core-valence triple-zeta basis set with all electrons being correlated (CCSD(T)(all)/cc-pwCVTZ). The optimized structural parameters have been corrected for the diffuse-function effects and extrapolated to the higher basis set (cc-pwCVQZ) using results of MP2 computations (named as best ab initio structure). The GED equilibrium structure remarkably agrees with the best ab initio one as well as with that one derived from microwave (MW) rotational constants by Puzzarini and Barone. Thus, it has been revealed that the precise experiment and coupled-cluster calculations yield the same results when accurate vibrational corrections (including anharmonic ones) are considered in the experimental structural analysis. Moreover, it has been shown that the equilibrium structure derived from the GED data, being in general of one order less accurate than that determined from the MW rotational constants, is still reliable and accurate.

  6. Financial Structure and Economic Welfare: Applied General Equilibrium Development Economics

    PubMed Central

    Townsend, Robert

    2010-01-01

    This review provides a common framework for researchers thinking about the next generation of micro-founded macro models of growth, inequality, and financial deepening, as well as direction for policy makers targeting microfinance programs to alleviate poverty. Topics include treatment of financial structure general equilibrium models: testing for as-if-complete markets or other financial underpinnings; examining dual-sector models with both a perfectly intermediated sector and a sector in financial autarky, as well as a second generation of these models that embeds information problems and other obstacles to trade; designing surveys to capture measures of income, investment/savings, and flow of funds; and aggregating individuals and households to the level of network, village, or national economy. The review concludes with new directions that overcome conceptual and computational limitations. PMID:21037939

  7. Equilibrium structure of white dwarfs at finite temperatures

    NASA Astrophysics Data System (ADS)

    Boshkayev, K. A.; Rueda, J. A.; Zhami, B. A.; Kalymova, Zh. A.; Balgymbekov, G. Sh.

    2016-03-01

    Recently, it has been shown by S. M. de Carvalho et al. (2014) that the deviations between the degenerate case and observations were already evident for 0.7-0.8 M⊙ white dwarfs. Such deviations were related to the neglected effects of finite temperatures on the structure of a white dwarf. Therefore, in this work by employing the Chandrasekhar equation of state taking into account the effects of temperature we show how the total pressure of the white dwarf matter depends on the mass density at different temperatures. Afterwards we construct equilibrium configurations of white dwarfs at finite temperatures. We obtain the mass-radius relations of white dwarfs for different temperatures by solving the Tolman-Oppenheimer-Volkoff equation, and compare them with the estimated masses and radii inferred from the Sloan Digital Sky Survey Data Release 4.

  8. The equilibrium molecular structures of 2-deoxyribose and fructose by the semiexperimental mixed estimation method and coupled-cluster computations.

    PubMed

    Vogt, Natalja; Demaison, Jean; Cocinero, Emilio J; Écija, Patricia; Lesarri, Alberto; Rudolph, Heinz Dieter; Vogt, Jürgen

    2016-06-21

    Fructose and deoxyribose (24 and 19 atoms, respectively) are too large for determining accurate equilibrium structures, either by high-level ab initio methods or by experiments alone. We show in this work that the semiexperimental (SE) mixed estimation (ME) method offers a valuable alternative for equilibrium structure determinations in moderate-sized molecules such as these monosaccharides or other biochemical building blocks. The SE/ME method proceeds by fitting experimental rotational data for a number of isotopologues, which have been corrected with theoretical vibration-rotation interaction parameters (αi), and predicate observations for the structure. The derived SE constants are later supplemented by carefully chosen structural parameters from medium level ab initio calculations, including those for hydrogen atoms. The combined data are then used in a weighted least-squares fit to determine an equilibrium structure (r). We applied the ME method here to fructose and 2-deoxyribose and checked the accuracy of the calculations for 2-deoxyribose against the high level ab initio r structure fully optimized at the CCSD(T) level. We show that the ME method allows determining a complete and reliable equilibrium structure for relatively large molecules, even when experimental rotational information includes a limited number of isotopologues. With a moderate computational cost the ME method could be applied to larger molecules, thereby improving the structural evidence for subtle orbital interactions such as the anomeric effect. PMID:27212641

  9. Efficient and accurate determination of lattice-vacancy diffusion coefficients via non equilibrium ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Sangiovanni, D. G.; Hellman, O.; Alling, B.; Abrikosov, I. A.

    2016-03-01

    We revisit the color-diffusion algorithm [Aeberhard et al., Phys. Rev. Lett. 108, 095901 (2012), 10.1103/PhysRevLett.108.095901] in non equilibrium ab initio molecular dynamics (NE-AIMD) and propose a simple efficient approach for the estimation of monovacancy jump rates in crystalline solids at temperatures well below melting. Color-diffusion applied to monovacancy migration entails that one lattice atom (colored atom) is accelerated toward the neighboring defect site by an external constant force F. Considering bcc molybdenum between 1000 and 2800 K as a model system, NE-AIMD results show that the colored-atom jump rate kNE increases exponentially with the force intensity F , up to F values far beyond the linear-fitting regime employed previously. Using a simple model, we derive an analytical expression which reproduces the observed kNE(F ) dependence on F . Equilibrium rates extrapolated by NE-AIMD results are in excellent agreement with those of unconstrained dynamics. The gain in computational efficiency achieved with our approach increases rapidly with decreasing temperatures and reaches a factor of 4 orders of magnitude at the lowest temperature considered in the present study.

  10. Development of Accurate Chemical Equilibrium Models for the Hanford Waste Tanks: New Thermodynamic Measurements and Model Applications

    SciTech Connect

    Felmy, Andrew R.; Mason, Marvin; Qafoku, Odeta; Xia, Yuanxian; Wang, Zheming; MacLean, Graham

    2003-03-27

    Developing accurate thermodynamic models for predicting the chemistry of the high-level waste tanks at Hanford is an extremely daunting challenge in electrolyte and radionuclide chemistry. These challenges stem from the extremely high ionic strength of the tank waste supernatants, presence of chelating agents in selected tanks, wide temperature range in processing conditions and the presence of important actinide species in multiple oxidation states. This presentation summarizes progress made to date in developing accurate models for these tank waste solutions, how these data are being used at Hanford and the important challenges that remain. New thermodynamic measurements on Sr and actinide complexation with specific chelating agents (EDTA, HEDTA and gluconate) will also be presented.

  11. Semiexperimental Equilibrium Structures for the Equatorial Conformers of N-Methylpiperidone and Tropinone by the Mixed Estimation Method

    NASA Astrophysics Data System (ADS)

    Demaison, Jean; Craig, Norman C.; Cocinero, Emilio J.; Grabow, Jens-Uwe; Lesarri, Alberto; Rudolph, H. D.

    2012-06-01

    N-methylpiperidone and tropinone, which contain a structural motif found in numerous alkaloids, are too large for determining an accurate equilibrium structure either by ab initio methods or by experiment. However, the ground state rotational constants of the parent species and of all isotopologues with a substituted heavy atom (13C, 15N, 18O) are known from microwave spectroscopy. These constants have been corrected for the rovibrational contribution calculated from an ab initio cubic force field. These semiexperimental equilibrium rotational constants have been supplemented by carefully chosen structural parameters from medium level ab initio calculations. In the mixed estimation method, the two sets of data have been used in a weighted least-squares fit to determine a reliable equilibrium structure for both molecules. This work shows that it is possible to determine reliable equilibrium structures for large molecules (34 degrees of freedom in the case of tropinone). The method could be applied without too much difficulty to still larger molecules. L. Evangelisti, A. Lesarri, M. K. Jahn, E. J. Cocinero, W. Caminati, J.-U. Grabow J. Phys. Chem. A 115, 9545-9551 (2011) E. J. Cocinero, A. Lesarri, P. Écija, J.-U. Grabow, J. A. Fernández, F. Castaño PCCP 12, 6076-6083 (2010)

  12. Accurate protein structure modeling using sparse NMR data and homologous structure information

    PubMed Central

    Thompson, James M.; Sgourakis, Nikolaos G.; Liu, Gaohua; Rossi, Paolo; Tang, Yuefeng; Mills, Jeffrey L.; Szyperski, Thomas; Montelione, Gaetano T.; Baker, David

    2012-01-01

    While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that allows robust modeling of protein structures of up to 225 residues by combining , 13C, and 15N backbone and 13Cβ chemical shift data, distance restraints derived from homologous structures, and a physically realistic all-atom energy function. Accurate models are distinguished from inaccurate models generated using incorrect sequence alignments by requiring that (i) the all-atom energies of models generated using the restraints are lower than models generated in unrestrained calculations and (ii) the low-energy structures converge to within 2.0 Å backbone rmsd over 75% of the protein. Benchmark calculations on known structures and blind targets show that the method can accurately model protein structures, even with very remote homology information, to a backbone rmsd of 1.2–1.9 Å relative to the conventional determined NMR ensembles and of 0.9–1.6 Å relative to X-ray structures for well-defined regions of the protein structures. This approach facilitates the accurate modeling of protein structures using backbone chemical shift data without need for side-chain resonance assignments and extensive analysis of NOESY cross-peak assignments. PMID:22665781

  13. Equilibrium structure in the presence of internal rotation: A case study of cis-methyl formate

    NASA Astrophysics Data System (ADS)

    Demaison, J.; Margulès, L.; Kleiner, I.; Császár, A. G.

    2010-02-01

    The Born-Oppenheimer (BO) equilibrium molecular structure ( reBO) of cis-methyl formate has been determined at the CCSD(T) level of electronic structure theory using Gaussian basis sets of at least quadruple-ζ quality and a core correlation correction. The quadratic, cubic and semi-diagonal quartic force field in normal coordinates has also been computed at the MP2 level employing a basis set of triple-ζ quality. A semi-experimental equilibrium structure ( reSE) has been derived from experimental ground-state rotational constants and the lowest-order rovibrational interaction parameters calculated from the ab initio cubic force field. To determine reSE structures, it is important to start from accurate ground-state rotational constants. Different spectroscopic methods, applicable in the presence of internal rotation and used in the literature to obtain "unperturbed" rotational constants from the analysis and fitting of the spectrum, are reviewed and compared. They are shown to be compatible though their precision may be different. The reBO and reSE structures are in good agreement showing that, in the particular case of cis-methyl formate, the methyl torsion can still be treated as a small-amplitude vibration. The best equilibrium structure obtained for cis-methyl formate is: r(C m-O) = 1.434 Å, r(O-C c) = 1.335 Å, r(C m-H s) = 1.083 Å, r(C m-H a) = 1.087 Å, r(C c-H) = 1.093 Å, r(C dbnd O) = 1.201 Å, ∠(COC) = 114.4°, ∠(CCH s) = 105.6°, ∠(CCH a) = 110.2°, ∠(OCH) = 109.6°, ∠(OCO) = 125.5°, and τ(H aCOC) = 60.3°. The accuracy is believed to be about 0.001 Å for the bond lengths and 0.1° for the angles.

  14. Vibration-rotation spectra of deuterated hypochlorous acid and the determination of the equilibrium structure

    NASA Astrophysics Data System (ADS)

    Deeley, C. M.

    1987-04-01

    Vibration-rotation spectra of the three fundamental vibrations of D 16O 35Cl have been measured at a resolution of 0.01 cm -1 to determine vibration-rotation constants. From these results values for the equilibrium rotational constants have been established and used, in conjunction with the equilibrium rotational constants for H 16O 35Cl (C. M. Deeley and I. M. Mills, J. Mol. Spectrosc.114, 368-376 (1985)), to determine the equilibrium structure of hypochlorous acid.

  15. A computationally efficient and accurate numerical representation of thermodynamic properties of steam and water for computations of non-equilibrium condensing steam flow in steam turbines

    NASA Astrophysics Data System (ADS)

    Hrubý, Jan

    2012-04-01

    Mathematical modeling of the non-equilibrium condensing transonic steam flow in the complex 3D geometry of a steam turbine is a demanding problem both concerning the physical concepts and the required computational power. Available accurate formulations of steam properties IAPWS-95 and IAPWS-IF97 require much computation time. For this reason, the modelers often accept the unrealistic ideal-gas behavior. Here we present a computation scheme based on a piecewise, thermodynamically consistent representation of the IAPWS-95 formulation. Density and internal energy are chosen as independent variables to avoid variable transformations and iterations. On the contrary to the previous Tabular Taylor Series Expansion Method, the pressure and temperature are continuous functions of the independent variables, which is a desirable property for the solution of the differential equations of the mass, energy, and momentum conservation for both phases.

  16. A Numerical Characterization of the Gravito-Electrostatic Sheath Equilibrium Structure in Solar Plasma

    NASA Astrophysics Data System (ADS)

    Karmakar, Pralay Kumar

    This article describes the equilibrium structure of the solar interior plasma (SIP) and solar wind plasma (SWP) in detail under the framework of the gravito-electrostatic sheath (GES) model. This model gives a precise definition of the solar surface boundary (SSB), surface origin mechanism of the subsonic SWP, and its supersonic acceleration. Equilibrium parameters like plasma potential, self-gravity, population density, flow, their gradients, and all the relevant inhomogeneity scale lengths are numerically calculated and analyzed as an initial value problem. Physical significance of the structure condition for the SSB is discussed. The plasma oscillation and Jeans time scales are also plotted and compared. In addition, different coupling parameters, and electric current profiles are also numerically studied. The current profiles exhibit an important behavior of directional reversibility, i.e., an electrodynamical transition from negative to positive value. It occurs beyond a few Jeans lengths away from the SSB. The virtual spherical surface lying at the current reversal point, where the net current becomes zero, has the property of a floating surface behavior of the real physical wall. Our investigation indicates that the SWP behaves as an ion current-carrying plasma system. The basic mechanism behind the GES formation and its distinctions from conventional plasma sheath are discussed. The electromagnetic properties of the Sun derived from our model with the most accurate available inputs are compared with those of others. These results are useful as an input element to study the properties of the linear and nonlinear dynamics of various solar plasma waves, oscillations and instabilities.

  17. Stellar and gaseous disc structures in cosmological galaxy equilibrium models

    NASA Astrophysics Data System (ADS)

    Rathaus, Ben; Sternberg, Amiel

    2016-05-01

    We present `radially resolved equilibrium models' for the growth of stellar and gaseous discs in cosmologically accreting massive haloes. Our focus is on objects that evolve to redshifts z ˜ 2. We solve the time-dependent equations that govern the radially dependent star formation rates, inflows and outflows from and to the inter- and circumgalactic medium, and inward radial gas flows within the discs. The stellar and gaseous discs reach equilibrium configurations on dynamical time-scales much shorter than variations in the cosmological dark matter halo growth and baryonic accretions rates. We show analytically that mass and global angular momentum conservation naturally give rise to exponential gas and stellar discs over many radial length-scales. As expected, the gaseous discs are more extended as set by the condition Toomre Q < 1 for star formation. The discs rapidly become baryon dominated. For massive, 5 × 1012 M⊙ haloes at redshift z = 2, we reproduced the typical observed star formation rates of ˜100 M⊙ yr-1, stellar masses ˜9 × 1010 M⊙, gas contents ˜1011 M⊙, half-mass sizes of 4.5 and 5.8 kpc for the stars and gas, and characteristic surface densities of 500 and 400 M⊙ pc-2 for the stars and gas.

  18. On Equilibrium Configurations in Continuum Mechanics of Structural Defects

    NASA Astrophysics Data System (ADS)

    Günther, H.

    We consider the determination of the theory by a second order tensor field gik and affinity fik. By variational principle for Einstein-Hilbert Lagrangian solid state equilibrium positions of the ideal and real crystal will be described. On account of external Galilei-invariance this theory affords an invariant three dimensional geometry at most being able to produce a stable static equilibrium of defects. The motion of defects is related to the theory of invariants of the internal group of field equations produced by this theory in strong analogy to Maxwell's electrodynamics. The elastic ether concept for the theory of light affords the idea of a gauge field approximation of continuum mechanics fitting linearized Einstein-Hilbert Lagrangian approach. The stress and strain space duality has to be understood on this background.Translated AbstractÜber Gleichgewichtskonfigurationen in der Kontinuumsmechanik der StrukturdefekteWir betrachten die Determinierung der Theorie durch ein Tensorfeld zweiter Ordnung gik und eine Affinität fik. Mit dem Variationsprinzip für die Einstein-Hilbertsche Lagrangefunktion werden Gleichgewichtszustände des idealen und realen Kristalls beschrieben. Auf Grund der äußeren Galilei-Invarianz liefert die Theorie eine invariante dreidimensionale Geometrie, welche höchstens stabile statische Gleichgewichtszustände hervorbringen kann. Die Bewegung der Defekte hängt mit der Invariantentheorie der inneren Gruppe der Feldgleichungen der Theorie in enger Analogie zur Maxwellschen Elektrodynamik zusammen. Das Konzept eines elastischen Äthers für die elektromagnetische Theorie des Lichtes liefert die Idee für einen eichfeldtheoretischen Zugang zur Kontinuumsmechanik, der die lineare Näherung des geometrischen Zugangs mit der Einstein-Hilbertschen Lagrangefunktion darstellt. Die Dualität des Spannungs- und Dehnungsraumes ist vor diesem Hintergrund zu sehen.

  19. Accurate molecular structures and infrared spectra of trans-2,3-dideuterooxirane, methyloxirane, and trans-2,3-dimethyloxirane

    SciTech Connect

    Barone, Vincenzo; Biczysko, Malgorzata Bloino, Julien; Puzzarini, Cristina

    2014-07-21

    Oxirane derivatives are the most used benchmarks for chiroptical spectroscopies in view of their small size and relative rigidity. The molecular structure, vibrational harmonic and anharmonic frequencies, and infrared intensities of the ground electronic states are analyzed in this paper. Equilibrium structure and harmonic force fields have been evaluated by means of high-level quantum-chemical calculations at the coupled-cluster level including single and double excitations together with a perturbative treatment of triples (CCSD(T)). Extrapolation to the complete basis-set limit as well as core-correlation effects have also been taken into account. Anharmonic contributions have been computed at the CCSD(T)/cc-pVTZ level for trans-2,3-dideuterooxirane. These data can serve as references to evaluate the accuracy of less expensive computational approaches rooted in the density functional theory (DFT). The latter have been used within hybrid CC/DFT approaches, which have been applied to simulate fully anharmonic infrared (IR) spectra. Finally, the best theoretical estimates of the equilibrium structures and vibrational wavenumbers are compared to the most accurate experimental data and show in all cases very good agreement, i.e., within 0.001 Å, 0.1 deg, 10 cm{sup −1}, and 0.5 km mol{sup −1}, for bond lengths, angles, wavenumbers, and IR intensities, respectively.

  20. Equilibrium structures of anisometric, quadrupolar particles confined to a monolayer.

    PubMed

    Heinemann, Thomas; Antlanger, Moritz; Mazars, Martial; Klapp, Sabine H L; Kahl, Gerhard

    2016-02-21

    We investigate the structural properties of a two-dimensional system of ellipsoidal particles carrying a linear quadrupole moment in their center. These particles represent a simple model for a variety of uncharged, non-polar conjugated organic molecules. Using optimization tools based on ideas of evolutionary algorithms, we first examine the ground state structures as we vary the aspect ratio of the particles and the pressure. Interestingly, we find, besides the intuitively expected T-like configurations, a variety of complex structures, characterized with up to three different particle orientations. In an effort to explore the impact of thermal fluctuations, we perform constant-pressure molecular dynamics simulations within a range of rather low temperatures. We observe that ground state structures formed by particles with a large aspect ratio are in particular suited to withstand fluctuations up to rather high temperatures. Our comprehensive investigations allow for a deeper understanding of molecular or colloidal monolayer arrangements under the influence of a typical electrostatic interaction on a coarse-grained level. PMID:26896992

  1. Equilibrium structures of anisometric, quadrupolar particles confined to a monolayer

    NASA Astrophysics Data System (ADS)

    Heinemann, Thomas; Antlanger, Moritz; Mazars, Martial; Klapp, Sabine H. L.; Kahl, Gerhard

    2016-02-01

    We investigate the structural properties of a two-dimensional system of ellipsoidal particles carrying a linear quadrupole moment in their center. These particles represent a simple model for a variety of uncharged, non-polar conjugated organic molecules. Using optimization tools based on ideas of evolutionary algorithms, we first examine the ground state structures as we vary the aspect ratio of the particles and the pressure. Interestingly, we find, besides the intuitively expected T-like configurations, a variety of complex structures, characterized with up to three different particle orientations. In an effort to explore the impact of thermal fluctuations, we perform constant-pressure molecular dynamics simulations within a range of rather low temperatures. We observe that ground state structures formed by particles with a large aspect ratio are in particular suited to withstand fluctuations up to rather high temperatures. Our comprehensive investigations allow for a deeper understanding of molecular or colloidal monolayer arrangements under the influence of a typical electrostatic interaction on a coarse-grained level.

  2. DNA viewed as an out-of-equilibrium structure

    NASA Astrophysics Data System (ADS)

    Provata, A.; Nicolis, C.; Nicolis, G.

    2014-05-01

    The complexity of the primary structure of human DNA is explored using methods from nonequilibrium statistical mechanics, dynamical systems theory, and information theory. A collection of statistical analyses is performed on the DNA data and the results are compared with sequences derived from different stochastic processes. The use of χ2 tests shows that DNA can not be described as a low order Markov chain of order up to r =6. Although detailed balance seems to hold at the level of a binary alphabet, it fails when all four base pairs are considered, suggesting spatial asymmetry and irreversibility. Furthermore, the block entropy does not increase linearly with the block size, reflecting the long-range nature of the correlations in the human genomic sequences. To probe locally the spatial structure of the chain, we study the exit distances from a specific symbol, the distribution of recurrence distances, and the Hurst exponent, all of which show power law tails and long-range characteristics. These results suggest that human DNA can be viewed as a nonequilibrium structure maintained in its state through interactions with a constantly changing environment. Based solely on the exit distance distribution accounting for the nonequilibrium statistics and using the Monte Carlo rejection sampling method, we construct a model DNA sequence. This method allows us to keep both long- and short-range statistical characteristics of the native DNA data. The model sequence presents the same characteristic exponents as the natural DNA but fails to capture spatial correlations and point-to-point details.

  3. DNA viewed as an out-of-equilibrium structure.

    PubMed

    Provata, A; Nicolis, C; Nicolis, G

    2014-05-01

    The complexity of the primary structure of human DNA is explored using methods from nonequilibrium statistical mechanics, dynamical systems theory, and information theory. A collection of statistical analyses is performed on the DNA data and the results are compared with sequences derived from different stochastic processes. The use of χ^{2} tests shows that DNA can not be described as a low order Markov chain of order up to r=6. Although detailed balance seems to hold at the level of a binary alphabet, it fails when all four base pairs are considered, suggesting spatial asymmetry and irreversibility. Furthermore, the block entropy does not increase linearly with the block size, reflecting the long-range nature of the correlations in the human genomic sequences. To probe locally the spatial structure of the chain, we study the exit distances from a specific symbol, the distribution of recurrence distances, and the Hurst exponent, all of which show power law tails and long-range characteristics. These results suggest that human DNA can be viewed as a nonequilibrium structure maintained in its state through interactions with a constantly changing environment. Based solely on the exit distance distribution accounting for the nonequilibrium statistics and using the Monte Carlo rejection sampling method, we construct a model DNA sequence. This method allows us to keep both long- and short-range statistical characteristics of the native DNA data. The model sequence presents the same characteristic exponents as the natural DNA but fails to capture spatial correlations and point-to-point details. PMID:25353737

  4. On calculating the equilibrium structure of molecular crystals.

    SciTech Connect

    Mattsson, Ann Elisabet; Wixom, Ryan R.; Mattsson, Thomas Kjell Rene

    2010-03-01

    The difficulty of calculating the ambient properties of molecular crystals, such as the explosive PETN, has long hampered much needed computational investigations of these materials. One reason for the shortcomings is that the exchange-correlation functionals available for Density Functional Theory (DFT) based calculations do not correctly describe the weak intermolecular van der Waals' forces present in molecular crystals. However, this weak interaction also poses other challenges for the computational schemes used. We will discuss these issues in the context of calculations of lattice constants and structure of PETN with a number of different functionals, and also discuss if these limitations can be circumvented for studies at non-ambient conditions.

  5. The accuracy of diffusion quantum Monte Carlo simulations in the determination of molecular equilibrium structures

    NASA Astrophysics Data System (ADS)

    Lu, Shih-I.

    2004-12-01

    For a test set of 17 first-row small molecules, the equilibrium structures are calculated with Ornstein-Uhlenbeck diffusion quantum Monte Carlo simulations guiding by trial wave functions constructed from floating spherical Gaussian orbitals and spherical Gaussian geminals. To measure performance of the Monte Carlo calculations, the mean deviation, the mean absolute deviation, the maximum absolute deviation, and the standard deviation of Monte Carlo calculated equilibrium structures with respect to empirical equilibrium structures are given. This approach is found to yield results having a uniformly high quality, being consistent with empirical equilibrium structures and surpassing calculated values from the coupled cluster model with single, double, and noniterative triple excitations [CCSD(T)] with the basis sets of cc-pCVQZ and cc-pVQZ. The nonrelativistic equilibrium atomization energies are also presented to assess performance of the calculated methods. The mean absolute deviations regarding experimental atomization energy are 0.16 and 0.21 kcal/mol for the Monte Carlo and CCSD(T)/cc-pCV(56)Z calculations, respectively.

  6. Dimensions and equilibrium structures of the primary component of the nonsynchronous binary systems

    NASA Astrophysics Data System (ADS)

    Pathania, A.; Medupe, T.

    2014-01-01

    Rotating stars and stars in the synchronous binaries have been extensively studied in literature. However, there are only few studies that have investigated the problems of the nonsynchronous binaries. In the present paper, we have made an attempt to study the various dimensions and equilibrium structures of the primary component of the nonsynchronous binaries. We have used the first approximation theory of Limber (1963) along with the methodology as that proposed by Mohan and Saxena (1983) for the present study. The objective of this paper is to check the effect of nonsynchronism on the various dimensions and equilibrium structures of the primary components of the binary systems. The results of the present study shows that there is change in the dimensions and equilibrium structures of the primary component of the binary systems due to nonsynchronism, and this change is more appreciable when the difference between the angular velocities of rotation and revolution is large.

  7. Assembly of nothing: equilibrium fluids with designed structured porosity.

    PubMed

    Lindquist, Beth A; Jadrich, Ryan B; Truskett, Thomas M

    2016-03-14

    Controlled micro- to meso-scale porosity is a common materials design goal with possible applications ranging from molecular gas adsorption to particle size selective permeability or solubility. Here, we use inverse methods of statistical mechanics to design an isotropic pair interaction that, in the absence of an external field, assembles particles into an inhomogeneous fluid matrix surrounding pores of prescribed size ordered in a lattice morphology. The pore size can be tuned via modification of temperature or particle concentration. Moreover, modulating density reveals a rich series of microphase-separated morphologies including pore- or particle-based lattices, pore- or particle-based columns, and bicontinuous or lamellar structures. Sensitivity of pore assembly to the form of the designed interaction potential is explored. PMID:26883309

  8. Tubular precipitation structures: materials synthesis under non-equilibrium conditions.

    PubMed

    Makki, Rabih; Roszol, László; Pagano, Jason J; Steinbock, Oliver

    2012-06-28

    Inorganic precipitation reactions are known to self-organize a variety of macroscopic structures, including hollow tubes. We discuss recent advances in this field with an emphasis on experiments similar to 'silica gardens'. These reactions involve metal salts and sodium silicate solution. Reactions triggered from reagent-loaded microbeads can produce tubes with inner radii of down to 3 μm. Distinct wall morphologies are reported. For pump-driven injection, three qualitatively different growth regimes exist. In one of these regimes, tubes assemble around a buoyant jet of reactant solution, which allows the quantitative prediction of the tube radius. Additional topics include relaxation oscillations and the templating of tube growth with pinned gas bubble and mechanical devices. The tube materials and their nano-to-micro architectures are discussed for the cases of silica/Cu(OH)(2) and silica/Zn(OH)(2)/ZnO tubes. The latter case shows photocatalytic activity and photoluminescence. PMID:22615464

  9. On the time needed to reach an equilibrium structure of the radiation belts

    DOE PAGESBeta

    Ripoll, J. -F.; Loran, V.; Cunningham, Gregory Scott; Reeves, Geoffrey D.; Shprits, Y. Y.

    2016-06-04

    In this paper, we complement the notion of equilibrium states of the radiation belts with a discussion on the dynamics and time needed to reach equilibrium. We solve for the equilibrium states obtained using 1D radial diffusion with recently developed hiss and chorus lifetimes at constant values of Kp = 1, 3 and 6. We find that the equilibrium states at moderately low Kp, when plotted vs L-shell (L) and energy (E), display the same interesting S-shape for the inner edge of the outer belt as recently observed by the Van Allen Probes. The S-shape is also produced as themore » radiation belts dynamically evolve toward the equilibrium state when initialized to simulate the buildup after a massive dropout or to simulate loss due to outward diffusion from a saturated state. Physically, this shape, intimately linked with the slot structure, is due to the dependence of electron loss rate (originating from wave-particle interactions) on both energy and L-shell. Equilibrium electron flux profiles are governed by the Biot number (τDiffusion/τloss), with large Biot number corresponding to low fluxes and low Biot number to large fluxes. The time it takes for the flux at a specific (L, E) to reach the value associated with the equilibrium state, starting from these different initial states, is governed by the initial state of the belts, the property of the dynamics (diffusion coefficients), and the size of the domain of computation. Its structure shows a rather complex scissor form in the (L, E) plane. The equilibrium value (phase space density or flux) is practically reachable only for selected regions in (L, E) and geomagnetic activity. Convergence to equilibrium requires hundreds of days in the inner belt for E > 300 keV and moderate Kp (≤3). It takes less time to reach equilibrium during disturbed geomagnetic conditions (Kp ≥ 3), when the system evolves faster. Restricting our interest to the slot region, below L = 4, we find that only small regions in (L, E) space

  10. Equilibrium Geometries and Electronic Structure of Small Silicon Monohydrides Clusters

    NASA Astrophysics Data System (ADS)

    Yang, Jucai; Bai, Xue; Li, Chunping; Xu, Wenguo; Xiao, Wensheng

    The geometries and energies of small silicon monohydride clusters (Si2H-Si10H) have been systematically investigated by density functional theory (DFT) scheme with DZP++ basis sets. Several possible geometric arrangements and electronic states have been considered for each cluster. The results on Si2H-Si4H are in good accordance with previous ab initio calculation. The geometry of ground state of Si2H is found to be a bridged C2v structure, and Si3H to be a bridged C2v, while Si4H a non-bridged Cs symmetry with 2A‧ state. The non-bridged geometries of ground state of Si5H-Si10H have been found to be corresponding to C2v (2B1), C2v (2B1), C5v (2A1), Cs (2A‧‧) (have two types), C1 (not symmetry), and Cs (2A‧), respectively. The results on Si5H, Si6H, Si8H and Si9H are different from previous calculations. Compared silicon clusters (Sin) with silicon monohydrides (SinH) clusters, the addition of a single hydrogen atom cannot cause great changes in the ground state geometries of Si2, Si3, Si4, Si7, Si9, and Si10 clusters, while in the ground state geometries of Si5, Si6 and Si8 clusters the change is great. The dissociation energies calculated indicates that Si4H, Si7H, and Si10H clusters are less stable than others.

  11. Equilibrium structure of the GeI/sub 4/ molecule

    SciTech Connect

    Giricheva, N.I.; Girichev, G.V.; Shlykov, S.A.; Titov, V.A.; Chusova, T.P.

    1988-09-01

    An electron-diffraction study has been made on the saturated vapor over solid GeI/sub 4/at 77 /plus minus/ 10/degree/C. The patterns have been interpreted on the assumption that the vapor contains only GeI/sub 4/ molecules. Three methods have been used to describe the measurements, and the corresponding parameter sets have been derived: (a) in terms of thermally averaged values (rg(Ge-I) = 2.515(5) /angstrom/, rg(I-I) = 4.093(9) /angstrom/, l(Ge-I) = 0.057(2) /angstrom/, l(I-I) = 0.149(4) /angstrom/); (b) in terms of a harmonic potential function (r/sub e//sup h/(Ge-I) = 2.507 /angstrom/, F/sub 11/ = 1.90, F/sub 22/ = 0.069, F/sub 33/ = 1.54, F/sub 44/ = 0.075 mdyn//angstrom/); and (c) in terms of an anharmonic potential function (r/sub e/(Ge-I) = 2.499 /angstrom/, F/sub 11/ = 1.79, F/sub 22/ = 0.058, F/sub 33/ = 1.49, F/sub 44/ = 0.095 mdyn//angstrom/, a/sub Ge-I/ = 2.28 /angstrom//sup /minus/1/, a/sub I-I/ = 0.32 /angstrom//sup /minus/1/). The diffraction studies confirm conclusions from spectral data on the tetrahedral structure of the GeI/sub 4/ molecule.

  12. Accurate measurements of vadose zone fluxes using automated equilibrium tension plate lysimeters: A synopsis of results from the Spydia research facility, New Zealand.

    NASA Astrophysics Data System (ADS)

    Wöhling, Thomas; Barkle, Greg; Stenger, Roland; Moorhead, Brian; Wall, Aaron; Clague, Juliet

    2014-05-01

    Automated equilibrium tension plate lysimeters (AETLs) are arguably the most accurate method to measure unsaturated water and contaminant fluxes below the root zone at the scale of up to 1 m². The AETL technique utilizes a porous sintered stainless-steel plate to provide a comparatively large sampling area with a continuously controlled vacuum that is in "equilibrium" with the surrounding vadose zone matric pressure to ensure measured fluxes represent those under undisturbed conditions. This novel lysimeter technique was used at an intensive research site for investigations of contaminant pathways from the land surface to the groundwater on a sheep and beef farm under pastoral land use in the Tutaeuaua subcatchment, New Zealand. The Spydia research facility was constructed in 2005 and was fully operational between 2006 and 2011. Extending from a central access caisson, 15 separately controlled AETLs with 0.2 m² surface area were installed at five depths between 0.4 m and 5.1 m into the undisturbed volcanic vadose zone materials. The unique setup of the facility ensured minimum interference of the experimental equipment and external factors with the measurements. Over the period of more than five years, a comprehensive data set was collected at each of the 15 AETL locations which comprises of time series of soil water flux, pressure head, volumetric water contents, and soil temperature. The soil water was regularly analysed for EC, pH, dissolved carbon, various nitrogen compounds (including nitrate, ammonia, and organic N), phosphorus, bromide, chloride, sulphate, silica, and a range of other major ions, as well as for various metals. Climate data was measured directly at the site (rainfall) and a climate station at 500m distance. The shallow groundwater was sampled at three different depths directly from the Spydia caisson and at various observation wells surrounding the facility. Two tracer experiments were conducted at the site in 2009 and 2010. In the 2009

  13. Precise equilibrium structure determination of hydrazoic acid (HN{sub 3}) by millimeter-wave spectroscopy

    SciTech Connect

    Amberger, Brent K.; Esselman, Brian J.; Woods, R. Claude; McMahon, Robert J.; Stanton, John F.

    2015-09-14

    The millimeter-wave spectrum of hydrazoic acid (HN{sub 3}) was analyzed in the frequency region of 235-450 GHz. Transitions from a total of 14 isotopologues were observed and fit using the A-reduced or S-reduced Hamiltonian. Coupled-cluster calculations were performed to obtain a theoretical geometry, as well as rotation-vibration interaction corrections. These calculated vibration-rotation correction terms were applied to the experimental rotational constants to obtain mixed theoretical/experimental equilibrium rotational constants (A{sub e}, B{sub e}, and C{sub e}). These equilibrium rotational constants were then used to obtain an equilibrium (R{sub e}) structure using a least-squares fitting routine. The R{sub e} structural parameters are consistent with a previously published R{sub s} structure, largely falling within the uncertainty limits of that R{sub s} structure. The present R{sub e} geometric parameters of HN{sub 3} are determined with exceptionally high accuracy, as a consequence of the large number of isotopologues measured experimentally and the sophisticated (coupled-cluster theoretical treatment (CCSD(T))/ANO2) of the vibration-rotation interactions. The R{sub e} structure exhibits remarkable agreement with the CCSD(T)/cc-pCV5Z predicted structure, validating both the accuracy of the ab initio method and the claimed uncertainties of the theoretical/experimental structure determination.

  14. Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids

    SciTech Connect

    Dunn, Nicholas J. H.; Noid, W. G.

    2015-12-28

    The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed “pressure-matching” variational principle to determine a volume-dependent contribution to the potential, U{sub V}(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing U{sub V}, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that U{sub V} accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the “simplicity” of the model.

  15. Peptide Length Determines Equilibrium Secondary Structure in Protein-Analogous Micelles

    NASA Astrophysics Data System (ADS)

    Tirrell, Matthew; Marullo, Rachel; Kastantin, Mark

    2013-03-01

    This work seeks improved bottom-up design of bioinspired materials built from peptide-amphiphiles, which are a class of bioconjugates whereby a biofunctional peptide is covalently attached to a hydrophobic moiety that drives self-assembly in aqueous solution. Specifically, this work highlights the importance of peptide length (i.e. molecular weight) in determining the equilibrium secondary structure of the peptide as well as the self-assembled (i.e. micelle) geometry. Peptides used here repeat a seven-amino acid sequence between one and four times to vary peptide length while maintaining similar peptide-peptide interactions. Without a hydrophobic tail, these peptides all exhibit a combination of random coil and α-helical structure. Upon self-assembly, however, short peptides are prone to β-sheet structure and cylindrical geometry while longer peptides remain helical in spheroidal micelles. The transition to β-sheets in short peptides is kinetic, whereby amphiphiles first self-assemble with helical peptide structure, then overcome an activation barrier as they transition to their equilibrium β-sheet structure at a rate that depends on both temperature and ionic strength. These results identify peptide length as an important control over equilibrium peptide secondary structure and micelle geometry. Furthermore, the kinetic nature of the helix-to-sheet transition opens the door for shape-changing bioinspired materials with tunable conversion rates.

  16. Formation of copper porous structures under near-equilibrium chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Kornyushchenko, A. S.; Natalich, V. V.; Perekrestov, V. I.

    2016-05-01

    The mechanism of copper structure formation under near-equilibrium conditions in a chemically-active medium-condensate system has been investigated. The desired conditions have been implemented using CVD system. Copper chloride CuCl2 was used as a source material, and mixture of hydrogen with nitrogen served as a working gas. The influence of the evaporation temperature, condensation temperature and state of the growth surface on the porous structures formation has been investigated. It has been established, that the structure formation mechanism is determined by layer-by-layer or normal crystal growth, nucleation and growth of whiskers, and also by partial intergrowth of structural elements.

  17. Relevant Models of Equilibrium Structures in One-Phase Regimes of Microemulsions.

    NASA Astrophysics Data System (ADS)

    Edwards, M. E.

    2000-11-01

    Although several studies have focused on equilibrium structures--domains--in one-phase regimes of dilutive microemulsions, the structures have not been completely determined. Here, we review the relevant continuum-statistical and continuum-mechanical models with the ultimate objective of their extension or modification. Presently, the models describe single droplet domains, two interacting droplets or dimer constructions, and thermal fluctuation description. Also, we present the rudiments of an interaction model which considers the undulations of two ellipsoidal droplets. A satisfactory model of equilibrium structures is essential if we are to further elucidate the behavior of microemulsions in various environments, such as, the case of microemulsions being located in a pulsed, external electric field: the phenomenon of static electro-optical Kerr effect. Currently, variations exist between relevant models and experimental results.

  18. Self-equilibrium and stability of regular truncated tetrahedral tensegrity structures

    NASA Astrophysics Data System (ADS)

    Zhang, J. Y.; Ohsaki, M.

    2012-10-01

    This paper presents analytical conditions of self-equilibrium and super-stability for the regular truncated tetrahedral tensegrity structures, nodes of which have one-to-one correspondence to the tetrahedral group. These conditions are presented in terms of force densities, by investigating the block-diagonalized force density matrix. The block-diagonalized force density matrix, with independent sub-matrices lying on its leading diagonal, is derived by making use of the tetrahedral symmetry via group representation theory. The condition for self-equilibrium is found by enforcing the force density matrix to have the necessary number of nullities, which is four for three-dimensional structures. The condition for super-stability is further presented by guaranteeing positive semi-definiteness of the force density matrix.

  19. Approximate analytic solutions for the ionization structure of a pressure equilibrium Strömgren sphere

    NASA Astrophysics Data System (ADS)

    Tinoco Arenas, A.; González Bolívar, M.; Medina Covarrubias, R.; Raga, A. C.

    2015-10-01

    We present analytic models for a photoionized region in pressure equilibrium with the surrounding, neutral material. The models are based on the assumption of a linear relation between the H ionization fraction and the square of the sound speed of the gas. We show that under these assumptions the "grey" radiative transfer equation has analytic solutions that provide the ionization structure and the density of the nebula as a function of radius.

  20. Accurate Electron Affinity of Iron and Fine Structures of Negative Iron ions

    PubMed Central

    Chen, Xiaolin; Luo, Zhihong; Li, Jiaming; Ning, Chuangang

    2016-01-01

    Ionization potential (IP) is defined as the amount of energy required to remove the most loosely bound electron of an atom, while electron affinity (EA) is defined as the amount of energy released when an electron is attached to a neutral atom. Both IP and EA are critical for understanding chemical properties of an element. In contrast to accurate IPs and structures of neutral atoms, EAs and structures of negative ions are relatively unexplored, especially for the transition metal anions. Here, we report the accurate EA value of Fe and fine structures of Fe− using the slow electron velocity imaging method. These measurements yield a very accurate EA value of Fe, 1235.93(28) cm−1 or 153.236(34) meV. The fine structures of Fe− were also successfully resolved. The present work provides a reliable benchmark for theoretical calculations, and also paves the way for improving the EA measurements of other transition metal atoms to the sub cm−1 accuracy. PMID:27138292

  1. Accurate Electron Affinity of Iron and Fine Structures of Negative Iron ions.

    PubMed

    Chen, Xiaolin; Luo, Zhihong; Li, Jiaming; Ning, Chuangang

    2016-01-01

    Ionization potential (IP) is defined as the amount of energy required to remove the most loosely bound electron of an atom, while electron affinity (EA) is defined as the amount of energy released when an electron is attached to a neutral atom. Both IP and EA are critical for understanding chemical properties of an element. In contrast to accurate IPs and structures of neutral atoms, EAs and structures of negative ions are relatively unexplored, especially for the transition metal anions. Here, we report the accurate EA value of Fe and fine structures of Fe(-) using the slow electron velocity imaging method. These measurements yield a very accurate EA value of Fe, 1235.93(28) cm(-1) or 153.236(34) meV. The fine structures of Fe(-) were also successfully resolved. The present work provides a reliable benchmark for theoretical calculations, and also paves the way for improving the EA measurements of other transition metal atoms to the sub cm(-1) accuracy. PMID:27138292

  2. Accurate Electron Affinity of Iron and Fine Structures of Negative Iron ions

    NASA Astrophysics Data System (ADS)

    Chen, Xiaolin; Luo, Zhihong; Li, Jiaming; Ning, Chuangang

    2016-05-01

    Ionization potential (IP) is defined as the amount of energy required to remove the most loosely bound electron of an atom, while electron affinity (EA) is defined as the amount of energy released when an electron is attached to a neutral atom. Both IP and EA are critical for understanding chemical properties of an element. In contrast to accurate IPs and structures of neutral atoms, EAs and structures of negative ions are relatively unexplored, especially for the transition metal anions. Here, we report the accurate EA value of Fe and fine structures of Fe‑ using the slow electron velocity imaging method. These measurements yield a very accurate EA value of Fe, 1235.93(28) cm‑1 or 153.236(34) meV. The fine structures of Fe‑ were also successfully resolved. The present work provides a reliable benchmark for theoretical calculations, and also paves the way for improving the EA measurements of other transition metal atoms to the sub cm‑1 accuracy.

  3. Electronic structure and bonding of HBeLi, HmgLi, and HCaLi in their bent equilibrium geometries.

    PubMed

    Penotti, Fabio E

    2012-01-14

    Compact, yet accurate, non-orthogonal multi-configuration wavefunctions have been computed for HBeLi, HMgLi, and HCaLi in their respective nonlinear equilibrium geometries. They appear to be dominated by just two configurations, "orbitally relaxed" versions of the single-configuration spin-coupled and generalized valence bond (GVB) wavefunctions, respectively, with a smaller contribution from a self-consistent field (SCF)-like configuration. Double excitations out of the main configurations, while required for quantitative accuracy, enter the wavefunction with such small weights that they do not alter the qualitative picture that emerges from the orbital structure of the two main configurations. For comparison, calculations have also been carried out with two orthogonality-free configurations as reference, and no GVB-like or SCF-like configuration. Atoms-in-molecules (AIM) topological analyses of the overall electron densities, and considerations of local energetics in the differential neighbourhood of the equilibrium geometries, have been used to provide independent assessments of the nature of bonding in these molecules. Orbital structure and AIM results together suggest the existence of three-centre two-electron M-H-M' bonds through hydrogen in all three molecules. Orbital pictures suggest these bonds are at least partially covalent, while a strict interpretation of values of the electron density Laplacian at AIM bond critical points would imply closed-shell interactions. Also for all three molecules, the orbital structures of the two main configurations suggest the presence of a one-electron two-centre bond between Li and the alkaline-earth atom. This bond may provide at least a partial explanation for the relative shortness of the inter-metallic distances, but is apparently too spread out to show up in AIM analyses of the total electron density. Considerations of local energetics support the more nuanced description of bonding that emerges, for these three

  4. Ribosomes in the balance: structural equilibrium ensures translational fidelity and proper gene expression

    PubMed Central

    Musalgaonkar, Sharmishtha; Moomau, Christine A.; Dinman, Jonathan D.

    2014-01-01

    At equilibrium, empty ribosomes freely transit between the rotated and un-rotated states. In the cell, the binding of two translation elongation factors to the same general region of the ribosome stabilizes one state over the other. These stabilized states are resolved by expenditure of energy in the form of GTP hydrolysis. A prior study employing mutants of a late assembling peripheral ribosomal protein suggested that ribosome rotational status determines its affinity for elongation factors, and hence translational fidelity and gene expression. Here, mutants of the early assembling integral ribosomal protein uL2 are used to test the generality of this hypothesis. rRNA structure probing analyses reveal that mutations in the uL2 B7b bridge region shift the equilibrium toward the rotated state, propagating rRNA structural changes to all of the functional centers of ribosome. Structural disequilibrium unbalances ribosome biochemically: rotated ribosomes favor binding of the eEF2 translocase and disfavor that of the elongation ternary complex. This manifests as specific translational fidelity defects, impacting the expression of genes involved in telomere maintenance. A model is presented describing how cyclic intersubunit rotation ensures the unidirectionality of translational elongation, and how perturbation of rotational equilibrium affects specific aspects of translational fidelity and cellular gene expression. PMID:25389262

  5. On the equilibrium structures of self-gravitating masses of gas containing axisymmetric magnetic fields

    NASA Technical Reports Server (NTRS)

    Lerche, I.; Low, B. C.

    1980-01-01

    The general equations describing the equilibrium shapes of self-gravitating gas clouds containing axisymmetric magnetic fields are presented. The general equations admit of a large class of solutions. It is shown that if one additional (ad hoc) asumption is made that the mass be spherically symmetrically distributed, then the gas pressure and the boundary conditions are sufficiently constraining that the general topological structure of the solution is effectively determined. The further assumption of isothermal conditions for this case demands that all solutions possess force-free axisymmetric magnetic fields. It is also shown how the construction of aspherical (but axisymmetric) configurations can be achieved in some special cases, and it is demonstrated that the detailed form of the possible equilibrium shapes depends upon the arbitrary choice of the functional form of the variation of the gas pressure along the field lines.

  6. CoMOGrad and PHOG: From Computer Vision to Fast and Accurate Protein Tertiary Structure Retrieval

    PubMed Central

    Karim, Rezaul; Aziz, Mohd. Momin Al; Shatabda, Swakkhar; Rahman, M. Sohel; Mia, Md. Abul Kashem; Zaman, Farhana; Rakin, Salman

    2015-01-01

    The number of entries in a structural database of proteins is increasing day by day. Methods for retrieving protein tertiary structures from such a large database have turn out to be the key to comparative analysis of structures that plays an important role to understand proteins and their functions. In this paper, we present fast and accurate methods for the retrieval of proteins having tertiary structures similar to a query protein from a large database. Our proposed methods borrow ideas from the field of computer vision. The speed and accuracy of our methods come from the two newly introduced features- the co-occurrence matrix of the oriented gradient and pyramid histogram of oriented gradient- and the use of Euclidean distance as the distance measure. Experimental results clearly indicate the superiority of our approach in both running time and accuracy. Our method is readily available for use from this website: http://research.buet.ac.bd:8080/Comograd/. PMID:26293226

  7. CoMOGrad and PHOG: From Computer Vision to Fast and Accurate Protein Tertiary Structure Retrieval.

    PubMed

    Karim, Rezaul; Aziz, Mohd Momin Al; Shatabda, Swakkhar; Rahman, M Sohel; Mia, Md Abul Kashem; Zaman, Farhana; Rakin, Salman

    2015-01-01

    The number of entries in a structural database of proteins is increasing day by day. Methods for retrieving protein tertiary structures from such a large database have turn out to be the key to comparative analysis of structures that plays an important role to understand proteins and their functions. In this paper, we present fast and accurate methods for the retrieval of proteins having tertiary structures similar to a query protein from a large database. Our proposed methods borrow ideas from the field of computer vision. The speed and accuracy of our methods come from the two newly introduced features- the co-occurrence matrix of the oriented gradient and pyramid histogram of oriented gradient- and the use of Euclidean distance as the distance measure. Experimental results clearly indicate the superiority of our approach in both running time and accuracy. Our method is readily available for use from this website: http://research.buet.ac.bd:8080/Comograd/. PMID:26293226

  8. CC/DFT Route toward Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as a Case Study.

    PubMed

    Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Cimino, Paola; Penocchio, Emanuele; Puzzarini, Cristina

    2015-09-01

    The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC

  9. Born energy, acid-base equilibrium, structure and interactions of end-grafted weak polyelectrolyte layers.

    PubMed

    Nap, R J; Tagliazucchi, M; Szleifer, I

    2014-01-14

    This work addresses the effect of the Born self-energy contribution in the modeling of the structural and thermodynamical properties of weak polyelectrolytes confined to planar and curved surfaces. The theoretical framework is based on a theory that explicitly includes the conformations, size, shape, and charge distribution of all molecular species and considers the acid-base equilibrium of the weak polyelectrolyte. Namely, the degree of charge in the polymers is not imposed but it is a local varying property that results from the minimization of the total free energy. Inclusion of the dielectric properties of the polyelectrolyte is important as the environment of a polymer layer is very different from that in the adjacent aqueous solution. The main effect of the Born energy contribution on the molecular organization of an end-grafted weak polyacid layer is uncharging the weak acid (or basic) groups and consequently decreasing the concentration of mobile ions within the layer. The magnitude of the effect increases with polymer density and, in the case of the average degree of charge, it is qualitatively equivalent to a small shift in the equilibrium constant for the acid-base equilibrium of the weak polyelectrolyte monomers. The degree of charge is established by the competition between electrostatic interactions, the polymer conformational entropy, the excluded volume interactions, the translational entropy of the counterions and the acid-base chemical equilibrium. Consideration of the Born energy introduces an additional energetic penalty to the presence of charged groups in the polyelectrolyte layer, whose effect is mitigated by down-regulating the amount of charge, i.e., by shifting the local-acid base equilibrium towards its uncharged state. Shifting of the local acid-base equilibrium and its effect on the properties of the polyelectrolyte layer, without considering the Born energy, have been theoretically predicted previously. Account of the Born energy leads

  10. Born energy, acid-base equilibrium, structure and interactions of end-grafted weak polyelectrolyte layers

    SciTech Connect

    Nap, R. J.; Tagliazucchi, M.; Szleifer, I.

    2014-01-14

    This work addresses the effect of the Born self-energy contribution in the modeling of the structural and thermodynamical properties of weak polyelectrolytes confined to planar and curved surfaces. The theoretical framework is based on a theory that explicitly includes the conformations, size, shape, and charge distribution of all molecular species and considers the acid-base equilibrium of the weak polyelectrolyte. Namely, the degree of charge in the polymers is not imposed but it is a local varying property that results from the minimization of the total free energy. Inclusion of the dielectric properties of the polyelectrolyte is important as the environment of a polymer layer is very different from that in the adjacent aqueous solution. The main effect of the Born energy contribution on the molecular organization of an end-grafted weak polyacid layer is uncharging the weak acid (or basic) groups and consequently decreasing the concentration of mobile ions within the layer. The magnitude of the effect increases with polymer density and, in the case of the average degree of charge, it is qualitatively equivalent to a small shift in the equilibrium constant for the acid-base equilibrium of the weak polyelectrolyte monomers. The degree of charge is established by the competition between electrostatic interactions, the polymer conformational entropy, the excluded volume interactions, the translational entropy of the counterions and the acid-base chemical equilibrium. Consideration of the Born energy introduces an additional energetic penalty to the presence of charged groups in the polyelectrolyte layer, whose effect is mitigated by down-regulating the amount of charge, i.e., by shifting the local-acid base equilibrium towards its uncharged state. Shifting of the local acid-base equilibrium and its effect on the properties of the polyelectrolyte layer, without considering the Born energy, have been theoretically predicted previously. Account of the Born energy leads

  11. Born energy, acid-base equilibrium, structure and interactions of end-grafted weak polyelectrolyte layers

    NASA Astrophysics Data System (ADS)

    Nap, R. J.; Tagliazucchi, M.; Szleifer, I.

    2014-01-01

    This work addresses the effect of the Born self-energy contribution in the modeling of the structural and thermodynamical properties of weak polyelectrolytes confined to planar and curved surfaces. The theoretical framework is based on a theory that explicitly includes the conformations, size, shape, and charge distribution of all molecular species and considers the acid-base equilibrium of the weak polyelectrolyte. Namely, the degree of charge in the polymers is not imposed but it is a local varying property that results from the minimization of the total free energy. Inclusion of the dielectric properties of the polyelectrolyte is important as the environment of a polymer layer is very different from that in the adjacent aqueous solution. The main effect of the Born energy contribution on the molecular organization of an end-grafted weak polyacid layer is uncharging the weak acid (or basic) groups and consequently decreasing the concentration of mobile ions within the layer. The magnitude of the effect increases with polymer density and, in the case of the average degree of charge, it is qualitatively equivalent to a small shift in the equilibrium constant for the acid-base equilibrium of the weak polyelectrolyte monomers. The degree of charge is established by the competition between electrostatic interactions, the polymer conformational entropy, the excluded volume interactions, the translational entropy of the counterions and the acid-base chemical equilibrium. Consideration of the Born energy introduces an additional energetic penalty to the presence of charged groups in the polyelectrolyte layer, whose effect is mitigated by down-regulating the amount of charge, i.e., by shifting the local-acid base equilibrium towards its uncharged state. Shifting of the local acid-base equilibrium and its effect on the properties of the polyelectrolyte layer, without considering the Born energy, have been theoretically predicted previously. Account of the Born energy leads

  12. Equilibrium and structural studies on metal complexes of carbohyrates and their derivatives.

    PubMed

    Nagy, L; Szorcsik, A

    2002-04-10

    A summary is presented of the studies of our group on metal complexes of carbohydrates (aldoses, ketoses, mono-, di- and polysaccharides) and their derivatives (aldonic, alduronic acids, polyalcohols, amino sugars, amino acid sugar adducts, AMP, ATP, etc.). The results are reported of equilibrium, electrochemical, solution and solid-state structural studies of complexes of transition metals [Cu(II), Fe(III), Ni(II), Zn(II), Co(II), Ag(I), Mn in different oxidation states and organotin(IV)]. The structural parameters (coordination number, bond distance, and Debye-Waller factor) obtained by extended X-ray absorption fine structure spectroscopic (EXAFS) spectroscopy are discussed in detail. The general rules concerning the formation and structure of such complexes are emphasized. PMID:11931957

  13. An equilibrium double-twist model for the radial structure of collagen fibrils.

    PubMed

    Brown, Aidan I; Kreplak, Laurent; Rutenberg, Andrew D

    2014-11-14

    Mammalian tissues contain networks and ordered arrays of collagen fibrils originating from the periodic self-assembly of helical 300 nm long tropocollagen complexes. The fibril radius is typically between 25 to 250 nm, and tropocollagen at the surface appears to exhibit a characteristic twist-angle with respect to the fibril axis. Similar fibril radii and twist-angles at the surface are observed in vitro, suggesting that these features are controlled by a similar self-assembly process. In this work, we propose a physical mechanism of equilibrium radius control for collagen fibrils based on a radially varying double-twist alignment of tropocollagen within a collagen fibril. The free-energy of alignment is similar to that of liquid crystalline blue phases, and we employ an analytic Euler-Lagrange and numerical free energy minimization to determine the twist-angle between the molecular axis and the fibril axis along the radial direction. Competition between the different elastic energy components, together with a surface energy, determines the equilibrium radius and twist-angle at the fibril surface. A simplified model with a twist-angle that is linear with radius is a reasonable approximation in some parameter regimes, and explains a power-law dependence of radius and twist-angle at the surface as parameters are varied. Fibril radius and twist-angle at the surface corresponding to an equilibrium free-energy minimum are consistent with existing experimental measurements of collagen fibrils. Remarkably, in the experimental regime, all of our model parameters are important for controlling equilibrium structural parameters of collagen fibrils. PMID:25238208

  14. Ice crystallization in ultrafine water-salt aerosols: nucleation, ice-solution equilibrium, and internal structure.

    PubMed

    Hudait, Arpa; Molinero, Valeria

    2014-06-01

    Atmospheric aerosols have a strong influence on Earth's climate. Elucidating the physical state and internal structure of atmospheric aqueous aerosols is essential to predict their gas and water uptake, and the locus and rate of atmospherically important heterogeneous reactions. Ultrafine aerosols with sizes between 3 and 15 nm have been detected in large numbers in the troposphere and tropopause. Nanoscopic aerosols arising from bubble bursting of natural and artificial seawater have been identified in laboratory and field experiments. The internal structure and phase state of these aerosols, however, cannot yet be determined in experiments. Here we use molecular simulations to investigate the phase behavior and internal structure of liquid, vitrified, and crystallized water-salt ultrafine aerosols with radii from 2.5 to 9.5 nm and with up to 10% moles of ions. We find that both ice crystallization and vitrification of the nanodroplets lead to demixing of pure water from the solutions. Vitrification of aqueous nanodroplets yields nanodomains of pure low-density amorphous ice in coexistence with vitrified solute rich aqueous glass. The melting temperature of ice in the aerosols decreases monotonically with an increase of solute fraction and decrease of radius. The simulations reveal that nucleation of ice occurs homogeneously at the subsurface of the water-salt nanoparticles. Subsequent ice growth yields phase-segregated, internally mixed, aerosols with two phases in equilibrium: a concentrated water-salt amorphous mixture and a spherical cap-like ice nanophase. The surface of the crystallized aerosols is heterogeneous, with ice and solution exposed to the vapor. Free energy calculations indicate that as the concentration of salt in the particles, the advance of the crystallization, or the size of the particles increase, the stability of the spherical cap structure increases with respect to the alternative structure in which a core of ice is fully surrounded by

  15. Accurate Structure Prediction and Conformational Analysis of Cyclic Peptides with Residue-Specific Force Fields.

    PubMed

    Geng, Hao; Jiang, Fan; Wu, Yun-Dong

    2016-05-19

    Cyclic peptides (CPs) are promising candidates for drugs, chemical biology tools, and self-assembling nanomaterials. However, the development of reliable and accurate computational methods for their structure prediction has been challenging. Here, 20 all-trans CPs of 5-12 residues selected from Cambridge Structure Database have been simulated using replica-exchange molecular dynamics with four different force fields. Our recently developed residue-specific force fields RSFF1 and RSFF2 can correctly identify the crystal-like conformations of more than half CPs as the most populated conformation. The RSFF2 performs the best, which consistently predicts the crystal structures of 17 out of 20 CPs with rmsd < 1.1 Å. We also compared the backbone (ϕ, ψ) sampling of residues in CPs with those in short linear peptides and in globular proteins. In general, unlike linear peptides, CPs have local conformational free energies and entropies quite similar to globular proteins. PMID:27128113

  16. Screened exchange hybrid density functional for accurate and efficient structures and interaction energies.

    PubMed

    Brandenburg, Jan Gerit; Caldeweyher, Eike; Grimme, Stefan

    2016-06-21

    We extend the recently introduced PBEh-3c global hybrid density functional [S. Grimme et al., J. Chem. Phys., 2015, 143, 054107] by a screened Fock exchange variant based on the Henderson-Janesko-Scuseria exchange hole model. While the excellent performance of the global hybrid is maintained for small covalently bound molecules, its performance for computed condensed phase mass densities is further improved. Most importantly, a speed up of 30 to 50% can be achieved and especially for small orbital energy gap cases, the method is numerically much more robust. The latter point is important for many applications, e.g., for metal-organic frameworks, organic semiconductors, or protein structures. This enables an accurate density functional based electronic structure calculation of a full DNA helix structure on a single core desktop computer which is presented as an example in addition to comprehensive benchmark results. PMID:27240749

  17. Accurate Damage Location in Complex Composite Structures and Industrial Environments using Acoustic Emission

    NASA Astrophysics Data System (ADS)

    Eaton, M.; Pearson, M.; Lee, W.; Pullin, R.

    2015-07-01

    The ability to accurately locate damage in any given structure is a highly desirable attribute for an effective structural health monitoring system and could help to reduce operating costs and improve safety. This becomes a far greater challenge in complex geometries and materials, such as modern composite airframes. The poor translation of promising laboratory based SHM demonstrators to industrial environments forms a barrier to commercial up take of technology. The acoustic emission (AE) technique is a passive NDT method that detects elastic stress waves released by the growth of damage. It offers very sensitive damage detection, using a sparse array of sensors to detect and globally locate damage within a structure. However its application to complex structures commonly yields poor accuracy due to anisotropic wave propagation and the interruption of wave propagation by structural features such as holes and thickness changes. This work adopts an empirical mapping technique for AE location, known as Delta T Mapping, which uses experimental training data to account for such structural complexities. The technique is applied to a complex geometry composite aerospace structure undergoing certification testing. The component consists of a carbon fibre composite tube with varying wall thickness and multiple holes, that was loaded under bending. The damage location was validated using X-ray CT scanning and the Delta T Mapping technique was shown to improve location accuracy when compared with commercial algorithms. The onset and progression of damage were monitored throughout the test and used to inform future design iterations.

  18. Influence of molecular structure on the properties of out-of-equilibrium oscillating enzymatic reaction networks.

    PubMed

    Wong, Albert S Y; Postma, Sjoerd G J; Vialshin, Ilia N; Semenov, Sergey N; Huck, Wilhelm T S

    2015-09-30

    Our knowledge of the properties and dynamics of complex molecular reaction networks, for example those found in living systems, considerably lags behind the understanding of elementary chemical reactions. In part, this is because chemical reactions networks are nonlinear systems that operate under conditions far from equilibrium. Of particular interest is the role of individual reaction rates on the stability of the network output. In this research we use a rational approach combined with computational methods, to produce complex behavior (in our case oscillations) and show that small changes in molecular structure are sufficient to impart large changes in network behavior. PMID:26352485

  19. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers

    PubMed Central

    Hattne, Johan; Echols, Nathaniel; Tran, Rosalie; Kern, Jan; Gildea, Richard J.; Brewster, Aaron S.; Alonso-Mori, Roberto; Glöckner, Carina; Hellmich, Julia; Laksmono, Hartawan; Sierra, Raymond G.; Lassalle-Kaiser, Benedikt; Lampe, Alyssa; Han, Guangye; Gul, Sheraz; DiFiore, Dörte; Milathianaki, Despina; Fry, Alan R.; Miahnahri, Alan; White, William E.; Schafer, Donald W.; Seibert, M. Marvin; Koglin, Jason E.; Sokaras, Dimosthenis; Weng, Tsu-Chien; Sellberg, Jonas; Latimer, Matthew J.; Glatzel, Pieter; Zwart, Petrus H.; Grosse-Kunstleve, Ralf W.; Bogan, Michael J.; Messerschmidt, Marc; Williams, Garth J.; Boutet, Sébastien; Messinger, Johannes; Zouni, Athina; Yano, Junko; Bergmann, Uwe; Yachandra, Vittal K.; Adams, Paul D.; Sauter, Nicholas K.

    2014-01-01

    X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and free from radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract statistically significant high-resolution signals from fewer diffraction measurements. PMID:24633409

  20. Polarity, cell division, and out-of-equilibrium dynamics control the growth of epithelial structures

    PubMed Central

    Cerruti, Benedetta; Puliafito, Alberto; Shewan, Annette M.; Yu, Wei; Combes, Alexander N.; Little, Melissa H.; Chianale, Federica; Primo, Luca; Serini, Guido; Mostov, Keith E.; Celani, Antonio

    2013-01-01

    The growth of a well-formed epithelial structure is governed by mechanical constraints, cellular apico-basal polarity, and spatially controlled cell division. Here we compared the predictions of a mathematical model of epithelial growth with the morphological analysis of 3D epithelial structures. In both in vitro cyst models and in developing epithelial structures in vivo, epithelial growth could take place close to or far from mechanical equilibrium, and was determined by the hierarchy of time-scales of cell division, cell–cell rearrangements, and lumen dynamics. Equilibrium properties could be inferred by the analysis of cell–cell contact topologies, and the nonequilibrium phenotype was altered by inhibiting ROCK activity. The occurrence of an aberrant multilumen phenotype was linked to fast nonequilibrium growth, even when geometric control of cell division was correctly enforced. We predicted and verified experimentally that slowing down cell division partially rescued a multilumen phenotype induced by altered polarity. These results improve our understanding of the development of epithelial organs and, ultimately, of carcinogenesis. PMID:24145168

  1. Equilibrium Structures of Differentially Rotating and Tidally Distorted White Dwarf Models of Stars

    NASA Astrophysics Data System (ADS)

    Lal, Arvind Kumar; Mohan, C.; Singh, V. P.

    2006-01-01

    In this paper we present a method for computing the equilibrium structures and various physical parameters of a primary component of the binary system assuming that the primary is more massive than the secondary and is rotating differentially according to the law of the w2 = b0 + b1 × s2 + b2 × s4, w being the angular velocity of rotation of a fluid element distant s from the axis of rotation and b0, b1, b2 suitably chosen numerical constants. This method utilizes the averaging approach of Kippenhahn and Thomas (1997) and the concept of Roche equipotentials in a manner earlier used by Mohan et al. (1997) to incorporate the effects of rotation and tidal distortions on the equilibrium structures of certain rotationally and tidally distorted stellar models. The use of the method has been illustrated by applying it to obtain the structures and some observable parameters of certain differentially rotating and tidally distorted binary systems whose primary component is assumed to be a white dwarf star.

  2. Surface structures of equilibrium restricted curvature model on two fractal substrates

    NASA Astrophysics Data System (ADS)

    Song, Li-Jian; Tang, Gang; Zhang, Yong-Wei; Han, Kui; Xun, Zhi-Peng; Xia, Hui; Hao, Da-Peng; Li, Yan

    2014-01-01

    With the aim to probe the effects of the microscopic details of fractal substrates on the scaling of discrete growth models, the surface structures of the equilibrium restricted curvature (ERC) model on Sierpinski arrowhead and crab substrates are analyzed by means of Monte Carlo simulations. These two fractal substrates have the same fractal dimension df, but possess different dynamic exponents of random walk zrw. The results show that the surface structure of the ERC model on fractal substrates are related to not only the fractal dimension df, but also to the microscopic structures of the substrates expressed by the dynamic exponent of random walk zrw. The ERC model growing on the two substrates follows the well-known Family—Vicsek scaling law and satisfies the scaling relations 2α + df asymp z asymp 2zrw. In addition, the values of the scaling exponents are in good agreement with the analytical prediction of the fractional Mullins—Herring equation.

  3. Accurate Inference of Subtle Population Structure (and Other Genetic Discontinuities) Using Principal Coordinates

    PubMed Central

    Reeves, Patrick A.; Richards, Christopher M.

    2009-01-01

    Background Accurate inference of genetic discontinuities between populations is an essential component of intraspecific biodiversity and evolution studies, as well as associative genetics. The most widely-used methods to infer population structure are model-based, Bayesian MCMC procedures that minimize Hardy-Weinberg and linkage disequilibrium within subpopulations. These methods are useful, but suffer from large computational requirements and a dependence on modeling assumptions that may not be met in real data sets. Here we describe the development of a new approach, PCO-MC, which couples principal coordinate analysis to a clustering procedure for the inference of population structure from multilocus genotype data. Methodology/Principal Findings PCO-MC uses data from all principal coordinate axes simultaneously to calculate a multidimensional “density landscape”, from which the number of subpopulations, and the membership within subpopulations, is determined using a valley-seeking algorithm. Using extensive simulations, we show that this approach outperforms a Bayesian MCMC procedure when many loci (e.g. 100) are sampled, but that the Bayesian procedure is marginally superior with few loci (e.g. 10). When presented with sufficient data, PCO-MC accurately delineated subpopulations with population Fst values as low as 0.03 (G'st>0.2), whereas the limit of resolution of the Bayesian approach was Fst = 0.05 (G'st>0.35). Conclusions/Significance We draw a distinction between population structure inference for describing biodiversity as opposed to Type I error control in associative genetics. We suggest that discrete assignments, like those produced by PCO-MC, are appropriate for circumscribing units of biodiversity whereas expression of population structure as a continuous variable is more useful for case-control correction in structured association studies. PMID:19172174

  4. Equilibrium Structures of Molecules Featuring Bonds Between Second-Row Elements %STRUCTURES of Molecules Containing More than One 2ND-ROW Elements

    NASA Astrophysics Data System (ADS)

    Thorwirth, Sven; Harding, Michael E.

    2010-06-01

    Equilibrium geometries of a set of molecules containing chemical bonds between second-row elements (Al, Si, P, S, Cl) have been evaluated at the CCSD(T) level of theory in combination with large basis sets. The results of these calculations are compared against equilibrium values from experiment. Purely experimental equilibrium structures are only available for very few molecules of this kind. Consequently, empirical equilibrium structural parameters for the majority of members of the set had to be determined using ground-state rotational constants corrected for zero-point vibrational effects. The latter were obtained by second-order vibrational perturbation theory employing coupled-cluster calculations of anharmonic force fields.

  5. DR-TAMAS: Diffeomorphic Registration for Tensor Accurate Alignment of Anatomical Structures.

    PubMed

    Irfanoglu, M Okan; Nayak, Amritha; Jenkins, Jeffrey; Hutchinson, Elizabeth B; Sadeghi, Neda; Thomas, Cibu P; Pierpaoli, Carlo

    2016-05-15

    In this work, we propose DR-TAMAS (Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures), a novel framework for intersubject registration of Diffusion Tensor Imaging (DTI) data sets. This framework is optimized for brain data and its main goal is to achieve an accurate alignment of all brain structures, including white matter (WM), gray matter (GM), and spaces containing cerebrospinal fluid (CSF). Currently most DTI-based spatial normalization algorithms emphasize alignment of anisotropic structures. While some diffusion-derived metrics, such as diffusion anisotropy and tensor eigenvector orientation, are highly informative for proper alignment of WM, other tensor metrics such as the trace or mean diffusivity (MD) are fundamental for a proper alignment of GM and CSF boundaries. Moreover, it is desirable to include information from structural MRI data, e.g., T1-weighted or T2-weighted images, which are usually available together with the diffusion data. The fundamental property of DR-TAMAS is to achieve global anatomical accuracy by incorporating in its cost function the most informative metrics locally. Another important feature of DR-TAMAS is a symmetric time-varying velocity-based transformation model, which enables it to account for potentially large anatomical variability in healthy subjects and patients. The performance of DR-TAMAS is evaluated with several data sets and compared with other widely-used diffeomorphic image registration techniques employing both full tensor information and/or DTI-derived scalar maps. Our results show that the proposed method has excellent overall performance in the entire brain, while being equivalent to the best existing methods in WM. PMID:26931817

  6. Pyrolysis of sulfur tetrafluoride over boron: Excited-state rotational spectra and equilibrium structure of fluorothioborine (FBS)

    NASA Astrophysics Data System (ADS)

    Bizzocchi, L.; Esposti, C. Degli

    2001-10-01

    The unstable FBS molecule has been produced in the gas phase by a high-temperature reaction between crystalline boron and sulfur tetrafluoride. Its rotational spectrum has been observed in the millimeter-wave region, from 75 to 460 GHz, for different isotopic species and vibrational states. All the excited states which approximately lie below 1700 cm-1, that are 1000 (F-B stretch), 0110 (FBS bend), 0001 (B=S stretch), 2000, 0200, 0220, 0310, 0330, 0400, 0420, 0440, 1110, 1200, and 1220, have been investigated for the most abundant isotopomer F11B32S. The analysis of the spectra has been performed taking simultaneously into account the Fermi interaction which couples the states ν1,ν2,ν3 with ν1-1, ν2+2,ν3, and l-type resonances between different sublevels of a given vibrational bending state. This procedure allowed us to calculate directly deperturbed parameters and, in addition, yielded reliable estimates of the vibrational energy difference between the interacting levels and of the normal coordinate cubic force constant k122. Rotational spectra in the ground and various excited states have been also recorded and analyzed for the less abundant isotopic species F10B32S, F11B34S, F10B34S, F11B33S, and F10B33S. The very weak spectrum in the 0001 state was successfully observed for the pair of isotopomers F11B32S and F10B32S, whose equilibrium rotational constants could be accurately calculated yielding the first evaluation of the equilibrium structure of fluorothioborine: re(F-B)=1.2762±0.0002 Å and re(B=S)=1.6091±0.0002 Å.

  7. The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures

    PubMed Central

    Holton, James M; Classen, Scott; Frankel, Kenneth A; Tainer, John A

    2014-01-01

    In macromolecular crystallography, the agreement between observed and predicted structure factors (Rcryst and Rfree) is seldom better than 20%. This is much larger than the estimate of experimental error (Rmerge). The difference between Rcryst and Rmerge is the R-factor gap. There is no such gap in small-molecule crystallography, for which calculated structure factors are generally considered more accurate than the experimental measurements. Perhaps the true noise level of macromolecular data is higher than expected? Or is the gap caused by inaccurate phases that trap refined models in local minima? By generating simulated diffraction patterns using the program MLFSOM, and including every conceivable source of experimental error, we show that neither is the case. Processing our simulated data yielded values that were indistinguishable from those of real data for all crystallographic statistics except the final Rcryst and Rfree. These values decreased to 3.8% and 5.5% for simulated data, suggesting that the reason for high R-factors in macromolecular crystallography is neither experimental error nor phase bias, but rather an underlying inadequacy in the models used to explain our observations. The present inability to accurately represent the entire macromolecule with both its flexibility and its protein-solvent interface may be improved by synergies between small-angle X-ray scattering, computational chemistry and crystallography. The exciting implication of our finding is that macromolecular data contain substantial hidden and untapped potential to resolve ambiguities in the true nature of the nanoscale, a task that the second century of crystallography promises to fulfill. Database Coordinates and structure factors for the real data have been submitted to the Protein Data Bank under accession 4tws. PMID:25040949

  8. Fuzzy Reasoning to More Accurately Determine Void Areas on Optical Micrographs of Composite Structures

    NASA Technical Reports Server (NTRS)

    Dominquez, Jesus A.; Tate, Lanetra C.; Wright, M. Clara; Caraccio, Anne

    2013-01-01

    Accomplishing the best-performing composite matrix (resin) requires that not only the processing method but also the cure cycle generate low-void-content structures. If voids are present, the performance of the composite matrix will be significantly reduced. This is usually noticed by significant reductions in matrix-dominated properties, such as compression and shear strength. Voids in composite materials are areas that are absent of the composite components: matrix and fibers. The characteristics of the voids and their accurate estimation are critical to determine for high performance composite structures. One widely used method of performing void analysis on a composite structure sample is acquiring optical micrographs or Scanning Electron Microscope (SEM) images of lateral sides of the sample and retrieving the void areas within the micrographs/images using an image analysis technique. Segmentation for the retrieval and subsequent computation of void areas within the micrographs/images is challenging as the gray-scaled values of the void areas are close to the gray-scaled values of the matrix leading to the need of manually performing the segmentation based on the histogram of the micrographs/images to retrieve the void areas. The use of an algorithm developed by NASA and based on Fuzzy Reasoning (FR) proved to overcome the difficulty of suitably differentiate void and matrix image areas with similar gray-scaled values leading not only to a more accurate estimation of void areas on composite matrix micrographs but also to a faster void analysis process as the algorithm is fully autonomous.

  9. Accurate airway segmentation based on intensity structure analysis and graph-cut

    NASA Astrophysics Data System (ADS)

    Meng, Qier; Kitsaka, Takayuki; Nimura, Yukitaka; Oda, Masahiro; Mori, Kensaku

    2016-03-01

    This paper presents a novel airway segmentation method based on intensity structure analysis and graph-cut. Airway segmentation is an important step in analyzing chest CT volumes for computerized lung cancer detection, emphysema diagnosis, asthma diagnosis, and pre- and intra-operative bronchoscope navigation. However, obtaining a complete 3-D airway tree structure from a CT volume is quite challenging. Several researchers have proposed automated algorithms basically based on region growing and machine learning techniques. However these methods failed to detect the peripheral bronchi branches. They caused a large amount of leakage. This paper presents a novel approach that permits more accurate extraction of complex bronchial airway region. Our method are composed of three steps. First, the Hessian analysis is utilized for enhancing the line-like structure in CT volumes, then a multiscale cavity-enhancement filter is employed to detect the cavity-like structure from the previous enhanced result. In the second step, we utilize the support vector machine (SVM) to construct a classifier for removing the FP regions generated. Finally, the graph-cut algorithm is utilized to connect all of the candidate voxels to form an integrated airway tree. We applied this method to sixteen cases of 3D chest CT volumes. The results showed that the branch detection rate of this method can reach about 77.7% without leaking into the lung parenchyma areas.

  10. conSSert: Consensus SVM Model for Accurate Prediction of Ordered Secondary Structure.

    PubMed

    Kieslich, Chris A; Smadbeck, James; Khoury, George A; Floudas, Christodoulos A

    2016-03-28

    Accurate prediction of protein secondary structure remains a crucial step in most approaches to the protein-folding problem, yet the prediction of ordered secondary structure, specifically beta-strands, remains a challenge. We developed a consensus secondary structure prediction method, conSSert, which is based on support vector machines (SVM) and provides exceptional accuracy for the prediction of beta-strands with QE accuracy of over 0.82 and a Q2-EH of 0.86. conSSert uses as input probabilities for the three types of secondary structure (helix, strand, and coil) that are predicted by four top performing methods: PSSpred, PSIPRED, SPINE-X, and RAPTOR. conSSert was trained/tested using 4261 protein chains from PDBSelect25, and 8632 chains from PISCES. Further validation was performed using targets from CASP9, CASP10, and CASP11. Our data suggest that poor performance in strand prediction is likely a result of training bias and not solely due to the nonlocal nature of beta-sheet contacts. conSSert is freely available for noncommercial use as a webservice: http://ares.tamu.edu/conSSert/ . PMID:26928531

  11. Beyond Ellipse(s): Accurately Modelling the Isophotal Structure of Galaxies with ISOFIT and CMODEL

    NASA Astrophysics Data System (ADS)

    Ciambur, B. C.

    2015-09-01

    This work introduces a new fitting formalism for isophotes that enables more accurate modeling of galaxies with non-elliptical shapes, such as disk galaxies viewed edge-on or galaxies with X-shaped/peanut bulges. Within this scheme, the angular parameter that defines quasi-elliptical isophotes is transformed from the commonly used, but inappropriate, polar coordinate to the “eccentric anomaly.” This provides a superior description of deviations from ellipticity, better capturing the true isophotal shape. Furthermore, this makes it possible to accurately recover both the surface brightness profile, using the correct azimuthally averaged isophote, and the two-dimensional model of any galaxy: the hitherto ubiquitous, but artificial, cross-like features in residual images are completely removed. The formalism has been implemented into the Image Reduction and Analysis Facility tasks Ellipse and Bmodel to create the new tasks “Isofit,” and “Cmodel.” The new tools are demonstrated here with application to five galaxies, chosen to be representative case-studies for several areas where this technique makes it possible to gain new scientific insight. Specifically: properly quantifying boxy/disky isophotes via the fourth harmonic order in edge-on galaxies, quantifying X-shaped/peanut bulges, higher-order Fourier moments for modeling bars in disks, and complex isophote shapes. Higher order (n > 4) harmonics now become meaningful and may correlate with structural properties, as boxyness/diskyness is known to do. This work also illustrates how the accurate construction, and subtraction, of a model from a galaxy image facilitates the identification and recovery of over-lapping sources such as globular clusters and the optical counterparts of X-ray sources.

  12. Highly Accurate Structure-Based Prediction of HIV-1 Coreceptor Usage Suggests Intermolecular Interactions Driving Tropism

    PubMed Central

    Kieslich, Chris A.; Tamamis, Phanourios; Guzman, Yannis A.; Onel, Melis; Floudas, Christodoulos A.

    2016-01-01

    HIV-1 entry into host cells is mediated by interactions between the V3-loop of viral glycoprotein gp120 and chemokine receptor CCR5 or CXCR4, collectively known as HIV-1 coreceptors. Accurate genotypic prediction of coreceptor usage is of significant clinical interest and determination of the factors driving tropism has been the focus of extensive study. We have developed a method based on nonlinear support vector machines to elucidate the interacting residue pairs driving coreceptor usage and provide highly accurate coreceptor usage predictions. Our models utilize centroid-centroid interaction energies from computationally derived structures of the V3-loop:coreceptor complexes as primary features, while additional features based on established rules regarding V3-loop sequences are also investigated. We tested our method on 2455 V3-loop sequences of various lengths and subtypes, and produce a median area under the receiver operator curve of 0.977 based on 500 runs of 10-fold cross validation. Our study is the first to elucidate a small set of specific interacting residue pairs between the V3-loop and coreceptors capable of predicting coreceptor usage with high accuracy across major HIV-1 subtypes. The developed method has been implemented as a web tool named CRUSH, CoReceptor USage prediction for HIV-1, which is available at http://ares.tamu.edu/CRUSH/. PMID:26859389

  13. The Ion-Specific, Non-Equilibrium Structural Behavior of DNA Hydrogels

    NASA Astrophysics Data System (ADS)

    Nguyen, Dan; Saleh, Omar

    The highly tunable, sequence-dependent hybridization of DNA has enabled construction of DNA hydrogels with applications ranging from drug delivery to responsive materials. Though many have examined the structural characteristics of DNA hydrogels at equilibrium, relatively little is known about their non-equilibrium behavior, apart from their degradation rates when delivering molecular payloads. Here, we examine the effect of changing salt concentration on the dynamic formation, ageing, and degradation of DNA hydrogels comprised of branched DNA nanostars with palindromic overhangs. First, we observe that hydrogel phase is sensitive to the presence of a single unpaired base on the overhang, resulting in either a percolated network or a liquid-liquid phase separated state at high salt concentrations. Particular to the percolated network, we can induce the system to either contract or relax by changing the salt concentration. Decreasing monovalent NaCl induces the network to irreversibly contract whereas decreasing divalent MgCl2 induces the network to reversibly expand; this behavior runs counter to what is expected solely from electrostatic screening. We qualitatively understand these results by assuming that the monovalent salt modulates the dynamic hybridization between nanostar binding partners, whereas the divalent salt drives the dramatic/reversible induction of the `stacked-X' conformation in the DNA nanostars. Biomolecular Science and Engineering Program.

  14. Equilibrium structure of solar magnetic flux tubes: Energy transport with multistream radiative transfer

    NASA Technical Reports Server (NTRS)

    Hasan, S. S.; Kalkofen, W.

    1994-01-01

    We examine the equilibrium structure of vertical intense magnetic flux tubes on the Sun. Assuming cylindrical geometry, we solve the magnetohydrostatic equations in the thin flux-tube approximation, allowing for energy transport by radiation and convection. The radiative transfer equation is solved in the six-stream approximation, assuming gray opacity and local thermodynamic equilibrium. This constitutes a significant improvement over a previous study, in which the transfer was solved using the multidimensional generalization of the Eddington approximation. Convection in the flux tube is treated using mixing-length theory, with an additional parameter alpha, characterizing the suppression of convective energy transport in the tube by the strong magnetic field. The equations are solved using the method of partial linearization. We present results for tubes with different values of the magnetic field strength and radius at a fixed depth in the atmosphere. In general, we find that, at equal geometric heights, the temperature on the tube axis, compared to the ambient medium, is higher in the photosphere and lower in the convection zone, with the difference becoming larger for thicker tubes. At equal optical depths the tubes are generally hotter than their surroundings. The results are comparatively insensitive to alpha but depend upon whether radiative and convective energy transport operate simultaneously or in separate layers. A comparison of our results with semiempirical models shows that the temperature and intensity contrast are in broad agreement. However, the field strengths of the flux-tube models are somewhat lower than the values inferred from observations.

  15. Microwave spectra of the deuterium isotopologues of cis-hexatriene and a semiexperimental equilibrium structure.

    PubMed

    Craig, Norman C; Chen, Yihui; Fuson, Hannah A; Tian, Hengfeng; van Besien, Herman; Conrad, Andrew R; Tubergen, Michael J; Rudolph, Heinz Dieter; Demaison, Jean

    2013-10-01

    Microwave transitions and ground state rotational constants are reported for five newly synthesized deuterium isotopologues of cis-1,3,5-hexatriene (cHTE). These rotational constants along with those of the parent and the three (13)C species are used with vibration-rotation constants calculated from an MP2/cc-pVTZ model to derive an equilibrium structure. That structure is improved by the mixed estimation method. In this method, internal coordinates from good-quality quantum chemical calculations (with appropriate uncertainties) are fit simultaneously with moments of inertia of the full set of isotopologues. The new structure of cHTE is confirmed to be planar and is stabilized by an interaction between the hydrogen atoms H2 and H5, which form a bond and participate in a six-membered ring. cHTE shows larger structural effects of π-electron delocalization than does butadiene with the effects being magnified in the center of the molecule. Thus, strong structural evidence now exists for an increase in π-electron delocalization as the polyene chain lengthens. PMID:23237234

  16. Accurate and rapid optical characterization of an anisotropic guided structure based on a neural method.

    PubMed

    Robert, Stéphane; Battie, Yann; Jamon, Damien; Royer, Francois

    2007-04-10

    Optimal performances of integrated optical devices are obtained by the use of an accurate and reliable characterization method. The parameters of interest, i.e., optical indices and thickness of the waveguide structure, are calculated from effective indices by means of an inversion procedure. We demonstrate how an artificial neural network can achieve such a process. The artificial neural network used is a multilayer perceptron. The first result concerns a simulated anisotropic waveguide. The accuracy in the determination of optical indices and waveguide thickness is 5 x 10(-5) and 4 nm, respectively. Then an experimental application on a silica-titania thin film is performed. In addition, effective indices are measured by m-lines spectroscopy. Finally, a comparison with a classical optimization algorithm demonstrates the robustness of the neural method. PMID:17384718

  17. Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.

    PubMed

    Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

    2016-02-01

    Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-`one-click' experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/. PMID:26894674

  18. Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations

    PubMed Central

    Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

    2016-01-01

    Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-‘one-click’ experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/. PMID:26894674

  19. Accurate response surface approximations for weight equations based on structural optimization

    NASA Astrophysics Data System (ADS)

    Papila, Melih

    Accurate weight prediction methods are vitally important for aircraft design optimization. Therefore, designers seek weight prediction techniques with low computational cost and high accuracy, and usually require a compromise between the two. The compromise can be achieved by combining stress analysis and response surface (RS) methodology. While stress analysis provides accurate weight information, RS techniques help to transmit effectively this information to the optimization procedure. The focus of this dissertation is structural weight equations in the form of RS approximations and their accuracy when fitted to results of structural optimizations that are based on finite element analyses. Use of RS methodology filters out the numerical noise in structural optimization results and provides a smooth weight function that can easily be used in gradient-based configuration optimization. In engineering applications RS approximations of low order polynomials are widely used, but the weight may not be modeled well by low-order polynomials, leading to bias errors. In addition, some structural optimization results may have high-amplitude errors (outliers) that may severely affect the accuracy of the weight equation. Statistical techniques associated with RS methodology are sought in order to deal with these two difficulties: (1) high-amplitude numerical noise (outliers) and (2) approximation model inadequacy. The investigation starts with reducing approximation error by identifying and repairing outliers. A potential reason for outliers in optimization results is premature convergence, and outliers of such nature may be corrected by employing different convergence settings. It is demonstrated that outlier repair can lead to accuracy improvements over the more standard approach of removing outliers. The adequacy of approximation is then studied by a modified lack-of-fit approach, and RS errors due to the approximation model are reduced by using higher order polynomials. In

  20. Processing and crystallographic structure of non-equilibrium Si-doped HfO{sub 2}

    SciTech Connect

    Hou, Dong; Fancher, Chris M.; Esteves, Giovanni; Jones, Jacob L.; Zhao, Lili

    2015-06-28

    Si-doped HfO{sub 2} was confirmed to exist as a non-equilibrium state. The crystallographic structures of Si-doped HfO{sub 2} were studied using high-resolution synchrotron X-ray diffraction and the Rietveld refinement method. Incorporation of Si into HfO{sub 2} and diffusion of Si out of (Hf,Si)O{sub 2} were determined as a function of calcination temperature. Higher thermal energy input at elevated calcination temperatures resulted in the formation of HfSiO{sub 4}, which is the expected major secondary phase in Si-doped HfO{sub 2}. The effect of SiO{sub 2} particle size (nano- and micron-sized) on the formation of Si-doped HfO{sub 2} was also determined. Nano-crystalline SiO{sub 2} was found to incorporate into HfO{sub 2} more readily.

  1. Internal rotation and equilibrium structure of 2-nitropropane from gas electron diffraction and quantum chemistry

    NASA Astrophysics Data System (ADS)

    Tarasov, Yu. I.; Kochikov, I. V.; Kovtun, D. M.; Ivanov, A. A.

    2009-03-01

    In this paper, the equilibrium structural parameters of the 2-nitropropane molecule and the barrier of internal rotation of the nitrogroup are determined from the gas electron diffraction data, with the use of quantum chemistry calculations and experimental vibrational frequencies, in the framework of the large-amplitude motion model for internal rotation. Quantum chemistry calculations at the MP2 and B3LYP levels of theory with various Pople and Dunning basis sets unambiguously predict the same minimum energy molecular conformation, with relatively close values of internal rotation barrier (375-525 cm -1). The results of present analysis show that the minimum of the potential function of the nitrogroup internal rotation is located in syn-H position when one of the oxygen atoms eclipses hydrogen atom that does not belong to any of CH 3 groups (dihedral angle H-C-N-O is zero). It has also been found that internal rotation is hindered, with the barrier height in the range of 220-560 cm -1 (0.6-1.6 kcal/mol) with the most probable value near 380 cm -1 (1.1 kcal/mol). The main equilibrium structure parameters in syn-H configuration are as follows (values in parentheses correspond to 3 times standard deviations): re(C-C) = 1.516(5) Å, re(C-N) = 1.501(5) Å, re (N dbnd O) = 1.225(4) Å, ∠C-C-N=108.7(1.0)°,∠O dbnd N dbnd O =124.8(0.4)°. We also provide thermally averaged parameters for comparison with the results of previous studies.

  2. An equilibrium analysis of the land use structure in the Yunnan Province, China

    NASA Astrophysics Data System (ADS)

    van Aken, H. M.; van Veldhoven, A. K.; Veth, C.; de Ruijter, W. P. M.; van Leeuwen, P. J.; Drijfhout, S. S.; Whittle, C. P.; Rouault, M.

    2014-06-01

    Global land use structure is changing rapidly due to unceasing population growth and accelerated urbanization, which leads to fierce competition between the rigid demand for built-up area and the protection of cultivated land, forest, and grassland. It has been a great challenge to realize the sustainable development of land resources. Based on a computable general equilibrium model of land use change with a social accounting matrix dataset, this study implemented an equilibrium analysis of the land use structure in the Yunnan Province during the period of 2008-2020 under three scenarios, the baseline scenario, low TFP (total factor productivity) scenario, and high TFP scenario. The results indicated that under all three scenarios, area of cultivated land declined significantly along with a remarkable expansion of built-up area, while areas of forest, grassland, and unused land increased slightly. The growth rate of TFP had first negative and then positive effects on the expansion of built-up area and decline of cultivated land as it increased. Moreover, the simulated changes of both cultivated land and built-up area were the biggest under the low TFP scenario, and far exceeded the limit in the Overall Plan for Land Utilization in the Yunnan Province in 2020. The scenario-based simulation results are of important reference value for policy-makers in making land use decisions, balancing the fierce competition between the protection of cultivated land and the increasing demand for built-up area, and guaranteeing food security, ecological security, and the sustainable development of land resources.

  3. An equilibrium analysis of the land use structure in the Yunnan Province, China

    NASA Astrophysics Data System (ADS)

    Luo, Jiao; Zhan, Jinyan; Lin, Yingzhi; Zhao, Chunhong

    2014-09-01

    Global land use structure is changing rapidly due to unceasing population growth and accelerated urbanization, which leads to fierce competition between the rigid demand for built-up area and the protection of cultivated land, forest, and grassland. It has been a great challenge to realize the sustainable development of land resources. Based on a computable general equilibrium model of land use change with a social accounting matrix dataset, this study implemented an equilibrium analysis of the land use structure in the Yunnan Province during the period of 2008-2020 under three scenarios, the baseline scenario, low TFP (total factor productivity) scenario, and high TFP scenario. The results indicated that under all three scenarios, area of cultivated land declined significantly along with a remarkable expansion of built-up area, while areas of forest, grassland, and unused land increased slightly. The growth rate of TFP had first negative and then positive effects on the expansion of built-up area and decline of cultivated land as it increased. Moreover, the simulated changes of both cultivated land and built-up area were the biggest under the low TFP scenario, and far exceeded the limit in the Overall Plan for Land Utilization in the Yunnan Province in 2020. The scenario-based simulation results are of important reference value for policy-makers in making land use decisions, balancing the fierce competition between the protection of cultivated land and the increasing demand for built-up area, and guaranteeing food security, ecological security, and the sustainable development of land resources.

  4. Discrete state model and accurate estimation of loop entropy of RNA secondary structures.

    PubMed

    Zhang, Jian; Lin, Ming; Chen, Rong; Wang, Wei; Liang, Jie

    2008-03-28

    Conformational entropy makes important contribution to the stability and folding of RNA molecule, but it is challenging to either measure or compute conformational entropy associated with long loops. We develop optimized discrete k-state models of RNA backbone based on known RNA structures for computing entropy of loops, which are modeled as self-avoiding walks. To estimate entropy of hairpin, bulge, internal loop, and multibranch loop of long length (up to 50), we develop an efficient sampling method based on the sequential Monte Carlo principle. Our method considers excluded volume effect. It is general and can be applied to calculating entropy of loops with longer length and arbitrary complexity. For loops of short length, our results are in good agreement with a recent theoretical model and experimental measurement. For long loops, our estimated entropy of hairpin loops is in excellent agreement with the Jacobson-Stockmayer extrapolation model. However, for bulge loops and more complex secondary structures such as internal and multibranch loops, we find that the Jacobson-Stockmayer extrapolation model has large errors. Based on estimated entropy, we have developed empirical formulae for accurate calculation of entropy of long loops in different secondary structures. Our study on the effect of asymmetric size of loops suggest that loop entropy of internal loops is largely determined by the total loop length, and is only marginally affected by the asymmetric size of the two loops. Our finding suggests that the significant asymmetric effects of loop length in internal loops measured by experiments are likely to be partially enthalpic. Our method can be applied to develop improved energy parameters important for studying RNA stability and folding, and for predicting RNA secondary and tertiary structures. The discrete model and the program used to calculate loop entropy can be downloaded at http://gila.bioengr.uic.edu/resources/RNA.html. PMID:18376982

  5. Can structured data fields accurately measure quality of care? The example of falls.

    PubMed

    Ganz, David A; Almeida, Shone; Roth, Carol P; Reuben, David B; Wenger, Neil S

    2012-01-01

    By automating collection of data elements, electronic health records may simplify the process of measuring the quality of medical care. Using data from a quality improvement initiative in primary care medical groups, we sought to determine whether the quality of care for falls and fear of falling in outpatients aged 75 and older could be accurately measured solely from codable (non-free-text) data in a structured visit note. A traditional medical record review by trained abstractors served as the criterion standard. Among 215 patient records reviewed, we found a structured visit note in 54% of charts within 3 mo of the date patients had been identified as having falls or fear of falling. The reliability of an algorithm based on codable data was at least good (kappa of at least 0.61) compared with full medical record review for three care processes recommended for patients with two falls or one fall with injury in the past year: orthostatic vital signs, vision test/eye examination, and home safety evaluation. However, the automated algorithm routinely underestimated quality of care. Performance standards based on automated measurement of quality of care from electronic health records need to account for documentation occurring in nonstructured form. PMID:23408222

  6. Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials.

    PubMed

    Boereboom, Jelle M; Potestio, Raffaello; Donadio, Davide; Bulo, Rosa E

    2016-08-01

    Adaptive quantum mechanical (QM)/molecular mechanical (MM) methods enable efficient molecular simulations of chemistry in solution. Reactive subregions are modeled with an accurate QM potential energy expression while the rest of the system is described in a more approximate manner (MM). As solvent molecules diffuse in and out of the reactive region, they are gradually included into (and excluded from) the QM expression. It would be desirable to model such a system with a single adaptive Hamiltonian, but thus far this has resulted in distorted structures at the boundary between the two regions. Solving this long outstanding problem will allow microcanonical adaptive QM/MM simulations that can be used to obtain vibrational spectra and dynamical properties. The difficulty lies in the complex QM potential energy expression, with a many-body expansion that contains higher order terms. Here, we outline a Hamiltonian adaptive multiscale scheme within the framework of many-body potentials. The adaptive expressions are entirely general, and complementary to all standard (nonadaptive) QM/MM embedding schemes available. We demonstrate the merit of our approach on a molecular system defined by two different MM potentials (MM/MM'). For the long-range interactions a numerical scheme is used (particle mesh Ewald), which yields energy expressions that are many-body in nature. Our Hamiltonian approach is the first to provide both energy conservation and the correct solvent structure everywhere in this system. PMID:27332140

  7. Equilibrium Structure of a Triblock Copolymer System Revealed by Mesoscale Simulation and Neutron Scattering

    SciTech Connect

    Do, Changwoo; Chen, Wei-Ren; Hong, Kunlun; Smith, Gregory Scott

    2013-01-01

    We have performed both mesoscale simulations and neutron scattering experiments on Pluronic L62, a poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO) triblock copolymer system in aqueous solution. The influence of simulation variables such PEO/PPO block ratio, interaction parameters, and coarse-graining methods is extensively investigated by covering all permutations of parameters found in the literatures. Upon increasing the polymer weight fraction from 50 wt% to 90 wt%, the equilibrium structure of the isotropic, reverse micellar, bicontinuous, worm-like micelle network, and lamellar phases are respectively predicted from the simulation depending on the choices of simulation parameters. Small angle neutron scattering (SANS) measurements show that the same polymer systems exhibit the spherical micellar, lamellar, and reverse micellar phases with the increase of the copolymer concentration at room temperature. Detailed structural analysis and comparison with simulations suggest that one of the simulation parameter sets can provide reasonable agreement with the experimentally observed structures.

  8. Equilibrium structure of a triblock copolymer system revealed by mesoscale simulation and neutron scattering

    NASA Astrophysics Data System (ADS)

    Do, Changwoo; Chen, Wei-Ren; Hong, Kunlun; Smith, Gregory S.

    2013-12-01

    We have performed both mesoscale simulations and neutron scattering experiments on Pluronic L62, a poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO) triblock copolymer system in aqueous solution. The influence of simulation variables such PEO/PPO block ratio, interaction parameters, and coarse-graining methods is extensively investigated by covering all permutations of parameters found in the literatures. Upon increasing the polymer weight fraction from 50 wt% to 90 wt%, the equilibrium structure of the isotropic, reverse micellar, bicontinuous, worm-like micelle network, and lamellar phases are respectively predicted from the simulation depending on the choices of simulation parameters. Small angle neutron scattering (SANS) measurements show that the same polymer systems exhibit the spherical micellar, lamellar, and reverse micellar phases with the increase of the copolymer concentration at room temperature. Detailed structural analysis and comparison with simulations suggest that one of the simulation parameter sets can provide reasonable agreement with the experimentally observed structures.

  9. Temperature structure of the tropical tropopause layer in radiative-convective equilibrium

    NASA Astrophysics Data System (ADS)

    Birner, Thomas

    2014-05-01

    The tropical tropopause layer (TTL) shows a curious stratification structure: temperature continues to decrease beyond the level of main convective outflow (~200 hPa) up to the cold point tropopause (~100 hPa), but TTL lapse rates are smaller than in the upper troposphere. A cold point tropopause well separated from the level of main convective outflow has previously been shown to be consistent with the detailed radiative balance in the TTL even if dynamical effects were absent. More generally, the cold tropical tropopause is controlled by adiabatic cooling due to large-scale upwelling (forced by extratropical or tropical waves). TTL cooling can also come from the large-scale hydrostatic response aloft deep convective heating as well as from overshooting convection. Here, results based on idealized radiative-convective equilibrium model simulations are presented, contrasting single-column with cloud-resolving simulations. While all of the above processes are capable of producing a TTL-like region in isolation, their combination is found to produce crucial feedbacks. In particular, both water vapour and ozone are found to have strong radiative effects on TTL temperatures, highlighting important feedbacks between transport circulations setting temperatures and tracer structures and the resulting tracer structures in turn affecting temperatures.

  10. Supramolecular Magnetic Brushes: The Impact of Dipolar Interactions on the Equilibrium Structure

    PubMed Central

    2015-01-01

    The equilibrium structure of supramolecular magnetic filament brushes is analyzed at two different scales. First, we study the density and height distributions for brushes with various grafting densities and chain lengths. We use Langevin dynamics simulations with a bead–spring model that takes into account the cross-links between the surface of the ferromagnetic particles, whose magnetization is characterized by a point dipole. Magnetic filament brushes are shown to be more compact near the substrate than nonmagnetic ones, with a bimodal height distribution for large grafting densities. This latter feature makes them also different from brushes with electric dipoles. Next, in order to explain the observed behavior at the filament scale, we introduce a graph theory analysis to elucidate for the first time the structure of the brush at the scale of individual beads. It turns out that, in contrast to nonmagnetic brushes, in which the internal structure is determined by random density fluctuations, magnetic forces introduce a certain order in the system. Because of their highly directional nature, magnetic dipolar interactions prevent some of the random connections to be formed. On the other hand, they favor a higher connectivity of the chains’ free and grafted ends. We show that this complex dipolar brush microstructure has a strong impact on the magnetic response of the brush, as any weak applied field has to compete with the dipole–dipole interactions within the crowded environment. PMID:26538768

  11. A microscopic, non-equilibrium, statistical field theory for cosmic structure formation

    NASA Astrophysics Data System (ADS)

    Bartelmann, Matthias; Fabis, Felix; Berg, Daniel; Kozlikin, Elena; Lilow, Robert; Viermann, Celia

    2016-04-01

    Building upon the recent pioneering work by Mazenko and by Das and Mazenko, we develop a microscopic, non-equilibrium, statistical field theory for initially correlated canonical ensembles of classical microscopic particles obeying Hamiltonian dynamics. Our primary target is cosmic structure formation, where initial Gaussian correlations in phase space are believed to be set by inflation. We give an exact expression for the generating functional of this theory and work out suitable approximations. We specify the initial correlations by a power spectrum and derive general expressions for the correlators of the density and the response field. We derive simple closed expressions for the lowest-order contributions to the nonlinear cosmological power spectrum, valid for arbitrary wave numbers. We further calculate the bispectrum expected in this theory within these approximations and the power spectrum of cosmic density fluctuations to first order in the gravitational interaction, using a recent improvement of the Zel’dovich approximation. We show that, with a modification motivated by the adhesion approximation, the nonlinear growth of the density power spectrum found in numerical simulations of cosmic structure evolution is reproduced well to redshift zero and for arbitrary wave numbers even within first-order perturbation theory. Our results present the first fully analytic calculation of the nonlinear power spectrum of cosmic structures.

  12. Equilibrium and Nonequilibrium Statistical Mechanics of Membranes, Liquid Crystal Films, and Other Layered Structures.

    NASA Astrophysics Data System (ADS)

    Chen, Chi-Ming

    In this thesis, we develop and analyze a continuum Landau theory for chiral and achiral lipid bilayers. This theory contains couplings between tangent-plane orientational order and curvature that lead to "rippled" phases with one-dimensional height modulations and to phases with two -dimensional height modulations. We calculate the mean -field phase diagrams by using both analytical and numerical methods. We generalize our theory to study the equilibrium phase diagrams of liquid crystal films. Both bulk smectics and freely suspended films are considered. For flexoelectric systems, continuous structural phase transitions are predicted among square-lattice, hexagonal, and distorted square-lattice phases as a function of the applied electric field. It is also shown that only uniform flat phases are predicted for thin films. One-dimensional ripple phases and two -dimensional square lattice phases can occur with increasing film thickness. Secondly we study the growth and instability of Myelin figures. For quasi-equilibrium growth, we predict a growth rate proportional to t^{-1/2 }, where t is the growth time. The proportional constant is inversely proportional to the viscosity of the fluid. Myelin figures are unstable under dehydration. The initial instability of myelin figures develops periodic arrays of bumps at the surface with a wave length of about 1 mum. This morphological change is induced by increasing the ratio of surface area to volume of myelin figures due to dehydration. We interpret this initial instability from energetical considerations and calculate the preferred wave length. Finally, we study theoretically the swelling kinetics of layered structures, particularly triblock copolymer mesogels. The gels are swollen by a solvent good for the bridging block but poor for the nonbridging block. At late stages the penetration front moves as in ordinary diffusion. However, the bending elasticity of the non -bridging layers leads to an initial t^{1/6 } relaxation

  13. COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples

    PubMed Central

    Yamagata, Koichi; Yamanishi, Ayako; Kokubu, Chikara; Takeda, Junji; Sese, Jun

    2016-01-01

    An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner. COSMOS also prioritizes the candidate SVs using strand-specific read-depth information. Performance tests on modeled tumor genomes revealed that COSMOS outperformed existing methods in terms of F-measure. We also applied COSMOS to an experimental mouse cell-based model, in which SVs were induced by genome engineering and gamma-ray irradiation, followed by polymerase chain reaction-based confirmation. The precision of COSMOS was 84.5%, while the next best existing method was 70.4%. Moreover, the sensitivity of COSMOS was the highest, indicating that COSMOS has great potential for cancer genome analysis. PMID:26833260

  14. Structural stability augmentation system design using BODEDIRECT: A quick and accurate approach

    NASA Technical Reports Server (NTRS)

    Goslin, T. J.; Ho, J. K.

    1989-01-01

    A methodology is presented for a modal suppression control law design using flight test data instead of mathematical models to obtain the required gain and phase information about the flexible airplane. This approach is referred to as BODEDIRECT. The purpose of the BODEDIRECT program is to provide a method of analyzing the modal phase relationships measured directly from the airplane. These measurements can be achieved with a frequency sweep at the control surface input while measuring the outputs of interest. The measured Bode-models can be used directly for analysis in the frequency domain, and for control law design. Besides providing a more accurate representation for the system inputs and outputs of interest, this method is quick and relatively inexpensive. To date, the BODEDIRECT program has been tested and verified for computational integrity. Its capabilities include calculation of series, parallel and loop closure connections between Bode-model representations. System PSD, together with gain and phase margins of stability may be calculated for successive loop closures of multi-input/multi-output systems. Current plans include extensive flight testing to obtain a Bode-model representation of a commercial aircraft for design of a structural stability augmentation system.

  15. Accurate prediction of lattice energies and structures of molecular crystals with molecular quantum chemistry methods.

    PubMed

    Fang, Tao; Li, Wei; Gu, Fangwei; Li, Shuhua

    2015-01-13

    We extend the generalized energy-based fragmentation (GEBF) approach to molecular crystals under periodic boundary conditions (PBC), and we demonstrate the performance of the method for a variety of molecular crystals. With this approach, the lattice energy of a molecular crystal can be obtained from the energies of a series of embedded subsystems, which can be computed with existing advanced molecular quantum chemistry methods. The use of the field compensation method allows the method to take long-range electrostatic interaction of the infinite crystal environment into account and make the method almost translationally invariant. The computational cost of the present method scales linearly with the number of molecules in the unit cell. Illustrative applications demonstrate that the PBC-GEBF method with explicitly correlated quantum chemistry methods is capable of providing accurate descriptions on the lattice energies and structures for various types of molecular crystals. In addition, this approach can be employed to quantify the contributions of various intermolecular interactions to the theoretical lattice energy. Such qualitative understanding is very useful for rational design of molecular crystals. PMID:26574207

  16. Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation

    PubMed Central

    Sharma, Virag; Elghafari, Anas; Hiller, Michael

    2016-01-01

    Identifying coding genes is an essential step in genome annotation. Here, we utilize existing whole genome alignments to detect conserved coding exons and then map gene annotations from one genome to many aligned genomes. We show that genome alignments contain thousands of spurious frameshifts and splice site mutations in exons that are truly conserved. To overcome these limitations, we have developed CESAR (Coding Exon-Structure Aware Realigner) that realigns coding exons, while considering reading frame and splice sites of each exon. CESAR effectively avoids spurious frameshifts in conserved genes and detects 91% of shifted splice sites. This results in the identification of thousands of additional conserved exons and 99% of the exons that lack inactivating mutations match real exons. Finally, to demonstrate the potential of using CESAR for comparative gene annotation, we applied it to 188 788 exons of 19 865 human genes to annotate human genes in 99 other vertebrates. These comparative gene annotations are available as a resource (http://bds.mpi-cbg.de/hillerlab/CESAR/). CESAR (https://github.com/hillerlab/CESAR/) can readily be applied to other alignments to accurately annotate coding genes in many other vertebrate and invertebrate genomes. PMID:27016733

  17. Straightforward and accurate technique for post-coupler stabilization in drift tube linac structures

    NASA Astrophysics Data System (ADS)

    Khalvati, Mohammad Reza; Ramberger, Suitbert

    2016-04-01

    The axial electric field of Alvarez drift tube linacs (DTLs) is known to be susceptible to variations due to static and dynamic effects like manufacturing tolerances and beam loading. Post-couplers are used to stabilize the accelerating fields of DTLs against tuning errors. Tilt sensitivity and its slope have been introduced as measures for the stability right from the invention of post-couplers but since then the actual stabilization has mostly been done by tedious iteration. In the present article, the local tilt-sensitivity slope TSn' is established as the principal measure for stabilization instead of tilt sensitivity or some visual slope, and its significance is developed on the basis of an equivalent-circuit diagram of the DTL. Experimental and 3D simulation results are used to analyze its behavior and to define a technique for stabilization that allows finding the best post-coupler settings with just four tilt-sensitivity measurements. CERN's Linac4 DTL Tank 2 and Tank 3 have been stabilized successfully using this technique. The final tilt-sensitivity error has been reduced from ±100 %/MHz down to ±3 %/MHz for Tank 2 and down to ±1 %/MHz for Tank 3. Finally, an accurate procedure for tuning the structure using slug tuners is discussed.

  18. Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation.

    PubMed

    Sharma, Virag; Elghafari, Anas; Hiller, Michael

    2016-06-20

    Identifying coding genes is an essential step in genome annotation. Here, we utilize existing whole genome alignments to detect conserved coding exons and then map gene annotations from one genome to many aligned genomes. We show that genome alignments contain thousands of spurious frameshifts and splice site mutations in exons that are truly conserved. To overcome these limitations, we have developed CESAR (Coding Exon-Structure Aware Realigner) that realigns coding exons, while considering reading frame and splice sites of each exon. CESAR effectively avoids spurious frameshifts in conserved genes and detects 91% of shifted splice sites. This results in the identification of thousands of additional conserved exons and 99% of the exons that lack inactivating mutations match real exons. Finally, to demonstrate the potential of using CESAR for comparative gene annotation, we applied it to 188 788 exons of 19 865 human genes to annotate human genes in 99 other vertebrates. These comparative gene annotations are available as a resource (http://bds.mpi-cbg.de/hillerlab/CESAR/). CESAR (https://github.com/hillerlab/CESAR/) can readily be applied to other alignments to accurately annotate coding genes in many other vertebrate and invertebrate genomes. PMID:27016733

  19. COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples.

    PubMed

    Yamagata, Koichi; Yamanishi, Ayako; Kokubu, Chikara; Takeda, Junji; Sese, Jun

    2016-05-01

    An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner. COSMOS also prioritizes the candidate SVs using strand-specific read-depth information. Performance tests on modeled tumor genomes revealed that COSMOS outperformed existing methods in terms of F-measure. We also applied COSMOS to an experimental mouse cell-based model, in which SVs were induced by genome engineering and gamma-ray irradiation, followed by polymerase chain reaction-based confirmation. The precision of COSMOS was 84.5%, while the next best existing method was 70.4%. Moreover, the sensitivity of COSMOS was the highest, indicating that COSMOS has great potential for cancer genome analysis. PMID:26833260

  20. Silicon Oxysulfide, OSiS: Rotational Spectrum, Quantum-Chemical Calculations, and Equilibrium Structure.

    PubMed

    Thorwirth, Sven; Mück, Leonie Anna; Gauss, Jürgen; Tamassia, Filippo; Lattanzi, Valerio; McCarthy, Michael C

    2011-06-01

    Silicon oxysulfide, OSiS, and seven of its minor isotopic species have been characterized for the first time in the gas phase at high spectral resolution by means of Fourier transform microwave spectroscopy. The equilibrium structure of OSiS has been determined from the experimental data using calculated vibration-rotation interaction constants. The structural parameters (rO-Si = 1.5064 Å and rSi-S = 1.9133 Å) are in very good agreement with values from high-level quantum chemical calculations using coupled-cluster techniques together with sophisticated additivity and extrapolation schemes. The bond distances in OSiS are very short in comparison with those in SiO and SiS. This unexpected finding is explained by the partial charges calculated for OSiS via a natural population analysis. The results suggest that electrostatic effects rather than multiple bonding are the key factors in determining bonding in this triatomic molecule. The data presented provide the spectroscopic information needed for radio astronomical searches for OSiS. PMID:26295414

  1. Metastable and equilibrium defect structure of II VI/GaAs interfaces

    NASA Astrophysics Data System (ADS)

    Schwartzman, A. F.; Sinclair, R.

    1991-07-01

    Defect characterization by high-resolution electron microscopy is presented for (001) epitaxy of the CdTe/GaAs and ZnTe/GaAs heterojunctions, before and after a long vacuum anneal. The annealed interface structure consists of a periodic array of perfect edge Lomer misfit dislocations, with spacing corresponding to a strain-free thin film. Since this is the most efficient manner to obtain complete relaxation, it represents the equilibrium microstructure. The as-deposited films are very thick, three to four orders of magnitude greater than the critical thicknesses, which are both less than a monolayer for these large lattice mismatch systems. Their microstructure corresponds to a metastable distribution of defects in that the thin film residual strain is nearly zero and neighboring defects can react to form Lomer misfits. A variety of defects exist both in the form of perfect misfit dislocations at the interface and extended defects into the thin film. The extended defects result from formation of stacking faults bounded by either Shockley or Frank partials, and more complicated defect structures due to interacting perfect and partial dislocations on intersecting slip planes. The purpose of this paper is to investigate the means by which complete stress relaxation can occur through dislocation reactions during annealing of very thick as-deposited films.

  2. Thermodynamics and equilibrium structure of Ne38 cluster: quantum mechanics versus classical.

    PubMed

    Predescu, Cristian; Frantsuzov, Pavel A; Mandelshtam, Vladimir A

    2005-04-15

    The equilibrium properties of classical Lennard-Jones (LJ38) versus quantum Ne38 Lennard-Jones clusters are investigated. The quantum simulations use both the path-integral Monte Carlo (PIMC) and the recently developed variational-Gaussian wave packet Monte Carlo (VGW-MC) methods. The PIMC and the classical MC simulations are implemented in the parallel tempering framework. The classical heat capacity Cv(T) curve agrees well with that of Neirotti et al. [J. Chem. Phys. 112, 10340 (2000)], although a much larger confining sphere is used in the present work. The classical Cv(T) shows a peak at about 6 K, interpreted as a solid-liquid transition, and a shoulder at approximately 4 K, attributed to a solid-solid transition involving structures from the global octahedral (Oh) minimum and the main icosahedral (C5v) minimum. The VGW method is used to locate and characterize the low energy states of Ne38, which are then further refined by PIMC calculations. Unlike the classical case, the ground state of Ne38 is a liquidlike structure. Among the several liquidlike states with energies below the two symmetric states (Oh and C5v), the lowest two exhibit strong delocalization over basins associated with at least two classical local minima. Because the symmetric structures do not play an essential role in the thermodynamics of Ne38, the quantum heat capacity is a featureless curve indicative of the absence of any structural transformations. Good agreement between the two methods, VGW and PIMC, is obtained. The present results are also consistent with the predictions by Calvo et al. [J. Chem. Phys. 114, 7312 (2001)] based on the quantum superposition method within the harmonic approximation. However, because of its approximate nature, the latter method leads to an incorrect assignment of the Ne38 ground state as well as to a significant underestimation of the heat capacity. PMID:15945633

  3. Vlasov Theory of the Equilibrium Structure of Tangential Discontinuities in Space Plasmas

    NASA Astrophysics Data System (ADS)

    Roth, M.; de Keyser, J.; Kuznetsova, M. M.

    1996-05-01

    Extensive theoretical work has been performed on the equilibrium structure of tangential discontinuities (TDs) in collisionless plasmas. This paper reviews kinetic models based on steady-state solutions of the Vlasov equation. It is shown that most of the existing models are special cases of a generalized multi-species model. In this generalized model all particle populations -from both outer regions and from inside the layer — are described using a unique formalism for the velocity distribution functions. Because of their historical importance, the Harris and Sestero models are reviewed and deduced from the generalized model. The Lee and Kan model is also a special case of the generalized model. The generalized model, however, is also able to describe TDs with velocity shear and large angles of magnetic field rotation. Such a multi-species model with a large number of free parameters and different gradient scales illustrates many observable features of TDs, including their multiscale fine structure. Particular attention is paid to the magnetopause. Observed magnetopause crossings are simulated. The effects of the relative flow velocity and asymmetrical magnetic field profiles on the structure of the magnetopause and on its stability with respect to tearing perturbations are discussed. We also present calculations that demonstrate the potential of the generalized model in explaining the origin of discrete auroral arcs. Numerical simulations of solar wind TDs with heavy ions and a large spectrum of thicknesses are also feasible. This indicates that such a model is of fundamental importance for understanding the detailed structure of solar wind TDs, like those observed by the interplanetary spacecraft ULYSSES. The problems associated with the one-dimensional, time-independent Vlasov approach are discussed and a variational principle is suggested to reduce the arbitrariness resulting from the large number of free parameters.

  4. Rotational spectra of rare isotopic species of fluoroiodomethane: Determination of the equilibrium structure from rotational spectroscopy and quantum-chemical calculations

    NASA Astrophysics Data System (ADS)

    Puzzarini, Cristina; Cazzoli, Gabriele; López, Juan Carlos; Alonso, José Luis; Baldacci, Agostino; Baldan, Alessandro; Stopkowicz, Stella; Cheng, Lan; Gauss, Jürgen

    2012-07-01

    Supported by accurate quantum-chemical calculations, the rotational spectra of the mono- and bi-deuterated species of fluoroiodomethane, CHDFI and CD2FI, as well as of the 13C-containing species, 13CH2FI, were recorded for the first time. Three different spectrometers were employed, a Fourier-transform microwave spectrometer, a millimeter/submillimter-wave spectrometer, and a THz spectrometer, thus allowing to record a huge portion of the rotational spectrum, from 5 GHz up to 1.05 THz, and to accurately determine the ground-state rotational and centrifugal-distortion constants. Sub-Doppler measurements allowed to resolve the hyperfine structure of the rotational spectrum and to determine the complete iodine quadrupole-coupling tensor as well as the diagonal elements of the iodine spin-rotation tensor. The present investigation of rare isotopic species of CH2FI together with the results previously obtained for the main isotopologue [C. Puzzarini, G. Cazzoli, J. C. López, J. L. Alonso, A. Baldacci, A. Baldan, S. Stopkowicz, L. Cheng, and J. Gauss, J. Chem. Phys. 134, 174312 (2011);, 10.1063/1.3583498 G. Cazzoli, A. Baldacci, A. Baldan, and C. Puzzarini, Mol. Phys. 109, 2245 (2011)], 10.1080/00268976.2011.609142 enabled us to derive a semi-experimental equilibrium structure for fluoroiodomethane by means of a least-squares fit procedure using the available experimental ground-state rotational constants together with computed vibrational corrections. Problems related to the missing isotopic substitution of fluorine and iodine were overcome thanks to the availability of an accurate theoretical equilibrium geometry (computed at the coupled-cluster singles and doubles level augmented by a perturbative treatment of triple excitations).

  5. Bayesian statistical treatment of the fluorescence of AFLP bands leads to accurate genetic structure inference.

    PubMed

    Gaggiotti, Oscar E

    2010-11-01

    Ever since the introduction of allozymes in the 1960s, evolutionary biologists and ecologists have continued to search for more powerful molecular markers to estimate important parameters such as effective population size and migration rates and to make inferences about the demographic history of populations, the relationships between individuals and the genetic architecture of phenotypic variation (Bensch & Akesson 2005; Bonin et al. 2007). Choosing a marker requires a thorough consideration of the trade-offs associated with the different techniques and the type of data obtained from them. Some markers can be very informative but require substantial amounts of start-up time (e.g. microsatellites), while others require very little time but are much less polymorphic. Amplified fragment length polymorphism (AFLP) is a firmly established molecular marker technique that falls in this latter category. AFLPs are widely distributed throughout the genome and can be used on organisms for which there is no a priori sequence information (Meudt & Clarke 2007). These properties together with their moderate cost and short start-up time have made them the method of choice for many molecular ecology studies of wild species (Bensch & Akesson 2005). However, they have a major disadvantage, they are dominant. This represents a very important limitation because many statistical genetics methods appropriate for molecular ecology studies require the use of codominant markers. In this issue, Foll et al. (2010) present an innovative hierarchical Bayesian method that overcomes this limitation. The proposed approach represents a comprehensive statistical treatment of the fluorescence of AFLP bands and leads to accurate inferences about the genetic structure of natural populations. Besides allowing a quasi-codominant treatment of AFLPs, this new method also solves the difficult problems posed by subjectivity in the scoring of AFLP bands. PMID:20958811

  6. Multiobjective optimization in quantitative structure-activity relationships: deriving accurate and interpretable QSARs.

    PubMed

    Nicolotti, Orazio; Gillet, Valerie J; Fleming, Peter J; Green, Darren V S

    2002-11-01

    Deriving quantitative structure-activity relationship (QSAR) models that are accurate, reliable, and easily interpretable is a difficult task. In this study, two new methods have been developed that aim to find useful QSAR models that represent an appropriate balance between model accuracy and complexity. Both methods are based on genetic programming (GP). The first method, referred to as genetic QSAR (or GPQSAR), uses a penalty function to control model complexity. GPQSAR is designed to derive a single linear model that represents an appropriate balance between the variance and the number of descriptors selected for the model. The second method, referred to as multiobjective genetic QSAR (MoQSAR), is based on multiobjective GP and represents a new way of thinking of QSAR. Specifically, QSAR is considered as a multiobjective optimization problem that comprises a number of competitive objectives. Typical objectives include model fitting, the total number of terms, and the occurrence of nonlinear terms. MoQSAR results in a family of equivalent QSAR models where each QSAR represents a different tradeoff in the objectives. A practical consideration often overlooked in QSAR studies is the need for the model to promote an understanding of the biochemical response under investigation. To accomplish this, chemically intuitive descriptors are needed but do not always give rise to statistically robust models. This problem is addressed by the addition of a further objective, called chemical desirability, that aims to reward models that consist of descriptors that are easily interpretable by chemists. GPQSAR and MoQSAR have been tested on various data sets including the Selwood data set and two different solubility data sets. The study demonstrates that the MoQSAR method is able to find models that are at least as good as models derived using standard statistical approaches and also yields models that allow a medicinal chemist to trade statistical robustness for chemical

  7. Quantum-chemical calculations and electron diffraction study of the equilibrium molecular structure of vitamin K3

    NASA Astrophysics Data System (ADS)

    Khaikin, L. S.; Tikhonov, D. S.; Grikina, O. E.; Rykov, A. N.; Stepanov, N. F.

    2014-05-01

    The equilibrium molecular structure of 2-methyl-1,4-naphthoquinone (vitamin K3) having C s symmetry is experimentally characterized for the first time by means of gas-phase electron diffraction using quantum-chemical calculations and data on the vibrational spectra of related compounds.

  8. Rotational spectroscopy of pyridazine and its isotopologs from 235-360 GHz: equilibrium structure and vibrational satellites.

    PubMed

    Esselman, Brian J; Amberger, Brent K; Shutter, Joshua D; Daane, Mitchell A; Stanton, John F; Woods, R Claude; McMahon, Robert J

    2013-12-14

    The rotational spectrum of pyridazine (o-C4H4N2), the ortho disubstituted nitrogen analog of benzene, has been measured and analyzed in the gas phase. For the ground vibrational state of the normal isotopolog, over 2000 individual rotational transitions have been identified between 238 and 360 GHz and have been fit to 13 parameters of a 6th-order centrifugal distortion Hamiltonian. All transitions in this frequency region can now be predicted from this model to near experimental accuracy, i.e., well enough for the purpose of any future radio-astronomical search for this species. Three isotopologs, [3-(13)C]-C4H4N2, [4-(13)C]-C4H4N2, and [1-(15)N]-C4H4N2, have been detected in natural abundance, and several hundred lines have been measured for each of these species and fit to 6th-order Hamiltonians. Ten additional isotopologs were synthesized with enhanced deuterium substitution and analyzed to allow for a complete structure determination. The equilibrium structure (Re) of pyridazine was obtained by correcting the experimental rotational constants for the effects of vibration-rotation coupling using interaction constants predicted from CCSD(T) calculations with an ANO0 basis set and further correcting for the effect of electron mass. The final Re structural parameters are determined with excellent accuracy, as evidenced by their ability to predict 28 independent moments of inertia (Ia and Ib for 14 isotopologs) very well from 9 structural parameters. The rotational spectra of the six lowest-energy fundamental vibrational satellites of the main isotopolog have been detected. The rotational spectra of the five lowest-energy vibrational satellites have been assigned and fit to yield accurate rotational and distortion constants, while the fit and assignment for the sixth is less complete. The resultant vibration-rotation interaction (α) constants are found to be in excellent agreement with ones predicted from coupled-cluster calculations, which proved to be the key

  9. Rotational spectroscopy of pyridazine and its isotopologs from 235–360 GHz: Equilibrium structure and vibrational satellites

    SciTech Connect

    Esselman, Brian J.; Amberger, Brent K.; Shutter, Joshua D.; Daane, Mitchell A.; Woods, R. Claude; McMahon, Robert J.; Stanton, John F.

    2013-12-14

    The rotational spectrum of pyridazine (o-C{sub 4}H{sub 4}N{sub 2}), the ortho disubstituted nitrogen analog of benzene, has been measured and analyzed in the gas phase. For the ground vibrational state of the normal isotopolog, over 2000 individual rotational transitions have been identified between 238 and 360 GHz and have been fit to 13 parameters of a 6th-order centrifugal distortion Hamiltonian. All transitions in this frequency region can now be predicted from this model to near experimental accuracy, i.e., well enough for the purpose of any future radio-astronomical search for this species. Three isotopologs, [3-{sup 13}C]-C{sub 4}H{sub 4}N{sub 2}, [4-{sup 13}C]-C{sub 4}H{sub 4}N{sub 2}, and [1-{sup 15}N]-C{sub 4}H{sub 4}N{sub 2}, have been detected in natural abundance, and several hundred lines have been measured for each of these species and fit to 6th-order Hamiltonians. Ten additional isotopologs were synthesized with enhanced deuterium substitution and analyzed to allow for a complete structure determination. The equilibrium structure (R{sub e}) of pyridazine was obtained by correcting the experimental rotational constants for the effects of vibration-rotation coupling using interaction constants predicted from CCSD(T) calculations with an ANO0 basis set and further correcting for the effect of electron mass. The final R{sub e} structural parameters are determined with excellent accuracy, as evidenced by their ability to predict 28 independent moments of inertia (I{sub a} and I{sub b} for 14 isotopologs) very well from 9 structural parameters. The rotational spectra of the six lowest-energy fundamental vibrational satellites of the main isotopolog have been detected. The rotational spectra of the five lowest-energy vibrational satellites have been assigned and fit to yield accurate rotational and distortion constants, while the fit and assignment for the sixth is less complete. The resultant vibration-rotation interaction (α) constants are found to

  10. Thin current sheets in collisionless plasma: Equilibrium structure, plasma instabilities, and particle acceleration

    SciTech Connect

    Zelenyi, L. M.; Malova, H. V.; Artemyev, A. V.; Popov, V. Yu.; Petrukovich, A. A.

    2011-02-15

    The review is devoted to plasma structures with an extremely small transverse size, namely, thin current sheets that have been discovered and investigated by spacecraft observations in the Earth's magnetotail in the last few decades. The formation of current sheets is attributed to complicated dynamic processes occurring in a collisionless space plasma during geomagnetic perturbations and near the magnetic reconnection regions. The models that describe thin current structures in the Earth's magnetotail are reviewed. They are based on the assumption of the quasi-adiabatic ion dynamics in a relatively weak magnetic field of the magnetotail neutral sheet, where the ions can become unmagnetized. It is shown that the ion distribution can be represented as a function of the integrals of particle motion-the total energy and quasi-adiabatic invariant. Various modifications of the initial equilibrium are considered that are obtained with allowance for the currents of magnetized electrons, the contribution of oxygen ions, the asymmetry of plasma sources, and the effects related to the non-Maxwellian particle distributions. The theoretical results are compared with the observational data from the Cluster spacecraft mission. Various plasma instabilities developing in thin current sheets are investigated. The evolution of the tearing mode is analyzed, and the parameter range in which the mode can grow are determined. The paradox of complete stabilization of the tearing mode in current sheets with a nonzero normal magnetic field component is thereby resolved based on the quasi-adiabatic model. It is shown that, over a wide range of current sheet parameters and the propagation directions of large-scale unstable waves, various modified drift instabilities-kink and sausage modes-can develop in the system. Based on the concept of a turbulent electromagnetic field excited as a result of the development and saturation of unstable waves, a mechanism for charged particle acceleration in

  11. Local atomic structure in equilibrium and supercooled liquid Zr[subscript 75.5]Pd[subscript 24.5

    SciTech Connect

    Mauro, N.A.; Fu, W.; Bendert, J.C.; Cheng, Y.Q.; Ma, E.; Kelton, K.F.

    2012-09-06

    Atomic structures were obtained in equilibrium and supercooled eutectic Zr{sub 75.5}Pd{sub 24.5} liquids by in situ high-energy synchrotron diffraction measurements using the beamline electrostatic levitation (BESL) technique, which provides a high-vacuum, containerless, environment. Reverse Monte Carlo fits to the x-ray static structure factors, constrained using partial pair correlation functions obtained from ab initio molecular dynamics simulations, indicate the presence of medium-range order (MRO) in the form of a strong tendency for Pd-Pd (solute-solute) avoidance. This order persists over the entire temperature range studied, from 170 C above the equilibrium liquidus temperature to 263 C below it. Further, a quantitative analysis of the atomic structures obtained indicates a modest degree of icosahedral-like local order around Pd atoms, with the clusters showing an increased tendency for face-sharing to form more extended structures with decreasing temperature.

  12. Dielectric-dependent Density Functionals for Accurate Electronic Structure Calculations of Molecules and Solids

    NASA Astrophysics Data System (ADS)

    Skone, Jonathan; Govoni, Marco; Galli, Giulia

    Dielectric-dependent hybrid [DDH] functionals have recently been shown to yield highly accurate energy gaps and dielectric constants for a wide variety of solids, at a computational cost considerably less than standard GW calculations. The fraction of exact exchange included in the definition of DDH functionals depends (self-consistently) on the dielectric constant of the material. In the present talk we introduce a range-separated (RS) version of DDH functionals where short and long-range components are matched using material dependent, non-empirical parameters. Comparing with state of the art GW calculations and experiment, we show that such RS hybrids yield accurate electronic properties of both molecules and solids, including energy gaps, photoelectron spectra and absolute ionization potentials. This work was supported by NSF-CCI Grant Number NSF-CHE-0802907 and DOE-BES.

  13. Solid-solid structural transformations in Lennard-Jones clusters: accurate simulations versus the harmonic superposition approximation.

    PubMed

    Sharapov, Vladimir A; Mandelshtam, Vladimir A

    2007-10-18

    We consider systems undergoing very-low-temperature solid-solid transitions associated with minima of similar energy but different symmetry, and separated by a high potential barrier. In such cases the well-known "broken-ergodicity" problem is often difficult to overcome, even using the most advanced Monte Carlo (MC) techniques, including the replica exchange method (REM). The methodology that we develop in this paper is suitable for the above specified cases and is numerically accurate and efficient. It is based on a new MC move implemented within the REM framework, in which trial points are generated analytically using an auxiliary harmonic superposition system that mimics well the true system at low temperatures. Due to the new move, the low-temperature random walks are able to frequently switch the relevant potential energy funnels leading to an efficient sampling. Numerically accurate results are obtained for a number of Lennard-Jones clusters, including those that have so far been treated only by the harmonic superposition approximation (HSA). The latter is believed to provide good estimates for low-temperature equilibrium properties but is manifestly uncontrollable and is difficult to validate. The present results provide a good test for the HSA and demonstrate its reliability, particularly for estimation of the solid-solid transition temperatures in most cases considered. PMID:17685597

  14. Structure and evolution of irradiated accretion disks. I - Static thermal equilibrium structure. II - Dynamical evolution of a thermally unstable torus

    NASA Technical Reports Server (NTRS)

    Tuchman, Y.; Mineshige, S.; Wheeler, J. C.

    1990-01-01

    The thermal equilibrum structure and dynamical behavior of externally irradiated accretion disks are investigated. For radiative disks only the surface layer is heated, while for convective disks the heat penetrates deeply into the disk. For sufficiently strong radiation and given irradiation flux F(irr), the disk is completely stabilized against thermal instabilities of the sort invoked to explain dwarf novae. For moderately strong irradiation there is still an unstable branch in the thermal equilibrium curve. In typical soft X-ray transients, the disk is unstable against the dwarf-nova type instability. Fixed F(irr) on accretion disk annuli reduces the amplitude and the quiescent times and increases the outburst duration of the resultant light curves. Varying F(irr) in proportion to the mass accretion rate at the disks's inner edge results in light curves with a plateau in the decay from outbursts. In the case when irradiation is suddenly switched on, a temperature inversion results which leads to the formation of an accretion corona.

  15. Equilibrium Sorption of Structurally Diverse Organic Ions to Bovine Serum Albumin.

    PubMed

    Henneberger, Luise; Goss, Kai-Uwe; Endo, Satoshi

    2016-05-17

    Reliable partitioning data are essential for assessing the bioaccumulation potential and the toxicity of chemicals. In contrast to neutral organic chemicals, the partitioning behavior of ionogenic organic chemicals (IOCs) is still a black box for environmental scientists. Partitioning to serum albumin, the major protein in blood plasma, strongly influences the freely dissolved concentration of many chemicals (including IOCs), which affects their transport and distribution in the body. Because consistent data sets for partitioning of IOCs are rarely available, bovine serum albumin-water partition coefficients (KBSA/w) were measured in this study for 45 anionic and 4 cationic organic chemicals, including various substituted benzoic and naphthoic acids, sulfonates and several pesticides and pharmaceuticals. The results of this study suggest that binding to BSA is substantially influenced by the three-dimensional structure of the chemicals and the position of substitutions on the sorbing molecules. For example, we found a difference of >1.5 log units between isomeric chemicals such as 3,4-dichlorobenzoic acid and 2,6-dichlorobenzoic acid, and 1-naphthoic acid and 2-naphthoic acid. Conventional modeling approaches (e.g., based on octanol-water partition coefficients) poorly predict log KBSA/w of organic ions (R(2) ≤ 0.5), partially because they do not capture the observed steric effects. Hence, alternative modeling strategies will be required for accurate prediction of serum albumin-water partition coefficients of organic ions. PMID:27098963

  16. PROMALS3D web server for accurate multiple protein sequence and structure alignments.

    PubMed

    Pei, Jimin; Tang, Ming; Grishin, Nick V

    2008-07-01

    Multiple sequence alignments are essential in computational sequence and structural analysis, with applications in homology detection, structure modeling, function prediction and phylogenetic analysis. We report PROMALS3D web server for constructing alignments for multiple protein sequences and/or structures using information from available 3D structures, database homologs and predicted secondary structures. PROMALS3D shows higher alignment accuracy than a number of other advanced methods. Input of PROMALS3D web server can be FASTA format protein sequences, PDB format protein structures and/or user-defined alignment constraints. The output page provides alignments with several formats, including a colored alignment augmented with useful information about sequence grouping, predicted secondary structures and consensus sequences. Intermediate results of sequence and structural database searches are also available. The PROMALS3D web server is available at: http://prodata.swmed.edu/promals3d/. PMID:18503087

  17. Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

    PubMed

    Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

    2009-12-24

    In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure. PMID:19950907

  18. Empirical anharmonic force field and equilibrium structure of hypochlorous acid, HOCl

    NASA Astrophysics Data System (ADS)

    Escribano, R. M.; Di Lonardo, G.; Fusina, L.

    1996-09-01

    The cubic and quartic force fields of HOCl are investigated on the basis of the most recent experimental data on vibration-rotation interaction constants and anharmonicity constants. Some discrepancies with respect to previously reported ab initio results are found and discussed. The geometrical parameters of this molecule are also evaluated from recent data on the equilibrium values of the moments of inertia.

  19. Seeking: Accurate Measurement Techniques for Deep-Bone Density and Structure

    NASA Technical Reports Server (NTRS)

    Sibonga, Jean

    2009-01-01

    We are seeking a clinically-useful technology with enough sensitivity to assess the microstructure of "spongy" bone that is found in the marrow cavities of whole bones. However, this technology must be for skeletal sites surrounded by layers of soft tissues, such as the spine and the hip. Soft tissue interferes with conventional imaging and using a more accessible area -- for example, the wrist or the ankle of limbs-- as a proxy for the less accessible skeletal regions, will not be accurate. A non-radioactive technology is strongly preferred.

  20. {ital Ab} {ital initio} investigation of the N{sub 2}{endash}HF complex: Accurate structure and energetics

    SciTech Connect

    Woon, D.E.; Dunning, T.H. Jr.; Peterson, K.A.

    1996-04-01

    Augmented correlation consistent basis sets of double (aug-cc-pVDZ), triple (aug-cc-pVTZ), and modified quadruple zeta (aug-cc-pVQZ{prime}) quality have been employed to describe the N{sub 2}{endash}HF potential energy surface at the Hartree{endash}Fock level and with single reference correlated wave functions including Mo/ller{endash}Plesset perturbation theory (MP2, MP3, MP4) and coupled cluster methods [CCSD, CCSD(T)]. The most accurate computed equilibrium binding energies {ital D}{sub {ital e}} are (with counterpoise correction) 810 cm{sup {minus}1} (MP4/aug-cc-pVQZ{prime}) and 788 cm{sup {minus}1} [CCSD(T)/aug-cc-pVQZ{prime}]. Estimated complete basis set limits of 814 cm{sup {minus}1} (MP4) and 793 cm{sup {minus}1} [CCSD(T)] indicate that the large basis set results are essentially converged. Harmonic frequencies and zero-point energies were determined through the aug-cc-pVTZ level. Combining the zero point energies computed at the aug-cc-pVTZ level with the equilibrium binding energies computed at the aug-cc-pVQZ{prime} level, we predict {ital D}{sub 0} values of 322 and 296 cm{sup {minus}1}, respectively, at the MP4 and CCSD(T) levels of theory. Using experimental anharmonic frequencies, on the other hand, the CCSD(T) value of {ital D}{sub 0} is increased to 415 cm{sup {minus}1}, in good agreement with the experimental value recently reported by Miller and co-workers, 398{plus_minus}2 cm{sup {minus}1}. {copyright} {ital 1996 American Institute of Physics.}

  1. Using Dielectric Properties to Design Nonempirical Hybrid Functionals for Accurate Electronic Structure

    NASA Astrophysics Data System (ADS)

    Skone, Jonathan; Govoni, Marco; Galli, Giulia

    2015-03-01

    Building upon a recently proposed self-consistent hybrid (sc-hybrid) functional, where the optimal dielectric screening is included self-consistently, we propose an improved form by incorporating range-separation of the exchange part. We discuss the choice of the non-empirical parameters defining range separation, and we present results for condensed media including semiconductors, amorphous insulators, and molecular crystals. We find that the range-separated sc-hybrid functional further improves upon the electronic gaps obtained with full-range sc-hybrids, thus providing an accurate functional for high throughput band gap engineering. This work was supported by NSF-CCI Grant Number NSF-CHE-0802907 and ARL Grant Number W911NF-12-2-0023.

  2. LOCUSTRA: accurate prediction of local protein structure using a two-layer support vector machine approach.

    PubMed

    Zimmermann, Olav; Hansmann, Ulrich H E

    2008-09-01

    Constraint generation for 3d structure prediction and structure-based database searches benefit from fine-grained prediction of local structure. In this work, we present LOCUSTRA, a novel scheme for the multiclass prediction of local structure that uses two layers of support vector machines (SVM). Using a 16-letter structural alphabet from de Brevern et al. (Proteins: Struct., Funct., Bioinf. 2000, 41, 271-287), we assess its prediction ability for an independent test set of 222 proteins and compare our method to three-class secondary structure prediction and direct prediction of dihedral angles. The prediction accuracy is Q16=61.0% for the 16 classes of the structural alphabet and Q3=79.2% for a simple mapping to the three secondary classes helix, sheet, and coil. We achieve a mean phi(psi) error of 24.74 degrees (38.35 degrees) and a median RMSDA (root-mean-square deviation of the (dihedral) angles) per protein chain of 52.1 degrees. These results compare favorably with related approaches. The LOCUSTRA web server is freely available to researchers at http://www.fz-juelich.de/nic/cbb/service/service.php. PMID:18763837

  3. A 3-D MHD equilibrium description of nonlinearly saturated ideal external kink/peeling structures in tokamaks

    NASA Astrophysics Data System (ADS)

    Cooper, W. A.; Graves, J. P.; Duval, B. P.; Porte, L.; Reimerdes, H.; Sauter, O.; Tran, T.-M.

    2015-12-01

    > Novel free boundary magnetohydrodynamic equilibrium states with spontaneous three-dimensional (3-D) deformations of the plasma-vacuum interface are computed. The structures obtained look like saturated ideal external kink/peeling modes. Large edge pressure gradients yield toroidal mode number distortions when the edge bootstrap current is large and higher corrugations when this current is small. Linear ideal MHD stability analyses confirm the nonlinear saturated ideal kink equilibrium states produced and we can identify the Pfirsch-Schlüter current as the main linear instability driving mechanism when the edge pressure gradient is large. The dominant non-axisymmetric component of this Pfirsch-Schlüter current drives a near resonant helical parallel current density ribbon that aligns with the near vanishing magnetic shear region caused by the edge bootstrap current. This current ribbon is a manifestation of the outer mode previously found on JET (Solano 2010). We claim that the equilibrium corrugations describe structures that are commonly observed in quiescent H-mode tokamak discharges.

  4. Equilibrium point defects in intermetallics with the [ital B]2 structure: NiAl and FeAl

    SciTech Connect

    Fu, C.L.; Ye, Y.; Yoo, M.H. ); Ho, K.M. )

    1993-09-01

    Equilibrium point defects and their relation to the contrasting mechanical behavior of NiAl and FeAl are investigated. For NiAl, the defect structure is dominated by two types of defects---monovacancies on the Ni sites and substitutional antisite defects on the Al sites. The defect structure of FeAl differs from that of NiAl in the occurrence of antisite defects at the transition-metal sites for Al-rich alloys and the tendency for vacancy clustering. The strong ordering (and brittleness) of NiAl is attributed mainly to the difference in atomic size between constituent atoms.

  5. Polyallelic structural variants can provide accurate, highly informative genetic markers focused on diagnosis and therapeutic targets: Accuracy vs. Precision.

    PubMed

    Roses, A D

    2016-02-01

    Structural variants (SVs) include all insertions, deletions, and rearrangements in the genome, with several common types of nucleotide repeats including single sequence repeats, short tandem repeats, and insertion-deletion length variants. Polyallelic SVs provide highly informative markers for association studies with well-phenotyped cohorts. SVs can influence gene regulation by affecting epigenetics, transcription, splicing, and/or translation. Accurate assays of polyallelic SV loci are required to define the range and allele frequency of variable length alleles. PMID:26517180

  6. Fast and accurate analysis of large-scale composite structures with the parallel multilevel fast multipole algorithm.

    PubMed

    Ergül, Özgür; Gürel, Levent

    2013-03-01

    Accurate electromagnetic modeling of complicated optical structures poses several challenges. Optical metamaterial and plasmonic structures are composed of multiple coexisting dielectric and/or conducting parts. Such composite structures may possess diverse values of conductivities and dielectric constants, including negative permittivity and permeability. Further challenges are the large sizes of the structures with respect to wavelength and the complexities of the geometries. In order to overcome these challenges and to achieve rigorous and efficient electromagnetic modeling of three-dimensional optical composite structures, we have developed a parallel implementation of the multilevel fast multipole algorithm (MLFMA). Precise formulation of composite structures is achieved with the so-called "electric and magnetic current combined-field integral equation." Surface integral equations are carefully discretized with piecewise linear basis functions, and the ensuing dense matrix equations are solved iteratively with parallel MLFMA. The hierarchical strategy is used for the efficient parallelization of MLFMA on distributed-memory architectures. In this paper, fast and accurate solutions of large-scale canonical and complicated real-life problems, such as optical metamaterials, discretized with tens of millions of unknowns are presented in order to demonstrate the capabilities of the proposed electromagnetic solver. PMID:23456127

  7. The role of non-equilibrium vibrational structures in electronic coherence and recoherence in pigment-protein complexes

    NASA Astrophysics Data System (ADS)

    Chin, A. W.; Prior, J.; Rosenbach, R.; Caycedo-Soler, F.; Huelga, S. F.; Plenio, M. B.

    2013-02-01

    Recent observations of oscillatory features in the optical response of photosynthetic complexes have revealed evidence for surprisingly long-lasting electronic coherences which can coexist with energy transport. These observations have ignited multidisciplinary interest in the role of quantum effects in biological systems, including the fundamental question of how electronic coherence can survive in biological surroundings. Here we show that the non-trivial spectral structures of protein fluctuations can generate non-equilibrium processes that lead to the spontaneous creation and sustenance of electronic coherence, even at physiological temperatures. Developing new advanced simulation tools to treat these effects, we provide a firm microscopic basis to successfully reproduce the experimentally observed coherence times in the Fenna-Matthews-Olson complex, and illustrate how detailed quantum modelling and simulation can shed further light on a wide range of other non-equilibrium processes which may be important in different photosynthetic systems.

  8. Accurate structural and spectroscopic characterization of prebiotic molecules: The neutral and cationic acetyl cyanide and their related species.

    PubMed

    Bellili, A; Linguerri, R; Hochlaf, M; Puzzarini, C

    2015-11-14

    In an effort to provide an accurate structural and spectroscopic characterization of acetyl cyanide, its two enolic isomers and the corresponding cationic species, state-of-the-art computational methods, and approaches have been employed. The coupled-cluster theory including single and double excitations together with a perturbative treatment of triples has been used as starting point in composite schemes accounting for extrapolation to the complete basis-set limit as well as core-valence correlation effects to determine highly accurate molecular structures, fundamental vibrational frequencies, and rotational parameters. The available experimental data for acetyl cyanide allowed us to assess the reliability of our computations: structural, energetic, and spectroscopic properties have been obtained with an overall accuracy of about, or better than, 0.001 Å, 2 kcal/mol, 1-10 MHz, and 11 cm(-1) for bond distances, adiabatic ionization potentials, rotational constants, and fundamental vibrational frequencies, respectively. We are therefore confident that the highly accurate spectroscopic data provided herein can be useful for guiding future experimental investigations and/or astronomical observations. PMID:26567669

  9. Fine structure in proton radioactivity: An accurate tool to ascertain the breaking of axial symmetry in {sup 145}Tm

    SciTech Connect

    Arumugam, P.; Ferreira, L. S.; Maglione, E.

    2008-10-15

    With a proper formalism for proton emission from triaxially deformed nuclei, we perform exact calculations of decay widths for the decays to ground and first excited 2{sup +} states in the daughter nucleus. Our results for rotational spectrum, decay width and fine structure in the case of the nucleus {sup 145}Tm lead for the first time to an accurate identification of triaxial deformation using proton emission. This work also puts in evidence the advantage of proton emission over the conventional probes to study nuclear structure at the proton drip-line.

  10. Discretely disordered photonic bandgap structures: a more accurate invariant measure calculation

    NASA Astrophysics Data System (ADS)

    Kissel, Glen J.

    2009-02-01

    In the one-dimensional optical analog to Anderson localization, a periodically layered medium has one or more parameters randomly disordered. Such a randomized system can be modeled by an infinite product of 2x2 random transfer matrices with the upper Lyapunov exponent of the matrix product identified as the localization factor (inverse localization length) for the model. The theorem of Furstenberg allows us, at least theoretically, to calculate this upper Lyapunov exponent. In Furstenberg's formula we not only integrate with respect to the probability measure of the random matrices, but also with respect to the invariant probability measure of the direction of the vector propagated by the random matrices. This invariant measure is difficult to find analytically, and, as a result, the most successful approach is to determine the invariant measure numerically. A Monte Carlo simulation which uses accumulated bin counts to track the direction of the propagated vector through a long chain of random matrices does a good job of estimating the invariant probability measure, but with a level of uncertainty. A potentially more accurate numerical technique by Froyland and Aihara obtains the invariant measure as a left eigenvector of a large sparse matrix containing probability values determined by the action of the random matrices on input vectors. We first apply these two techniques to a random Fibonacci sequence whose Lyapunov exponent was determined by Viswanath. We then demonstrate these techniques on a quarter-wave stack model with binary discrete disorder in layer thickness, and compare results to the continuously disordered counterpart.

  11. Accurate Fabrication of Hydroxyapatite Bone Models with Porous Scaffold Structures by Using Stereolithography

    NASA Astrophysics Data System (ADS)

    Maeda, Chiaki; Tasaki, Satoko; Kirihara, Soshu

    2011-05-01

    Computer graphic models of bioscaffolds with four-coordinate lattice structures of solid rods in artificial bones were designed by using a computer aided design. The scaffold models composed of acryl resin with hydroxyapatite particles at 45vol. % were fabricated by using stereolithography of a computer aided manufacturing. After dewaxing and sintering heat treatment processes, the ceramics scaffold models with four-coordinate lattices and fine hydroxyapatite microstructures were obtained successfully. By using a computer aided analysis, it was found that bio-fluids could flow extensively inside the sintered scaffolds. This result shows that the lattice structures will realize appropriate bio-fluid circulations and promote regenerations of new bones.

  12. Accurate Structure and Dynamics of the Metal-Site of Paramagnetic Metalloproteins from NMR Parameters Using Natural Bond Orbitals

    PubMed Central

    2012-01-01

    A natural bond orbital (NBO) analysis of unpaired electron spin density in metalloproteins is presented, which allows a fast and robust calculation of paramagnetic NMR parameters. Approximately 90% of the unpaired electron spin density occupies metal–ligand NBOs, allowing the majority of the density to be modeled by only a few NBOs that reflect the chemical bonding environment. We show that the paramagnetic relaxation rate of protons can be calculated accurately using only the metal–ligand NBOs and that these rates are in good agreement with corresponding rates measured experimentally. This holds, in particular, for protons of ligand residues where the point-dipole approximation breaks down. To describe the paramagnetic relaxation of heavy nuclei, also the electron spin density in the local orbitals must be taken into account. Geometric distance restraints for 15N can be derived from the paramagnetic relaxation enhancement and the Fermi contact shift when local NBOs are included in the analysis. Thus, the NBO approach allows us to include experimental paramagnetic NMR parameters of 15N nuclei as restraints in a structure optimization protocol. We performed a molecular dynamics simulation and structure determination of oxidized rubredoxin using the experimentally obtained paramagnetic NMR parameters of 15N. The corresponding structures obtained are in good agreement with the crystal structure of rubredoxin. Thus, the NBO approach allows an accurate description of the geometric structure and the dynamics of metalloproteins, when NMR parameters are available of nuclei in the immediate vicinity of the metal-site. PMID:22329704

  13. Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction

    PubMed Central

    Braun, Tatjana; Koehler Leman, Julia; Lange, Oliver F.

    2015-01-01

    Recent work has shown that the accuracy of ab initio structure prediction can be significantly improved by integrating evolutionary information in form of intra-protein residue-residue contacts. Following this seminal result, much effort is put into the improvement of contact predictions. However, there is also a substantial need to develop structure prediction protocols tailored to the type of restraints gained by contact predictions. Here, we present a structure prediction protocol that combines evolutionary information with the resolution-adapted structural recombination approach of Rosetta, called RASREC. Compared to the classic Rosetta ab initio protocol, RASREC achieves improved sampling, better convergence and higher robustness against incorrect distance restraints, making it the ideal sampling strategy for the stated problem. To demonstrate the accuracy of our protocol, we tested the approach on a diverse set of 28 globular proteins. Our method is able to converge for 26 out of the 28 targets and improves the average TM-score of the entire benchmark set from 0.55 to 0.72 when compared to the top ranked models obtained by the EVFold web server using identical contact predictions. Using a smaller benchmark, we furthermore show that the prediction accuracy of our method is only slightly reduced when the contact prediction accuracy is comparatively low. This observation is of special interest for protein sequences that only have a limited number of homologs. PMID:26713437

  14. Structure and dynamics of concentration fluctuations in a non-equilibrium dense colloidal suspension.

    PubMed

    Giavazzi, Fabio; Savorana, Giovanni; Vailati, Alberto; Cerbino, Roberto

    2016-08-21

    Linearised fluctuating hydrodynamics describes effectively the concentration non-equilibrium fluctuations (NEF) arising during a diffusion process driven by a small concentration gradient. However, fluctuations in the presence of large gradients are not yet fully understood. Here we study the giant concentration NEF arising when a dense aqueous colloidal suspension is allowed to diffuse into an overlying layer of pure water. We use differential dynamic microscopy to determine both the statics and the dynamics of the fluctuations for several values of the wave-vector q. At small q, NEF are quenched by buoyancy, which prevents their full development and sets an upper timescale to their temporal relaxation. At intermediate q, the mean squared amplitude of NEF is characterised by a power law exponent -4, and fluctuations relax diffusively with diffusion coefficient D1. At large q, the amplitude of NEF vanishes and equilibrium concentration fluctuations are recovered, enabling a straightforward determination of the osmotic compressibility of the suspension during diffusion. In this q-range we also find that the relaxation of the fluctuations occurs with a diffusion coefficient D2 significantly different from D1. Both diffusion coefficients exhibit time-dependence with D1 increasing monotonically (by about 15%) and D2 showing the opposite behaviour (about 17% decrease). At equilibrium, the two coefficients coincide as expected. While the decrease of D2 is compatible with a diffusive evolution of the concentration profile, the increase of D1 is still not fully understood and may require considering nonlinearities that are neglected in current theories for highly stressed colloids. PMID:27425869

  15. Network diffusion accurately models the relationship between structural and functional brain connectivity networks

    PubMed Central

    Abdelnour, Farras; Voss, Henning U.; Raj, Ashish

    2014-01-01

    The relationship between anatomic connectivity of large-scale brain networks and their functional connectivity is of immense importance and an area of active research. Previous attempts have required complex simulations which model the dynamics of each cortical region, and explore the coupling between regions as derived by anatomic connections. While much insight is gained from these non-linear simulations, they can be computationally taxing tools for predicting functional from anatomic connectivities. Little attention has been paid to linear models. Here we show that a properly designed linear model appears to be superior to previous non-linear approaches in capturing the brain’s long-range second order correlation structure that governs the relationship between anatomic and functional connectivities. We derive a linear network of brain dynamics based on graph diffusion, whereby the diffusing quantity undergoes a random walk on a graph. We test our model using subjects who underwent diffusion MRI and resting state fMRI. The network diffusion model applied to the structural networks largely predicts the correlation structures derived from their fMRI data, to a greater extent than other approaches. The utility of the proposed approach is that it can routinely be used to infer functional correlation from anatomic connectivity. And since it is linear, anatomic connectivity can also be inferred from functional data. The success of our model confirms the linearity of ensemble average signals in the brain, and implies that their long-range correlation structure may percolate within the brain via purely mechanistic processes enacted on its structural connectivity pathways. PMID:24384152

  16. Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information

    PubMed Central

    Pollastri, Gianluca; Martin, Alberto JM; Mooney, Catherine; Vullo, Alessandro

    2007-01-01

    Background Structural properties of proteins such as secondary structure and solvent accessibility contribute to three-dimensional structure prediction, not only in the ab initio case but also when homology information to known structures is available. Structural properties are also routinely used in protein analysis even when homology is available, largely because homology modelling is lower throughput than, say, secondary structure prediction. Nonetheless, predictors of secondary structure and solvent accessibility are virtually always ab initio. Results Here we develop high-throughput machine learning systems for the prediction of protein secondary structure and solvent accessibility that exploit homology to proteins of known structure, where available, in the form of simple structural frequency profiles extracted from sets of PDB templates. We compare these systems to their state-of-the-art ab initio counterparts, and with a number of baselines in which secondary structures and solvent accessibilities are extracted directly from the templates. We show that structural information from templates greatly improves secondary structure and solvent accessibility prediction quality, and that, on average, the systems significantly enrich the information contained in the templates. For sequence similarity exceeding 30%, secondary structure prediction quality is approximately 90%, close to its theoretical maximum, and 2-class solvent accessibility roughly 85%. Gains are robust with respect to template selection noise, and significant for marginal sequence similarity and for short alignments, supporting the claim that these improved predictions may prove beneficial beyond the case in which clear homology is available. Conclusion The predictive system are publicly available at the address . PMID:17570843

  17. Non-equilibrium structures induced by ion irradiation in Ni[sub 4]Mo

    SciTech Connect

    Bellon, P. ); Okamoto, P.R. ); Schumacher, G. )

    1992-11-01

    We have studied the stability of equilibrium and metastable ordered phases (called LRO and SRO respectively) in Ni[sub 4]Mo during 500-keV Ne or 250-keV He irradiations. Some irradiations were performed in situ, allowing thus to follow the evolution of the samples, which were characterized by Transmission Electron Microscopy. Dynamical equilibrium phase diagrams are built, by varying the irradiation flux, temperature and dose. At a fixed ion flux, there exists a temperature range were a mixed'' ordered state is stabilized, and remains stable up to the maximum doses reached (1.7 dpa). This state, which cannot be obtained by electron irradiation, consists in the coexistence of the two ordered phases at a very fine scale ([le] 2nm). Comparison with results already reported after electron irradiation is made, stressing the role played by displacement cascades in our results. Furthermore we observed alignment of dislocation loops along, the [001] c-axis of the quadratic LRO phase.

  18. Non-equilibrium structures induced by ion irradiation in Ni{sub 4}Mo

    SciTech Connect

    Bellon, P.; Schumacher, G.

    1992-11-01

    We have studied the stability of equilibrium and metastable ordered phases (called LRO and SRO respectively) in Ni{sub 4}Mo during 500-keV Ne or 250-keV He irradiations. Some irradiations were performed in situ, allowing thus to follow the evolution of the samples, which were characterized by Transmission Electron Microscopy. Dynamical equilibrium phase diagrams are built, by varying the irradiation flux, temperature and dose. At a fixed ion flux, there exists a temperature range were a ``mixed`` ordered state is stabilized, and remains stable up to the maximum doses reached (1.7 dpa). This state, which cannot be obtained by electron irradiation, consists in the coexistence of the two ordered phases at a very fine scale ({le} 2nm). Comparison with results already reported after electron irradiation is made, stressing the role played by displacement cascades in our results. Furthermore we observed alignment of dislocation loops along, the [001] c-axis of the quadratic LRO phase.

  19. Pseudo-Newtonian models for the equilibrium structures of rotating relativistic stars

    NASA Astrophysics Data System (ADS)

    Kim, Jinho; Il Kim, Hee; Mok Lee, Hyung

    2009-10-01

    We obtain equilibrium solutions for rotating compact stars, including special relativistic effects. The gravity is assumed to be Newtonian, but we use the active mass density, which takes into account all energies such as the motion of the fluid, internal energy and pressure energy in addition to the rest-mass energy, in computing the gravitational potential using Poisson's equation. Such a treatment could be applicable to neutron stars with relativistic motions or a relativistic equation of state. We applied Hachisu's self-consistent field (SCF) method to find spheroidal as well as toroidal sequences of equilibrium solutions. Our solutions show better agreement with general relativistic solutions than the Newtonian relativistic hydrodynamic approach, which does not take into account the active mass. Physical quantities such as the peak density and equatorial radii in our solutions agree with the general relativistic ones to within 5 per cent. Therefore our approach can be used as a simple alternative to the fully relativistic one when a large number of model calculations is necessary, as it requires much fewer computational resources.

  20. Equilibrium Shaping

    NASA Astrophysics Data System (ADS)

    Izzo, Dario; Petazzi, Lorenzo

    2006-08-01

    We present a satellite path planning technique able to make identical spacecraft aquire a given configuration. The technique exploits a behaviour-based approach to achieve an autonomous and distributed control over the relative geometry making use of limited sensorial information. A desired velocity is defined for each satellite as a sum of different contributions coming from generic high level behaviours: forcing the final desired configuration the behaviours are further defined by an inverse dynamic calculation dubbed Equilibrium Shaping. We show how considering only three different kind of behaviours it is possible to acquire a number of interesting formations and we set down the theoretical framework to find the entire set. We find that allowing a limited amount of communication the technique may be used also to form complex lattice structures. Several control feedbacks able to track the desired velocities are introduced and discussed. Our results suggest that sliding mode control is particularly appropriate in connection with the developed technique.

  1. A new class of atomic basis functions for accurate electronic structure calculations of molecules

    NASA Astrophysics Data System (ADS)

    Laikov, Dimitri N.

    2005-11-01

    A new general approach is developed for obtaining systematic sequences of atomic single-particle basis sets for use in correlated electronic structure calculations of molecules. All the constituent functions are defined as the solutions of variational problems and are of three types: a minimal Hartree-Fock set, additional functions to represent low-lying excited configurations, and general functions for describing electron correlation. The latter are determined to minimize a functional derived from the closed-shell second-order correlation energy expression. Generally-contracted Gaussian expansions are developed to approximate these general functions in the non-relativistic case and within a scalar-relativistic approximation.

  2. Structural investigation of trifuoromethyl substituted bis(β-diketonato)-dichlorotitanium(IV) complexes displaying a mono-dinuclear equilibrium hydrolysis reaction

    NASA Astrophysics Data System (ADS)

    Kuhn, Annemarie; Conradie, Jeanet

    2015-10-01

    Mononuclear Ti(β-diketonato)2Cl2 complexes with CF3-containing β-diketonato ligands, exhibit a monomer-hydrolysed dinuclear complex equilibrium when dissolved in CDCl3 containing trace amounts of water. This result is in contrast to the more electron rich derivatives with non CF3-containing β-diketonato ligands, for example, Ti(acac)2Cl2, which exsists only as the monomer in CDCl3 solution. The X-ray structure of the μ-oxo bridged hydrolysed dinuclear complex {Ti(CF3COCHCOCH3)2Cl}2(μ-O) reveals that the two mononuclear Ti units forming the dinuclear structure, both adopt a cis-trans-cis configuration with the CF3 groups of the trifluoroacetylacetonate ligands in trans positions. In solution both mononuclear Ti(β-diketonato)2Cl2 and hydrolysed dinuclear {Ti(β-diketonato)2Cl}2(μ-O) complexes exist as equilibrium mixtures of isomers. DFT calculations, used to determine the stability of the isomers, showed that for monomeric bis(β-diketonato)-titanium(IV) complexes, there is agreement with experimental solid state structures, in that the most stable DFT calculated isomer, of a specific complex, formed in the solid state. However for the dinuclear {Ti(CF3COCHCOCH3)2Cl}2(μ-O) complex, DFT calculations revealed that although most of the 10 isomers are experimentally possible due to the small energy difference obtained between the isomers, an isomer of higher energy formed in the solid state, suggesting that the equilibrium reaction between the monomer and hydrolysed dinuclear complex may contribute to the formation of the less stable dinuclear isomer {Ti(CF3COCHCOCH3)2Cl}2(μ-O) (1111).

  3. The Dirac equation in electronic structure calculations: Accurate evaluation of DFT predictions for actinides

    SciTech Connect

    Wills, John M; Mattsson, Ann E

    2012-06-06

    Brooks, Johansson, and Skriver, using the LMTO-ASA method and considerable insight, were able to explain many of the ground state properties of the actinides. In the many years since this work was done, electronic structure calculations of increasing sophistication have been applied to actinide elements and compounds, attempting to quantify the applicability of DFT to actinides and actinide compounds and to try to incorporate other methodologies (i.e. DMFT) into DFT calculations. Through these calculations, the limits of both available density functionals and ad hoc methodologies are starting to become clear. However, it has also become clear that approximations used to incorporate relativity are not adequate to provide rigorous tests of the underlying equations of DFT, not to mention ad hoc additions. In this talk, we describe the result of full-potential LMTO calculations for the elemental actinides, comparing results obtained with a full Dirac basis with those obtained from scalar-relativistic bases, with and without variational spin-orbit. This comparison shows that the scalar relativistic treatment of actinides does not have sufficient accuracy to provide a rigorous test of theory and that variational spin-orbit introduces uncontrolled errors in the results of electronic structure calculations on actinide elements.

  4. Accurate structure prediction of peptide–MHC complexes for identifying highly immunogenic antigens

    SciTech Connect

    Park, Min-Sun; Park, Sung Yong; Miller, Keith R.; Collins, Edward J.; Lee, Ha Youn

    2013-11-01

    Designing an optimal HIV-1 vaccine faces the challenge of identifying antigens that induce a broad immune capacity. One factor to control the breadth of T cell responses is the surface morphology of a peptide–MHC complex. Here, we present an in silico protocol for predicting peptide–MHC structure. A robust signature of a conformational transition was identified during all-atom molecular dynamics, which results in a model with high accuracy. A large test set was used in constructing our protocol and we went another step further using a blind test with a wild-type peptide and two highly immunogenic mutants, which predicted substantial conformational changes in both mutants. The center residues at position five of the analogs were configured to be accessible to solvent, forming a prominent surface, while the residue of the wild-type peptide was to point laterally toward the side of the binding cleft. We then experimentally determined the structures of the blind test set, using high resolution of X-ray crystallography, which verified predicted conformational changes. Our observation strongly supports a positive association of the surface morphology of a peptide–MHC complex to its immunogenicity. Our study offers the prospect of enhancing immunogenicity of vaccines by identifying MHC binding immunogens.

  5. Effect of the cation model on the equilibrium structure of poly-L-glutamate in aqueous sodium chloride solution

    NASA Astrophysics Data System (ADS)

    Marchand, Gabriel; Soetens, Jean-Christophe; Jacquemin, Denis; Bopp, Philippe A.

    2015-12-01

    We demonstrate that different sets of Lennard-Jones parameters proposed for the Na+ ion, in conjunction with the empirical combining rules routinely used in simulation packages, can lead to essentially different equilibrium structures for a deprotonated poly-L-glutamic acid molecule (poly-L-glutamate) dissolved in a 0.3M aqueous NaCl solution. It is, however, difficult to discriminate a priori between these model potentials; when investigating the structure of the Na+-solvation shell in bulk NaCl solution, all parameter sets lead to radial distribution functions and solvation numbers in broad agreement with the available experimental data. We do not find any such dependency of the equilibrium structure on the parameters associated with the Cl- ion. This work does not aim at recommending a particular set of parameters for any particular purpose. Instead, it stresses the model dependence of simulation results for complex systems such as biomolecules in solution and thus the difficulties if simulations are to be used for unbiased predictions, or to discriminate between contradictory experiments. However, this opens the possibility of validating a model specifically in view of analyzing experimental data believed to be reliable.

  6. Effect of the cation model on the equilibrium structure of poly-L-glutamate in aqueous sodium chloride solution.

    PubMed

    Marchand, Gabriel; Soetens, Jean-Christophe; Jacquemin, Denis; Bopp, Philippe A

    2015-12-14

    We demonstrate that different sets of Lennard-Jones parameters proposed for the Na(+) ion, in conjunction with the empirical combining rules routinely used in simulation packages, can lead to essentially different equilibrium structures for a deprotonated poly-L-glutamic acid molecule (poly-L-glutamate) dissolved in a 0.3M aqueous NaCl solution. It is, however, difficult to discriminate a priori between these model potentials; when investigating the structure of the Na(+)-solvation shell in bulk NaCl solution, all parameter sets lead to radial distribution functions and solvation numbers in broad agreement with the available experimental data. We do not find any such dependency of the equilibrium structure on the parameters associated with the Cl(-) ion. This work does not aim at recommending a particular set of parameters for any particular purpose. Instead, it stresses the model dependence of simulation results for complex systems such as biomolecules in solution and thus the difficulties if simulations are to be used for unbiased predictions, or to discriminate between contradictory experiments. However, this opens the possibility of validating a model specifically in view of analyzing experimental data believed to be reliable. PMID:26671388

  7. Accurate structural study of langasite-family Ca3TaGa3Si2O14 crystal

    NASA Astrophysics Data System (ADS)

    Dudka, A. P.

    2016-03-01

    An accurate X-ray diffraction study of Ca3TaGa3Si2O14 single crystal has been performed using two datasets obtained on a diffractometer equipped with a CCD area detector ( a = 8.1056(2) Å, c = 4.9800(1) Å, sp. gr. P321, Z = 1, R/ wR = 0.486/0.488%). A model structure is determined which is characterized by a high degree of reproducibility of structural parameters. Each site in Ca3TaGa3Si2O14 is occupied by atoms of only one type. Nevertheless, its structural feature is asymmetric disordering of sites of Ca, Ta, Ga, and two out of three oxygen atoms occupying special and general sites. A transition of some part of Ca atoms (~3%) from 3 e sites on the twofold symmetry axis to general 6 g sites is revealed.

  8. A FIB-nanotomography method for accurate 3D reconstruction of open nanoporous structures.

    PubMed

    Mangipudi, K R; Radisch, V; Holzer, L; Volkert, C A

    2016-04-01

    We present an automated focused ion beam nanotomography method for nanoporous microstructures with open porosity, and apply it to reconstruct nanoporous gold (np-Au) structures with ligament sizes on the order of a few tens of nanometers. This method uses serial sectioning of a well-defined wedge-shaped geometry to determine the thickness of individual slices from the changes in the sample width in successive cross-sectional images. The pore space of a selected region of the np-Au is infiltrated with ion-beam-deposited Pt composite before serial sectioning. The cross-sectional images are binarized and stacked according to the individual slice thicknesses, and then processed using standard reconstruction methods. For the image conditions and sample geometry used here, we are able to determine the thickness of individual slices with an accuracy much smaller than a pixel. The accuracy of the new method based on actual slice thickness is assessed by comparing it with (i) a reconstruction using the same cross-sectional images but assuming a constant slice thickness, and (ii) a reconstruction using traditional FIB-tomography method employing constant slice thickness. The morphology and topology of the structures are characterized using ligament and pore size distributions, interface shape distribution functions, interface normal distributions, and genus. The results suggest that the morphology and topology of the final reconstructions are significantly influenced when a constant slice thickness is assumed. The study reveals grain-to-grain variations in the morphology and topology of np-Au. PMID:26906523

  9. A molecular dynamics computer simulation study of room-temperature ionic liquids. I. Equilibrium solvation structure and free energetics

    NASA Astrophysics Data System (ADS)

    Shim, Y.; Choi, M. Y.; Kim, Hyung J.

    2005-01-01

    Solvation in 1-ethyl-3-methylmidazolium chloride and in 1-ethyl-3-methylimidazolium hexafluorophosphate near equilibrium is investigated via molecular dynamics computer simulations with diatomic and benzenelike molecules employed as probe solutes. It is found that electrostriction plays an important role in both solvation structure and free energetics. The angular and radial distributions of cations and anions become more structured and their densities near the solute become enhanced as the solute charge separation grows. Due to the enhancement in structural rigidity induced by electrostriction, the force constant associated with solvent configuration fluctuations relevant to charge shift and transfer processes is also found to increase. The effective polarity and reorganization free energies of these ionic liquids are analyzed and compared with those of highly polar acetonitrile. Their screening behavior of electric charges is also investigated.

  10. Structuring energy supply and demand networks in a general equilibrium model to simulate global warming control strategies

    SciTech Connect

    Hamilton, S.; Veselka, T.D.; Cirillo, R.R.

    1991-01-01

    Global warming control strategies which mandate stringent caps on emissions of greenhouse forcing gases can substantially alter a country's demand, production, and imports of energy products. Although there is a large degree of uncertainty when attempting to estimate the potential impact of these strategies, insights into the problem can be acquired through computer model simulations. This paper presents one method of structuring a general equilibrium model, the ENergy and Power Evaluation Program/Global Climate Change (ENPEP/GCC), to simulate changes in a country's energy supply and demand balance in response to global warming control strategies. The equilibrium model presented in this study is based on the principle of decomposition, whereby a large complex problem is divided into a number of smaller submodules. Submodules simulate energy activities and conversion processes such as electricity production. These submodules are linked together to form an energy supply and demand network. Linkages identify energy and fuel flows among various activities. Since global warming control strategies can have wide reaching effects, a complex network was constructed. The network represents all energy production, conversion, transportation, distribution, and utilization activities. The structure of the network depicts interdependencies within and across economic sectors and was constructed such that energy prices and demand responses can be simulated. Global warming control alternatives represented in the network include: (1) conservation measures through increased efficiency; and (2) substitution of fuels that have high greenhouse gas emission rates with fuels that have lower emission rates. 6 refs., 4 figs., 4 tabs.

  11. Voronoi-cell finite difference method for accurate electronic structure calculation of polyatomic molecules on unstructured grids

    SciTech Connect

    Son, Sang-Kil

    2011-03-01

    We introduce a new numerical grid-based method on unstructured grids in the three-dimensional real-space to investigate the electronic structure of polyatomic molecules. The Voronoi-cell finite difference (VFD) method realizes a discrete Laplacian operator based on Voronoi cells and their natural neighbors, featuring high adaptivity and simplicity. To resolve multicenter Coulomb singularity in all-electron calculations of polyatomic molecules, this method utilizes highly adaptive molecular grids which consist of spherical atomic grids. It provides accurate and efficient solutions for the Schroedinger equation and the Poisson equation with the all-electron Coulomb potentials regardless of the coordinate system and the molecular symmetry. For numerical examples, we assess accuracy of the VFD method for electronic structures of one-electron polyatomic systems, and apply the method to the density-functional theory for many-electron polyatomic molecules.

  12. Structure of the flux lines lattice in NbSe2 : Equilibrium state and influence of the magnetic history

    NASA Astrophysics Data System (ADS)

    Pautrat, A.; Aburas, M.; Simon, Ch.; Mathieu, P.; Brûlet, A.; Dewhurst, C. D.; Bhattacharya, S.; Higgins, M. J.

    2009-05-01

    We have performed small-angle neutron scattering of the flux line lattice (FLL) in a Fe-doped NbSe2 sample which presents a large peak effect in the critical current. The scattered intensity and the width of the Bragg peaks of the equilibrium FLL indicate an ordered structure in the peak effect zone. The history dependence in the FLL structure has been studied using field-cooled and zero-field-cooled procedures, and each state shows the same intensity of Bragg scattering and good orientational order. These results strongly suggest that the peak effect is unrelated to a bulk-disordering transition and confirm the role of a heterogeneous distribution of screening current.

  13. Solution structure of a modified 2′,5′-linked RNA hairpin involved in an equilibrium with duplex

    PubMed Central

    Plevnik, Miha; Gdaniec, Zofia; Plavec, Janez

    2005-01-01

    The isomerization of phosphodiester functionality of nucleic acids from 3′,5′- to a less common 2′,5′-linkage influences the complex interplay of stereoelectronic effects that drive pseudorotational equilibrium of sugar rings and thus affect the conformational propensities for compact or more extended structures. The present study highlights the subtle balance of non-covalent forces at play in structural equilibrium of 2′,5′-linked RNA analogue, 3′-O-(2-methoxyethyl) substituted dodecamer *CG*CGAA*U*U*CG*CG, 3′-MOE-2′,5′-RNA, where all cytosines and uracils are methylated at C5. The NMR and UV spectroscopic studies have shown that 3′-MOE-2′,5′-RNA adopts both hairpin and duplex secondary structures, which are involved in a dynamic exchange that is slow on the NMR timescale and exhibits strand and salt concentration as well as pH dependence. Unusual effect of pH over a narrow physiological range is observed for imino proton resonances with exchange broadening observed at lower pH and relatively sharp lines observed at higher pH. The solution structure of 3′-MOE-2′,5′-RNA hairpin displays a unique and well-defined loop, which is stabilized by Watson–Crick A5·*U8 base pair and by n → π* stacking interactions of O4′ lone-pair electrons of A6 and *U8 with aromatic rings of A5 and *U7, respectively. In contrast, the stem region of 3′-MOE-2′,5′-RNA hairpin is more flexible. Our data highlight the important feature of backbone modifications that can have pronounced effects on interstrand association of nucleic acids. PMID:15788747

  14. Partition Equilibrium

    NASA Astrophysics Data System (ADS)

    Feldman, Michal; Tennenholtz, Moshe

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

  15. Using equilibrium isotope effects to detect intramolecular OH/OH hydrogen bonds: structural and solvent effects.

    PubMed

    Vasquez, Thomas E; Bergset, Jon M; Fierman, Matthew B; Nelson, Alshakim; Roth, Joshua; Khan, Saeed I; O'Leary, Daniel J

    2002-03-27

    A comparative (1)H NMR study of partially deuterated 1,3- and 1,4-diols has demonstrated that intramolecular hydrogen bonds of different geometry can give rise to equilibrium isotope shifts of opposite sign in hydrogen-bond-accepting solvents such as DMSO-d(6), acetone-d(6), and THF-d(8). The sign inversion is interpreted in terms of the ability of solvent molecules to form competitive intermolecular hydrogen bonds with the diol and in terms of the limiting chemical shifts for the interior and exterior hydroxyl groups. Deuterium is shown to prefer the intermolecular solvent hydrogen bond by 10.9 +/- 0.5 cal/mol for 1,4-diol 3 dissolved in DMSO-d(6) at room temperature. Pyridine-d(5) is shown to be capable of amplifying positive (downfield) isotope shifts measured in DMSO-d(6), in some cases by as much as a factor of 3. Its use is demonstrated for the assignment of the syn or anti relative configuration of 2,4-pentanediol and for the amplification of isotope shifts used to detect intramolecular hydrogen bonds in alpha- and beta-cyclodextrin. Studies in apolar solvents such as CD(2)Cl(2) and benzene-d(6) reveal that the isotope shift is negative (upfield) for all hydrogen bond geometries studied. Larger isotope shifts are measured in benzene-d(6), and a rationale for this amplification is presented. The use of apolar solvents is particularly useful for assigning the syn or anti configuration of 2,4-pentanediol. PMID:11902884

  16. Field induced changes in the ring/chain equilibrium of hydrogen bonded structures: 5-methyl-3-heptanol.

    PubMed

    Young-Gonzales, Amanda R; Richert, Ranko

    2016-08-21

    Using non-linear dielectric techniques, we have measured the dynamics of 5-methyl-3-heptanol at a temperature at which the Kirkwood correlation factor gK indicates the coexistence of ring- and chain-like hydrogen-bonded structures. Steady state permittivity spectra recorded in the presence of a high dc bias electric field (17 MV/m) reveal that both the amplitude and the time constant are increased by about 10% relative to the low field limit. This change is attributed to the field driven conversion from ring-like to the more polar chain-like structures, and a direct observation of its time dependence shows that the ring/chain structural transition occurs on a time scale that closely matches that of the dielectric Debye peak. This lends strong support to the picture that places fluctuations of the end-to-end vector of hydrogen bonded structures at the origin of the Debye process, equivalent to fluctuations of the net dipole moment or gK. Recognizing that changes in the ring/chain equilibrium constant also impact the spectral separation between Debye and α-process may explain the difference in their temperature dependence whenever gK is sensitive to temperature, i.e., when the structural motifs of hydrogen bonding change considerably. PMID:27544115

  17. Extraction of accurate structure-factor amplitudes from Laue data: wavelength normalization with wiggler and undulator X-ray sources.

    PubMed

    Srajer, V; Crosson, S; Schmidt, M; Key, J; Schotte, F; Anderson, S; Perman, B; Ren, Z; Teng, T Y; Bourgeois, D; Wulff, M; Moffat, K

    2000-07-01

    Wavelength normalization is an essential part of processing of Laue X-ray diffraction data and is critically important for deriving accurate structure-factor amplitudes. The results of wavelength normalization for Laue data obtained in nanosecond time-resolved experiments at the ID09 beamline at the European Synchrotron Radiation Facility, Grenoble, France, are presented. Several wiggler and undulator insertion devices with complex spectra were used. The results show that even in the most challenging cases, such as wiggler/undulator tandems or single-line undulators, accurate wavelength normalization does not require unusually redundant Laue data and can be accomplished using typical Laue data sets. Single-line undulator spectra derived from Laue data compare well with the measured incident X-ray spectra. Successful wavelength normalization of the undulator data was also confirmed by the observed signal in nanosecond time-resolved experiments. Single-line undulators, which are attractive for time-resolved experiments due to their high peak intensity and low polychromatic background, are compared with wigglers, based on data obtained on the same crystal. PMID:16609201

  18. Semiclassical shell-structure moment of inertia for equilibrium rotation of a simple Fermi system

    SciTech Connect

    Magner, A. G.; Sitdikov, A. S. Khamzin, A. A.; Bartel, J.

    2010-08-15

    Semiclassical shell-structure components of the collectivemoment of inertia are derived within the mean-field cranking model in the adiabatic approximation in terms of the free-energy shell corrections through those of a rigid body for the statistically equilibriumrotation of a Fermi system at finite temperature by using the nonperturbative extended Gutzwiller periodic-orbit theory. Their analytical structure in terms of the equatorial and 3-dimensional periodic orbits for the axially symmetric harmonic oscillator potential is in perfect agreement with the quantum results for different critical bifurcation deformations and different temperatures.

  19. A subsurface structure change associated with the eruptive activity at Sakurajima Volcano, Japan, inferred from an accurately controlled source

    NASA Astrophysics Data System (ADS)

    Maeda, Yuta; Yamaoka, Koshun; Miyamachi, Hiroki; Watanabe, Toshiki; Kunitomo, Takahiro; Ikuta, Ryoya; Yakiwara, Hiroshi; Iguchi, Masato

    2015-07-01

    Temporal variations of Green functions associated with the eruptive activity at Sakurajima Volcano, Japan, were estimated using an accurately controlled routinely operated signal system (ACROSS). We deconvolved 400 s waveforms of the ACROSS signal at nearby stations by a known source time function and stacked the results based on the time relative to individual eruptions and the eruption intervals; the quantities obtained by this procedure are Green functions corresponding to various stages of the eruptive activity. We found an energy decrease in the later phase of the Green functions in active eruptive periods. This energy decrease, localized in the 2-6 s window of the Green functions, is difficult to explain by contamination from volcanic earthquakes and tremors. The decrease could be more reasonably attributed to a subsurface structure change caused by the volcanic activity.

  20. Helical equilibrium

    SciTech Connect

    Yoshikawa, S.

    1981-08-01

    A straight, helical plasma equilibrium equation is solved numerically for a plasma with a helical magnetic axis. As is expected, by a suitable choice of the plasma boundary, the vacuum configuration is made line ..integral.. dl/B stable. As the plasma pressure increases, the line ..integral.. dl/B criterion will improve (again as expected). There is apparently no limit on the plasma ..beta.. from the equilibrium consideration. Thus helical-axis stellarator ..beta.. will presumably be limited by MHD stability ..beta.., and not by equilibrium ..beta...

  1. From Alfvén waves to kinetic Alfvén waves in an inhomogeneous equilibrium structure

    NASA Astrophysics Data System (ADS)

    Pucci, F.; Vásconez, C. L.; Pezzi, O.; Servidio, S.; Valentini, F.; Matthaeus, W. H.; Malara, F.

    2016-02-01

    Kinetic Alfvén waves are believed to primary form fluctuations in a hydromagnetic turbulence at scales of the order of the ion inertial length. We study a model where an initial Alfvén wave propagates inside an equilibrium structure which is inhomogeneous in the direction perpendicular to the equilibrium magnetic field. In a previous paper this situation has been considered in a particular configuration where the initial wave vector is parallel to the magnetic field and the wave is polarized perpendicular to the inhomogeneity direction. Here we consider other configurations, with a different polarization and possible initial oblique propagation. We employ numerical simulations, using both a Hall-magnetohydrodynamics and a Hybrid Vlasov-Maxwell model. Results show that in all the considered cases the time evolution leads to the formation of kinetic Alfvén waves within the inhomogeneity regions, which are identified by a comparison with analytical linear theory results. Then, in this context the formation of kinetic Alfvén waves seems to be a general phenomenon which could be also extended to more complex situations, like turbulence. Kinetic simulations show that kinetic Alfvén waves modify the ion distribution function, generating temperature anisotropy of both parallel and perpendicular to the local magnetic field as well as particle beams aligned along the local magnetic field. These results could be relevant both in the solar corona and in large-scale structures of the solar wind, where Alfvénic fluctuations are present along with large-scale inhomogeneities.

  2. From Alfvén waves to kinetic Alfvén waves in an inhomogeneous equilibrium structure

    NASA Astrophysics Data System (ADS)

    Pucci, Francesco; Vasconez, Christian L.; Pezzi, Oreste; Servidio, Sergio; Valentini, Francesco; Matthaeus, William H.; Malara, Francesco

    2016-04-01

    Kinetic Alfvén waves are believed to primary form fluctuations in a hydromagnetic turbulence at scales of the order of the ion inertial length. We study a model where an initial Alfvén wave propagates inside an equilibrium structure which is inhomogeneous in the direction perpendicular to the equilibrium magnetic field. In a previous paper [1] this situation has been considered in a particular configuration where the initial wavevector is parallel to the magnetic field and the wave is polarized perpendicular to the inhomogeneity direction. Here, we consider other configurations, with a different polarization and possible initial oblique propagation. We employ numerical simulations, using both a Hall-Magnetohydrodynamics and a Hybrid Vlasov-Maxwell model. Results show that in all the considered cases the time evolution leads to the formation of Kinetic Alfvén waves within the inhomogeneity regions, which are identified by a comparison with analytical linear theory results. Then, in this context the formation of Kinetic Alfvén waves seems to be a general phenomenon which could be also extended to more complex situations, like turbulence. Kinetic simulations show that Kinetic Alfvén waves modify the ion distribution function, generating temperature anisotropy of both parallel and perpendicular to the local magnetic field as well as particle beams aligned along the local magnetic field. These results could be relevant both in the solar corona and in large-scale structures of the solar wind, where Alfvénic fluctuations are present along with large-scale inhomogeneities. [1] C. Vasconez et al., Kinetic Alfvén waves generation by large-scale phase-mixing, The Astrophysical Journal 815.1, 7 (2015).

  3. Equilibrium and metastable structures of Nickel/Silicon Dioxide/Silicon and Nickel/Silicon interfaces

    NASA Astrophysics Data System (ADS)

    Thron, Andrew Malachi

    Solid-state dewetting occurs in thin continuous metal films when capillary instabilities drive the nucleation and growth of holes. Dewetting of thick (>100nm) metals films has extensively been studied and is well understood, however the dewetting of ultra-thin films is not well understood. Recent studies have shown that Ni films less than 5nm thick do not dewet at the same temperatures as thicker Ni films, however it is not well understood why. A fundamental understanding of the dewetting behavior of ultra-thin metal films has key relevance in applications such as catalysis and complimentary metal-oxide semiconductor (CMOS) transistors. Self-assembly of metal islands can be created through the solid-state dewetting of thin metal films on a support substrate. These metal islands are used as catalyst to grow arrays of nanotubes and nanowires. Solid-state dewetting degrades the functional properties of NiSi films, which are used as contacts to the source and drain in CMOS transistors. Once the transistors are processed above 650°C the NiSi film will agglomerate, degrading the contacts to the source and drain. Alloying NiSi with refractory metals increases the dewetting temperature to over 900°C. The effect of Pt on the NiSi/Si interface structure and how the interface structure changes the functional properties of the interface is not understood. In this thesis Transmission Electron Microscopy (TEM) and aberration corrected Scanning TEM (STEM) are used to study the interface structure of ultra-thin films. In-Situ annealing, inside the TEM is used to observe morphological changes in ultra-thin Ni films sputtered onto SiO2/Si substrates. A new Aduro Double tilt heating holder, made by Protochips Inc., is implemented for studying solid-state dewetting, in situ. The Aduro heating holder is based off a Microelectromechanical systems (MEMS) design, where ultra-fast and controlled heating rates are obtained by resistively heating a SiC membrane with a low thermal mass

  4. Learning the Structure of High-Dimensional Manifolds with Self-Organizing Maps for Accurate Information Extraction

    NASA Astrophysics Data System (ADS)

    Zhang, Lili

    This work aims to improve the capability of accurate information extraction from high-dimensional data, with a specific neural learning paradigm, the Self-Organizing Map (SOM). The SOM is an unsupervised learning algorithm that can faithfully sense the manifold structure and support supervised learning of relevant information from the data. Yet open problems regarding SOM learning exist. We focus on the following two issues. (1) Evaluation of topology preservation. Topology preservation is essential for SOMs in faithful representation of manifold structure. However, in reality, topology violations are not unusual, especially when the data have complicated structure. Measures capable of accurately quantifying and informatively expressing topology violations are lacking. One contribution of this work is a new measure, the Weighted Differential Topographic Function (WDTF), which differentiates an existing measure, the Topographic Function (TF), and incorporates detailed data distribution as an importance weighting of violations to distinguish severe violations from insignificant ones. Another contribution is an interactive visual tool, TopoView, which facilitates the visual inspection of violations on the SOM lattice. We show the effectiveness of the combined use of the WDTF and TopoView through a simple two-dimensional data set and two hyperspectral images. (2) Learning multiple latent variables from high-dimensional data. We use an existing two-layer SOM-hybrid supervised architecture, which captures the manifold structure in its SOM hidden layer, and then, uses its output layer to perform the supervised learning of latent variables. In the customary way, the output layer only uses the strongest output of the SOM neurons. This severely limits the learning capability. We allow multiple, k, strongest responses of the SOM neurons for the supervised learning. Moreover, the fact that different latent variables can be best learned with different values of k motivates a

  5. Simulation Study of the Non-Equilibrium Structure Formation In Magnetorheological Fluids.

    NASA Astrophysics Data System (ADS)

    Mohebi, M.; Jamasbi, N.; Liu, Jing

    1998-03-01

    A molecular dynamics model is presented to understand the structural formation of MR fluids which includes viscous drag of the surrounding liquid and the thermal motion of the particles. The simulation results indicate that the complexity of the lateral pattern as viewed in the direction of the applied field increases with the rate of application of the external magnetic field. We have also found that the maximum range for attractive interaction (escape distance) for two initially straight chains increases with temperature. Furthermore, we used our model to understand the role of volume fraction and cell thickness in the structural transition between column and bent wall formations. These results are relevant to understand the mechanisms and conditions for the formation of labyrinthine and columnar patterns experimentally observed in MR fluids.

  6. Effect of substituents and structural modification on conformational equilibrium in bis-quinolizidine system

    NASA Astrophysics Data System (ADS)

    Wysocka, Waleria; Brukwicki, Tadeusz; Włodarczak, Jacek

    2012-06-01

    On the basis of literature interpretation of 13C NMR and 1H NMR spectra of bis-quinolizidine alkaloids, the values of free enthalpy ΔG of conformational equilibria of those compounds were calculated. The results were analysed together with the X-ray and DFT data to discuss the effects of different substituents attached to the sparteine system in various positions as well as the effects of structural modifications on conformational equilibria. The measure of the effect was expressed by ΔΔG value, defined as the difference in ΔG of the compound under consideration and its parent compound without a given substituent.

  7. Femtosecond structural transformation of phase-change materials far from equilibrium monitored by coherent phonons

    PubMed Central

    Hase, Muneaki; Fons, Paul; Mitrofanov, Kirill; Kolobov, Alexander V.; Tominaga, Junji

    2015-01-01

    Multicomponent chalcogenides, such as quasi-binary GeTe–Sb2Te3 alloys, are widely used in optical data storage media in the form of rewritable optical discs. Ge2Sb2Te5 (GST) in particular has proven to be one of the best-performing materials, whose reliability allows more than 106 write–erase cycles. Despite these industrial applications, the fundamental kinetics of rapid phase change in GST remain controversial, and active debate continues over the ultimate speed limit. Here we explore ultrafast structural transformation in a photoexcited GST superlattice, where GeTe and Sb2Te3 are spatially separated, using coherent phonon spectroscopy with pump–pump–probe sequences. By analysing the coherent phonon spectra in different time regions, complex structural dynamics upon excitation are observed in the GST superlattice (but not in GST alloys), which can be described as the mixing of Ge sites from two different coordination environments. Our results suggest the possible applicability of GST superlattices for ultrafast switching devices. PMID:26403198

  8. An effective continuum approach for modeling non-equilibrium structural evolution of protein nanofiber networks.

    PubMed

    Cheng, Liang; Englander, Ongi; Paravastu, Anant; Oates, William S

    2011-08-01

    We quantify the formation and evolution of protein nanofibers using a new phase field modeling framework and compare the results to transmission electron microscopy measurements (TEM) and time-dependent growth measurements given in the literature. The modeling framework employs a set of effective continuum equations combined with underlying nanoscale forces and chemical potential relations governing protein nanofiber formation in solution. Calculations based on the theoretical framework are implemented numerically using a nonlinear finite element phase field modeling approach that couples homogenized protein molecular structure via a vector order parameter with chemical potential relations that describe interactions between the nanofibers and the surrounding solution. Homogenized, anisotropic molecular and chemical flux relations are found to be critical in obtaining nanofiber growth from seed particles or a random monomer bath. In addition, the model predicts both sigmoidal and first-order growth kinetics for protein nanofibers for unseeded and seeded models, respectively. These simulations include quantitative predictions on time scales of typical protein self-assembly behavior which qualitatively match TEM measurements of the RADA16-I protein and growth rate measurements for amyloid nanofibers from the literature. For comparisons with experiments, the numerical model performs multiple nanofiber protein evolution simulations with a characteristic length scale of ∼2.4 nm and characteristic time scale of ∼9.1 h. These results provide a new modeling tool that couples underlying monomer structure with self-assembling nanofiber behavior that is compatible with various external loadings and chemical environments. PMID:21823733

  9. An effective continuum approach for modeling non-equilibrium structural evolution of protein nanofiber networks

    NASA Astrophysics Data System (ADS)

    Cheng, Liang; Englander, Ongi; Paravastu, Anant; Oates, William S.

    2011-08-01

    We quantify the formation and evolution of protein nanofibers using a new phase field modeling framework and compare the results to transmission electron microscopy measurements (TEM) and time-dependent growth measurements given in the literature. The modeling framework employs a set of effective continuum equations combined with underlying nanoscale forces and chemical potential relations governing protein nanofiber formation in solution. Calculations based on the theoretical framework are implemented numerically using a nonlinear finite element phase field modeling approach that couples homogenized protein molecular structure via a vector order parameter with chemical potential relations that describe interactions between the nanofibers and the surrounding solution. Homogenized, anisotropic molecular and chemical flux relations are found to be critical in obtaining nanofiber growth from seed particles or a random monomer bath. In addition, the model predicts both sigmoidal and first-order growth kinetics for protein nanofibers for unseeded and seeded models, respectively. These simulations include quantitative predictions on time scales of typical protein self-assembly behavior which qualitatively match TEM measurements of the RADA16-I protein and growth rate measurements for amyloid nanofibers from the literature. For comparisons with experiments, the numerical model performs multiple nanofiber protein evolution simulations with a characteristic length scale of ˜2.4 nm and characteristic time scale of ˜9.1 h. These results provide a new modeling tool that couples underlying monomer structure with self-assembling nanofiber behavior that is compatible with various external loadings and chemical environments.

  10. Femtosecond structural transformation of phase-change materials far from equilibrium monitored by coherent phonons.

    PubMed

    Hase, Muneaki; Fons, Paul; Mitrofanov, Kirill; Kolobov, Alexander V; Tominaga, Junji

    2015-01-01

    Multicomponent chalcogenides, such as quasi-binary GeTe-Sb2Te3 alloys, are widely used in optical data storage media in the form of rewritable optical discs. Ge2Sb2Te5 (GST) in particular has proven to be one of the best-performing materials, whose reliability allows more than 10(6) write-erase cycles. Despite these industrial applications, the fundamental kinetics of rapid phase change in GST remain controversial, and active debate continues over the ultimate speed limit. Here we explore ultrafast structural transformation in a photoexcited GST superlattice, where GeTe and Sb2Te3 are spatially separated, using coherent phonon spectroscopy with pump-pump-probe sequences. By analysing the coherent phonon spectra in different time regions, complex structural dynamics upon excitation are observed in the GST superlattice (but not in GST alloys), which can be described as the mixing of Ge sites from two different coordination environments. Our results suggest the possible applicability of GST superlattices for ultrafast switching devices. PMID:26403198

  11. Femtosecond structural transformation of phase-change materials far from equilibrium monitored by coherent phonons

    NASA Astrophysics Data System (ADS)

    Hase, Muneaki; Fons, Paul; Mitrofanov, Kirill; Kolobov, Alexander V.; Tominaga, Junji

    2015-09-01

    Multicomponent chalcogenides, such as quasi-binary GeTe-Sb2Te3 alloys, are widely used in optical data storage media in the form of rewritable optical discs. Ge2Sb2Te5 (GST) in particular has proven to be one of the best-performing materials, whose reliability allows more than 106 write-erase cycles. Despite these industrial applications, the fundamental kinetics of rapid phase change in GST remain controversial, and active debate continues over the ultimate speed limit. Here we explore ultrafast structural transformation in a photoexcited GST superlattice, where GeTe and Sb2Te3 are spatially separated, using coherent phonon spectroscopy with pump-pump-probe sequences. By analysing the coherent phonon spectra in different time regions, complex structural dynamics upon excitation are observed in the GST superlattice (but not in GST alloys), which can be described as the mixing of Ge sites from two different coordination environments. Our results suggest the possible applicability of GST superlattices for ultrafast switching devices.

  12. Quantum chemical calculation of the equilibrium structures of small metal atom clusters

    NASA Technical Reports Server (NTRS)

    Kahn, L. R.

    1981-01-01

    A decomposition of the molecular energy is presented that is motivated by the atom superposition and electron delocalization physical model of chemical binding. The energy appears in physically transparent form consisting of a classical electrostatic interaction, a zero order two electron exchange interaction, a relaxation energy, and the atomic energies. Detailed formulae are derived in zero and first order of approximation. The formulation extends beyond first order to any chosen level of approximation leading, in principle, to the exact energy. The structure of this energy decomposition lends itself to the fullest utilization of the solutions to the atomic sub problems to simplify the calculation of the molecular energy. If nonlinear relaxation effects remain minor, the molecular energy calculation requires at most the calculation of two center, two electron integrals. This scheme thus affords the prospects of substantially reducing the computational effort required for the calculation of molecular energies.

  13. The equilibrium structure of thin magnetic flux tubes. II. [in sun and late stars

    NASA Technical Reports Server (NTRS)

    Kalkofen, W.; Rosner, R.; Ferrari, A.; Massaglia, S.

    1986-01-01

    The thermal structure of the medium inside thin, vertical magnetic flux tubes embedded in a given external atmosphere is investigated, assuming cylindrical symmetry and a depth-independent plasma beta. The variation with tube radius of the temperature on the tube axis is computed and the temperature on the tube wall is estimated. The temperature variation across the flux tube is found to be due to the depth variation of the intensity and to the density stratification of the atmosphere. Since the temperature difference between the axis and the wall is small in thin flux tubes (of the order of 10 percent), the horizontal temperature gradient may often be neglected and the temperature in a tube of given radius may be described by a single function of depth. Thus, a more detailed numerical treatment of the radiative transfer within thin flux tubes can be substantially simplified by neglecting horizontal temperature differences within the flux tube proper.

  14. THE DIAGNOSTIC O VI ABSORPTION LINE IN DIFFUSE PLASMAS: COMPARISON OF NON-EQUILIBRIUM IONIZATION STRUCTURE SIMULATIONS TO FUSE DATA

    SciTech Connect

    De Avillez, Miguel A.; Breitschwerdt, Dieter

    2012-12-20

    The nature of the interstellar O VI in the Galactic disk is studied by means of a multi-fluid hydrodynamical approximation, tracing the detailed time-dependent evolution of the ionization structure of the plasma. Our focus is to explore the signature of any non-equilibrium ionization condition present in the interstellar medium using the diagnostic O VI ion. A detailed comparison between the simulations and FUSE data is carried out by taking lines of sight (LOS) measurements through the simulated Galactic disk, covering an extent of 4 kpc from different vantage points. The simulation results bear a striking resemblance with the observations: (1) the N(O VI) distribution with distance and angle fall within the minimum and maximum values of the FUSE data; (2) the column density dispersion with distance is constant for all the LOS, showing a mild decrease at large distances; (3) O VI has a clumpy distribution along the LOS; and (4) the time-averaged midplane density for distances >400 pc has a value of (1.3-1.4) Multiplication-Sign 10{sup -8} cm{sup -3}. The highest concentration of O VI by mass occurs in the thermally stable (10{sup 3.9} K < T {<=} 10{sup 4.2} K; 20%) and unstable (10{sup 4.2} K < T < 10{sup 5} K; 50%) regimes, both well below its peak temperature in collisional ionization equilibrium, with the corresponding volume filling factors oscillating with time between 8%-20% and 4%-5%, respectively. These results may also be relevant for intergalactic metal absorption systems at high redshifts.

  15. One-photon mass-analyzed threshold ionization (MATI) spectroscopy of pyridine: Determination of accurate ionization energy and cationic structure

    SciTech Connect

    Lee, Yu Ran; Kang, Do Won; Kim, Hong Lae E-mail: hlkim@kangwon.ac.kr; Kwon, Chan Ho E-mail: hlkim@kangwon.ac.kr

    2014-11-07

    Ionization energies and cationic structures of pyridine were intensively investigated utilizing one-photon mass-analyzed threshold ionization (MATI) spectroscopy with vacuum ultraviolet radiation generated by four-wave difference frequency mixing in Kr. The present one-photon high-resolution MATI spectrum of pyridine demonstrated a much finer and richer vibrational structure than that of the previously reported two-photon MATI spectrum. From the MATI spectrum and photoionization efficiency curve, the accurate ionization energy of the ionic ground state of pyridine was confidently determined to be 73 570 ± 6 cm{sup −1} (9.1215 ± 0.0007 eV). The observed spectrum was almost completely assigned by utilizing Franck-Condon factors and vibrational frequencies calculated through adjustments of the geometrical parameters of cationic pyridine at the B3LYP/cc-pVTZ level. A unique feature unveiled through rigorous analysis was the prominent progression of the 10 vibrational mode, which corresponds to in-plane ring bending, and the combination of other totally symmetric fundamentals with the ring bending overtones, which contribute to the geometrical change upon ionization. Notably, the remaining peaks originate from the upper electronic state ({sup 2}A{sub 2}), as predicted by high-resolution photoelectron spectroscopy studies and symmetry-adapted cluster configuration interaction calculations. Based on the quantitatively good agreement between the experimental and calculated results, it was concluded that upon ionization the pyridine cation in the ground electronic state should have a planar structure of C{sub 2v} symmetry through the C-N axis.

  16. Towards Efficient and Accurate Description of Many-Electron Problems: Developments of Static and Time-Dependent Electronic Structure Methods

    NASA Astrophysics Data System (ADS)

    Ding, Feizhi

    Understanding electronic behavior in molecular and nano-scale systems is fundamental to the development and design of novel technologies and materials for application in a variety of scientific contexts from fundamental research to energy conversion. This dissertation aims to provide insights into this goal by developing novel methods and applications of first-principle electronic structure theory. Specifically, we will present new methods and applications of excited state multi-electron dynamics based on the real-time (RT) time-dependent Hartree-Fock (TDHF) and time-dependent density functional theory (TDDFT) formalism, and new development of the multi-configuration self-consist field theory (MCSCF) for modeling ground-state electronic structure. The RT-TDHF/TDDFT based developments and applications can be categorized into three broad and coherently integrated research areas: (1) modeling of the interaction between moleculars and external electromagnetic perturbations. In this part we will first prove both analytically and numerically the gauge invariance of the TDHF/TDDFT formalisms, then we will present a novel, efficient method for calculating molecular nonlinear optical properties, and last we will study quantum coherent plasmon in metal namowires using RT-TDDFT; (2) modeling of excited-state charge transfer in molecules. In this part, we will investigate the mechanisms of bridge-mediated electron transfer, and then we will introduce a newly developed non-equilibrium quantum/continuum embedding method for studying charge transfer dynamics in solution; (3) developments of first-principles spin-dependent many-electron dynamics. In this part, we will present an ab initio non-relativistic spin dynamics method based on the two-component generalized Hartree-Fock approach, and then we will generalized it to the two-component TDDFT framework and combine it with the Ehrenfest molecular dynamics approach for modeling the interaction between electron spins and nuclear

  17. Molecular polymorphism: microwave spectra, equilibrium structures, and an astronomical investigation of the HNCS isomeric family.

    PubMed

    McGuire, Brett A; Martin-Drumel, Marie-Aline; Thorwirth, Sven; Brünken, Sandra; Lattanzi, Valerio; Neill, Justin L; Spezzano, Silvia; Yu, Zhenhong; Zaleski, Daniel P; Remijan, Anthony J; Pate, Brooks H; McCarthy, Michael C

    2016-08-10

    The rotational spectra of thioisocyanic acid (HNCS), and its three energetic isomers (HSCN, HCNS, and HSNC) have been observed at high spectral resolution by a combination of chirped-pulse and Fabry-Pérot Fourier-transform microwave spectroscopy between 6 and 40 GHz in a pulsed-jet discharge expansion. Two isomers, thiofulminic acid (HCNS) and isothiofulminic acid (HSNC), calculated here to be 35-37 kcal mol(-1) less stable than the ground state isomer HNCS, have been detected for the first time. Precise rotational, centrifugal distortion, and nitrogen hyperfine coupling constants have been determined for the normal and rare isotopic species of both molecules; all are in good agreement with theoretical predictions obtained at the coupled cluster level of theory. On the basis of isotopic spectroscopy, precise molecular structures have been derived for all four isomers by correcting experimental rotational constants for the effects of rotation-vibration interaction calculated theoretically. Formation and isomerization pathways have also been investigated; the high abundance of HSCN relative to ground state HNCS, and the detection of strong lines of SH using CH3CN and H2S, suggest that HSCN is preferentially produced by the radical-radical reaction HS + CN. A radio astronomical search for HSCN and its isomers has been undertaken toward the high-mass star-forming region Sgr B2(N) in the Galactic Center with the 100 m Green Bank Telescope. While we find clear evidence for HSCN, only a tentative detection of HNCS is proposed, and there is no indication of HCNS or HSNC at the same rms noise level. HSCN, and tentatively HNCS, displays clear deviations from a single-excitation temperature model, suggesting weak masing may be occurring in some transitions in this source. PMID:27478937

  18. Diagnosis of equilibrium magnetic profiles, current transport, and internal structures in a reversed-field pinch using electron temperature fluctuations

    NASA Astrophysics Data System (ADS)

    Parke, Eli

    Due to long fast ion confinement times, neutral beam injection (NBI) on the Madison Symmetric Torus (MST) yields large fast ion populations with substantial density gradients. Novel application of the unique high-rep-rate (>10 kHz) Thomson scattering diagnostic on MST has enabled characterization of a newly observed beam-driven instability, and detailed measurement of equilibrium changes caused by the fast ion population. While previous work has focused on high-frequency energetic particle modes (EPMs), recent observations indicate that fast ions drive a bursting instability near the plasma rotation frequency under appropriate conditions. The mode chirps strongly, with a frequency of approximately 7 kHz in the plasma reference frame at peak amplitude. Bursts are correlated with EPM activity and core neutral particle analyzer signals drop by 30% during a burst, suggesting that this mode participates in avalanches of the higher frequency EPMs and drives enhanced fast ion transport. Electron temperature fluctuations correlated with this low-frequency mode exhibit a core-peaked structure with a sensitive dependence on the safety factor q. Although this mode has not yet been positively identified, its characteristics and internal structure are suggestive of an internal kink (fishbone) or beta-induced Alfven eigenmode. In addition to driving EPMs, the large fast ion population also modifies the current profile. An increase in on-axis current density driven by NBI is offset by a reduction in the mid-radius, leading to net-zero current drive. This results in a slight flattening of the safety factor profile, observed by precise measurement of the rational surface locations of the dominant tearing modes; these are identified from the phase flip in correlated electron temperature fluctuations recorded by Thomson scattering. For the core n = 6 rational surface, an inward shift of 1.1 +/- 0.6 cm is observed, with an estimated reduction in q0 of 5%. This technique provides a

  19. The relativistic equations of stellar structure and evolution. Stars with degenerate neutron cores. 1: Structure of equilibrium models

    NASA Technical Reports Server (NTRS)

    Thorne, K. S.; Zytkow, A. N.

    1976-01-01

    The general relativistic equations of stellar structure and evolution are reformulated in a notation which makes easy contact with Newtonian theory. Also, a general relativistic version of the mixing-length formalism for convection is presented. Finally, it is argued that in previous work on spherical systems general relativity theorists have identified the wrong quantity as "total mass-energy inside radius r."

  20. Equilibrium structure and relative stability of glyceraldehyde conformers: Gas-phase electron diffraction (GED) and quantum-chemical studies

    NASA Astrophysics Data System (ADS)

    Vogt, Natalja; Atavin, Evgenii G.; Rykov, Anatolii N.; Popov, Evgenii V.; Vilkov, Lev V.

    2009-11-01

    For the first time, the five dimensional (5-D) analysis of potential energy surface (PES) from quantum-chemical calculations was carried out to predict reliably the various glyceraldehyde (GLA) conformers. 36 conformers with relative stabilities up to 38 kJ/mol were found in the B3LYP approximation. According to results of MP2/cc-pVQZ calculations, the molecule exists at the experimental temperature of 388 K as a mixture of five conformers in the ratio I:II:III:IV:V = 63:18:4:10:5. Contrary to the theoretical conclusion of Lovas et al., the conformer IV is predicted to be more stable than the conformer III. Our result can explain why the conformer IV could be detected in the microwave (MW) spectroscopic experiment by Lovas et al., whereas the conformer III could not. For the first time, thermal-average and equilibrium structural parameters of GLA (main conformer) have been determined from gas-phase electron diffraction (GED) data. Vibrational corrections to the experimental bond lengths were determined using quadratic and cubic force constants from high-level ab initio calculations (MP2/cc-pVTZ). It was shown that the experimental intensities are sensitive to the contribution of the second conformer (27(15)%). Rotational constants calculated from MP2/cc-pVQZ geometries were found to be in excellent agreement with the experimental rotational constants corrected for anharmonic effects.

  1. Molybdena deposited on titania by equilibrium deposition filtration: structural evolution of oxo-molybdenum(vi) sites with temperature.

    PubMed

    Tsilomelekis, George; Panagiotou, George D; Stathi, Panagiota; Kalampounias, Angelos G; Bourikas, Kyriakos; Kordulis, Christos; Deligiannakis, Yiannis; Boghosian, Soghomon; Lycourghiotis, Alexis

    2016-09-14

    The equilibrium deposition filtration (EDF) method, an advanced catalyst synthesis route that is based on a molecular level approach, can be used for tailoring the oxometallic phase deposited on a porous oxide support. Here, the EDF method is used for synthesizing (MoOx)n/TiO2 catalysts. In situ Raman spectroscopy in the temperature range of 25-450 °C, low temperature (77 K) EPR spectroscopy and DR-UV spectroscopy are used for studying the evolution of the structural configuration of oxo-Mo(VI) species on TiO2 with increasing temperature as well as the influence of the supported (MoOx)n species on the photo-generation of electrons and holes of TiO2. This study concerns (MoOx)n/TiO2 samples in which the surface densities after calcination are 0.3, 2.6 and 3.9 Mo per nm(2), thereby covering a very wide range of submonolayer coverage. The gradual heat treatment of the catalysts results in a transformation of the initially (prior to drying) deposited species and the pertinent species evolution at the nano-level is discussed by means of a number of mechanisms including anchoring, association, cleavage and surface diffusion. PMID:27523593

  2. Millimeter Wave Spectroscopy and Equilibrium Structure Determination of Pyrimidine (m-C_4H_4N_2)

    NASA Astrophysics Data System (ADS)

    Heim, Zachary N.; Amberger, Brent K.; Esselman, Brian J.; Woods, R. Claude; McMahon, Robert J.

    2015-06-01

    Pyrimidine, the meta substituted dinitrogen analog of benzene, has been studied in the mm-wave region from 260 - 360 GHz, expanding on previous studies up to 337 GHz. The spectra of all four of the singly-substituted 13C and 15N isotopologues were observed in natural abundance. Samples of deuterium enriched pyrimidine were synthesized, giving access to several deuterium-substituted isotopologues. The experimental rotational constants have been corrected for vibration-rotation coupling and electron mass. The vibration-rotation corrections were calculated with an anharmonic frequency calculation at the CCSD[T]/ANO1 level using CFOUR. An equilibrium structure determination has been performed using the corrected rotational constants with the xrefit module of CFOUR. Several vibrational satellites of pyrimidine have also been studied. Their rotational constants have been compared to those obtained computationally. Z. Kisiel, L. Pszczolkowski, I. R. Medvedev, M. Winnewisser, F. C. De Lucia, E. Herbst, J. Mol. Spectrosc. 233, 231-243 (2005). G. L. Blackman, R. D. Brown, F. R. Burden, J. Mol. Spectrosc. 35, 444-454 (1970). W. Caminati, D. Damiani, Chem. Phys. Lett. 179, 460-462 (1991).

  3. Non-Newtonian behavior and molecular structure of Cooee bitumen under shear flow: A non-equilibrium molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Lemarchand, Claire A.; Bailey, Nicholas P.; Todd, Billy D.; Daivis, Peter J.; Hansen, Jesper S.

    2015-06-01

    The rheology and molecular structure of a model bitumen (Cooee bitumen) under shear are investigated in the non-Newtonian regime using non-equilibrium molecular dynamics simulations. The shear viscosity, normal stress differences, and pressure of the bitumen mixture are computed at different shear rates and different temperatures. The model bitumen is shown to be a shear-thinning fluid at all temperatures. In addition, the Cooee model is able to reproduce experimental results showing the formation of nanoaggregates composed of stacks of flat aromatic molecules in bitumen. These nanoaggregates are immersed in a solvent of saturated hydrocarbon molecules. At a fixed temperature, the shear-shinning behavior is related not only to the inter- and intramolecular alignments of the solvent molecules but also to the decrease of the average size of the nanoaggregates at high shear rates. The variation of the viscosity with temperature at different shear rates is also related to the size and relative composition of the nanoaggregates. The slight anisotropy of the whole sample due to the nanoaggregates is considered and quantified. Finally, the position of bitumen mixtures in the broad literature of complex systems such as colloidal suspensions, polymer solutions, and associating polymer networks is discussed.

  4. Accurate Method for Determining Adhesion of Cantilever Beams

    SciTech Connect

    Michalske, T.A.; de Boer, M.P.

    1999-01-08

    Using surface micromachined samples, we demonstrate the accurate measurement of cantilever beam adhesion by using test structures which are adhered over long attachment lengths. We show that this configuration has a deep energy well, such that a fracture equilibrium is easily reached. When compared to the commonly used method of determining the shortest attached beam, the present method is much less sensitive to variations in surface topography or to details of capillary drying.

  5. Accurate method for determining adhesion of cantilever beams

    SciTech Connect

    de Boer, M.P.; Michalske, T.A.

    1999-07-01

    Using surface micromachined samples, we demonstrate the accurate measurement of cantilever beam adhesion by using test structures which are adhered over long attachment lengths. We show that this configuration has a deep energy well, such that a fracture equilibrium is easily reached. When compared to the commonly used method of determining the shortest attached beam, the present method is much less sensitive to variations in surface topography or to details of capillary drying. {copyright} {ital 1999 American Institute of Physics.}

  6. Dynamic non-equilibrium wall-modeling for large eddy simulation at high Reynolds numbers

    NASA Astrophysics Data System (ADS)

    Kawai, Soshi; Larsson, Johan

    2013-01-01

    A dynamic non-equilibrium wall-model for large-eddy simulation at arbitrarily high Reynolds numbers is proposed and validated on equilibrium boundary layers and a non-equilibrium shock/boundary-layer interaction problem. The proposed method builds on the prior non-equilibrium wall-models of Balaras et al. [AIAA J. 34, 1111-1119 (1996)], 10.2514/3.13200 and Wang and Moin [Phys. Fluids 14, 2043-2051 (2002)], 10.1063/1.1476668: the failure of these wall-models to accurately predict the skin friction in equilibrium boundary layers is shown and analyzed, and an improved wall-model that solves this issue is proposed. The improvement stems directly from reasoning about how the turbulence length scale changes with wall distance in the inertial sublayer, the grid resolution, and the resolution-characteristics of numerical methods. The proposed model yields accurate resolved turbulence, both in terms of structure and statistics for both the equilibrium and non-equilibrium flows without the use of ad hoc corrections. Crucially, the model accurately predicts the skin friction, something that existing non-equilibrium wall-models fail to do robustly.

  7. Development of Accurate Chemical Equilibrium Models for Oxalate Species to High Ionic Strength in the System: Na-Ba-Ca-Mn-Sr-Cl-NO3-PO4-SO4-H2O at 25°C

    SciTech Connect

    Qafoku, Odeta; Felmy, Andrew R.

    2007-01-01

    The development of an accurate aqueous thermodynamic model is described for oxalate species in the Na-Ba-Ca-Mn-Sr-Cl-NO3-PO4-SO4-H2O system at 25°C. The model is valid to high ionic strength (as high as 10m) and from very acid (10m H2SO4) to neutral and basic conditions. The model is based upon the equations of Pitzer and co-workers. The necessary ion-interaction parameters are determined by comparison with experimental data taken from the literature or determined in this study. The proposed aqueous activity and solubility model is valid for a range of applications from interpretation of studies on mineral dissolution at circumneutral pH to the dissolution of high-level waste tank sludges under acidic conditions.

  8. Nuclear structure with accurate chiral perturbation theory nucleon-nucleon potential: Application to 6Li and 10B

    SciTech Connect

    Navratil, P; Caurier, E

    2003-10-14

    The authors calculate properties of A = 6 system using the accurate charge-dependent nucleon-nucleon (NN) potential at fourth order of chiral perturbation theory. By application of the ab initio no-core shell model (NCSM) and a variational calculation in the harmonic oscillator basis with basis size up to 16 {h_bar}{Omega} they obtain the {sup 6}Li binding energy of 28.5(5) MeV and a converged excitation spectrum. Also, they calculate properties of {sup 10}B using the same NN potential in a basis space of up to 8 {h_bar}{Omega}. The results are consistent with results obtained by standard accurate NN potentials and demonstrate a deficiency of Hamiltonians consisting of only two-body terms. At this order of chiral perturbation theory three-body terms appear. It is expected that inclusion of such terms in the Hamiltonian will improve agreement with experiment.

  9. Development of Accurate Chemical Equilibrium Models for the Hanford Waste Tanks: The System Na-Ca-Sr-OH-CO3-NO3-EDTA-HEDTA-H2O from 25 to 75°C

    SciTech Connect

    Felmy, Andrew R.; Mason, Marvin J.; Qafoku, Odeta; Dixon, David A.

    2005-04-19

    This symposium manuscript describes the development of an accurate aqueous thermodynamic model for predicting the speciation of Sr in the waste tanks at the Hanford site. A systematic approach is described that details the studies performed to define the most important inorganic and organic complexation reactions as well as the effects of other important metal ions that compete with Sr for complexation reactions with the chelates. By using this approach we were able to define a reduced set of inorganic complexation, organic complexation, and competing metal reactions that best represent the much more complex waste tank chemical system. A summary is presented of the final thermodynamic model for the system Na-Ca-Sr-OH-CO3-NO3-EDTA-HEDTA-H2O from 25 to 75 ºC that was previously published in a variety of sources. Previously unpublished experimental data are also given for the competing metal Ni as well for certain chemical systems, Na-Sr-CO3-PO4-H2O, and for the solubility of amorphous iron hydroxide in the presence of several organic chelating agents. These data were not used in model development but were key to the final selection of the specific chemical systems prioritized for detailed study.

  10. PSSP-RFE: accurate prediction of protein structural class by recursive feature extraction from PSI-BLAST profile, physical-chemical property and functional annotations.

    PubMed

    Li, Liqi; Cui, Xiang; Yu, Sanjiu; Zhang, Yuan; Luo, Zhong; Yang, Hua; Zhou, Yue; Zheng, Xiaoqi

    2014-01-01

    Protein structure prediction is critical to functional annotation of the massively accumulated biological sequences, which prompts an imperative need for the development of high-throughput technologies. As a first and key step in protein structure prediction, protein structural class prediction becomes an increasingly challenging task. Amongst most homological-based approaches, the accuracies of protein structural class prediction are sufficiently high for high similarity datasets, but still far from being satisfactory for low similarity datasets, i.e., below 40% in pairwise sequence similarity. Therefore, we present a novel method for accurate and reliable protein structural class prediction for both high and low similarity datasets. This method is based on Support Vector Machine (SVM) in conjunction with integrated features from position-specific score matrix (PSSM), PROFEAT and Gene Ontology (GO). A feature selection approach, SVM-RFE, is also used to rank the integrated feature vectors through recursively removing the feature with the lowest ranking score. The definitive top features selected by SVM-RFE are input into the SVM engines to predict the structural class of a query protein. To validate our method, jackknife tests were applied to seven widely used benchmark datasets, reaching overall accuracies between 84.61% and 99.79%, which are significantly higher than those achieved by state-of-the-art tools. These results suggest that our method could serve as an accurate and cost-effective alternative to existing methods in protein structural classification, especially for low similarity datasets. PMID:24675610

  11. Structure elucidation of degradation products of the antibiotic amoxicillin with ion trap MS(n) and accurate mass determination by ESI TOF.

    PubMed

    Nägele, Edgar; Moritz, Ralf

    2005-10-01

    Today, it is necessary to identify relevant compounds appearing in discovery and development of new drug substances in the pharmaceutical industry. For that purpose, the measurement of accurate molecular mass and empirical formula calculation is very important for structure elucidation in addition to other available analytical methods. In this work, the identification and confirmation of degradation products in a finished dosage form of the antibiotic drug amoxicillin obtained under stress conditions will be demonstrated. Structure elucidation is performed utilizing liquid chromatography (LC) ion trap MS/MS and MS3 together with accurate mass measurement of the molecular ions and of the collision induced dissociation (CID) fragments by liquid chromatography electro spray ionization time-of-flight mass spectrometry (LC/ESI-TOF). PMID:16099170

  12. RCK: accurate and efficient inference of sequence- and structure-based protein–RNA binding models from RNAcompete data

    PubMed Central

    Orenstein, Yaron; Wang, Yuhao; Berger, Bonnie

    2016-01-01

    Motivation: Protein–RNA interactions, which play vital roles in many processes, are mediated through both RNA sequence and structure. CLIP-based methods, which measure protein–RNA binding in vivo, suffer from experimental noise and systematic biases, whereas in vitro experiments capture a clearer signal of protein RNA-binding. Among them, RNAcompete provides binding affinities of a specific protein to more than 240 000 unstructured RNA probes in one experiment. The computational challenge is to infer RNA structure- and sequence-based binding models from these data. The state-of-the-art in sequence models, Deepbind, does not model structural preferences. RNAcontext models both sequence and structure preferences, but is outperformed by GraphProt. Unfortunately, GraphProt cannot detect structural preferences from RNAcompete data due to the unstructured nature of the data, as noted by its developers, nor can it be tractably run on the full RNACompete dataset. Results: We develop RCK, an efficient, scalable algorithm that infers both sequence and structure preferences based on a new k-mer based model. Remarkably, even though RNAcompete data is designed to be unstructured, RCK can still learn structural preferences from it. RCK significantly outperforms both RNAcontext and Deepbind in in vitro binding prediction for 244 RNAcompete experiments. Moreover, RCK is also faster and uses less memory, which enables scalability. While currently on par with existing methods in in vivo binding prediction on a small scale test, we demonstrate that RCK will increasingly benefit from experimentally measured RNA structure profiles as compared to computationally predicted ones. By running RCK on the entire RNAcompete dataset, we generate and provide as a resource a set of protein–RNA structure-based models on an unprecedented scale. Availability and Implementation: Software and models are freely available at http://rck.csail.mit.edu/ Contact: bab@mit.edu Supplementary information

  13. A Small Area In-Situ MEMS Test Structure to Accurately Measure Fracture Strength by Electrostatic Probing

    SciTech Connect

    Bitsie, Fernando; Jensen, Brian D.; de Boer, Maarten

    1999-07-15

    We have designed, fabricated, tested and modeled a first generation small area test structure for MEMS fracture studies by electrostatic rather than mechanical probing. Because of its small area, this device has potential applications as a lot monitor of strength or fatigue of the MEMS structural material. By matching deflection versus applied voltage data to a 3-D model of the test structure, we develop high confidence that the local stresses achieved in the gage section are greater than 1 GPa. Brittle failure of the polycrystalline silicon was observed.

  14. Accurate 3D rigid-body target motion and structure estimation by using GMTI/HRR with template information

    NASA Astrophysics Data System (ADS)

    Wu, Shunguang; Hong, Lang

    2008-04-01

    A framework of simultaneously estimating the motion and structure parameters of a 3D object by using high range resolution (HRR) and ground moving target indicator (GMTI) measurements with template information is given. By decoupling the motion and structure information and employing rigid-body constraints, we have developed the kinematic and measurement equations of the problem. Since the kinematic system is unobservable by using only one scan HRR and GMTI measurements, we designed an architecture to run the motion and structure filters in parallel by using multi-scan measurements. Moreover, to improve the estimation accuracy in large noise and/or false alarm environments, an interacting multi-template joint tracking (IMTJT) algorithm is proposed. Simulation results have shown that the averaged root mean square errors for both motion and structure state vectors have been significantly reduced by using the template information.

  15. Equilibrium and Orientation in Cephalopods.

    ERIC Educational Resources Information Center

    Budelmann, Bernd-Ulrich

    1980-01-01

    Describes the structure of the equilibrium receptor system in cephalopods, comparing it to the vertebrate counterpart--the vestibular system. Relates the evolution of this complex system to the competition of cephalopods with fishes. (CS)

  16. Accurate determination of the fine-structure intervals in the 3P ground states of C-13 and C-12 by far-infrared laser magnetic resonance

    NASA Technical Reports Server (NTRS)

    Cooksy, A. L.; Saykally, R. J.; Brown, J. M.; Evenson, K. M.

    1986-01-01

    Accurate values are presented for the fine-structure intervals in the 3P ground state of neutral atomic C-12 and C-13 as obtained from laser magnetic resonance spectroscopy. The rigorous analysis of C-13 hyperfine structure, the measurement of resonant fields for C-12 transitions at several additional far-infrared laser frequencies, and the increased precision of the C-12 measurements, permit significant improvement in the evaluation of these energies relative to earlier work. These results will expedite the direct and precise measurement of these transitions in interstellar sources and should assist in the determination of the interstellar C-12/C-13 abundance ratio.

  17. Functional connectivity and structural covariance between regions of interest can be measured more accurately using multivariate distance correlation.

    PubMed

    Geerligs, Linda; Cam-Can; Henson, Richard N

    2016-07-15

    Studies of brain-wide functional connectivity or structural covariance typically use measures like the Pearson correlation coefficient, applied to data that have been averaged across voxels within regions of interest (ROIs). However, averaging across voxels may result in biased connectivity estimates when there is inhomogeneity within those ROIs, e.g., sub-regions that exhibit different patterns of functional connectivity or structural covariance. Here, we propose a new measure based on "distance correlation"; a test of multivariate dependence of high dimensional vectors, which allows for both linear and non-linear dependencies. We used simulations to show how distance correlation out-performs Pearson correlation in the face of inhomogeneous ROIs. To evaluate this new measure on real data, we use resting-state fMRI scans and T1 structural scans from 2 sessions on each of 214 participants from the Cambridge Centre for Ageing & Neuroscience (Cam-CAN) project. Pearson correlation and distance correlation showed similar average connectivity patterns, for both functional connectivity and structural covariance. Nevertheless, distance correlation was shown to be 1) more reliable across sessions, 2) more similar across participants, and 3) more robust to different sets of ROIs. Moreover, we found that the similarity between functional connectivity and structural covariance estimates was higher for distance correlation compared to Pearson correlation. We also explored the relative effects of different preprocessing options and motion artefacts on functional connectivity. Because distance correlation is easy to implement and fast to compute, it is a promising alternative to Pearson correlations for investigating ROI-based brain-wide connectivity patterns, for functional as well as structural data. PMID:27114055

  18. The molecular structure, equilibrium conformation and barrier to internal rotation in decachloroferrocene, Fe(η-C₅Cl₅)₂, determined by gas electron diffraction.

    PubMed

    Phillips, Leo; Cooper, Mervyn K; Haaland, Arne; Samdal, Svein; Giricheva, Nina I; Girichev, Georgiy V

    2010-05-21

    The molecular structure of decachloroferrocene has been determined by gas electron diffraction supported by quantum chemical calculations. The equilibrium conformation has staggered ligand rings and D(5d) symmetry. The barrier to internal rotation is, however, only 0.8(2) kJ mol⁻¹. This barrier is so low that even at room temperature the vast majority of molecules in the gas phase would have sufficient thermal energy to undergo virtually non-hindered internal rotation. While the eclipsed equilibrium conformation of unsubstituted ferrocene is determined by attractive dispersion interaction between the two cyclopentadienyl ligands, the staggered equilibrium conformation of Fe(η-C₅Cl₅)₂ is due to steric repulsion between Cl atoms at different rings. The ligands are non-planar: the C-Cl bonds are bent 3.7(3)° out of the plane of the C₅ ring away from the metal atom. The Fe-C, C-C and C-Cl bond distances (r(a)) are: 205.0(4) pm, 143.4(3) pm and 170.2(4) pm respectively. PMID:20372696

  19. Rotation spectrum and high resolution infrared spectra of the fundamental bands of 121SbD 3. Determination of the ground state and equilibrium structures. Ab initio calculations of the spectroscopic parameters

    NASA Astrophysics Data System (ADS)

    Canè, E.; Di Lonardo, G.; Fusina, L.; Jerzembeck, W.; Bürger, H.; Breidung, J.; Thiel, W.

    2006-01-01

    The high resolution infrared spectrum of 121SbD 3, recorded between 20 and 350 cm -1 and in the regions of bending and stretching fundamental bands, centred at 600 and 1350 cm -1, has been analysed. Splittings of the K″=3, 6 lines have been observed both in the rotation and ro-vibration spectra. A large number of 'perturbation allowed' transitions with selection rules Δ(k-ℓ)=±3, ±6 and ±9 have been identified in all fundamental bands. Accurate ground state molecular parameters have been determined fitting simultaneously the rotational transitions and about 9000 ground state combination differences obtained from lines assigned in the ro-vibrational spectra. The A and B reductions of the rotational Hamiltonian have been applied in the analysis of the ground state. They provided almost equivalent results. The molecular parameters of the 1 1, 2 1, 3 1 and 4 1 states have been obtained from the simultaneous analysis of the ν1 ( A1)/ ν3 ( E) stretching and of the ν2 ( A1)/ ν4 ( E) bending dyads. In fact, the corresponding excited states are affected by strong perturbations due to Coriolis and k-type rovibrational interactions that have been treated explicitly in the model adopted for the analysis. Improved effective ground state and equilibrium geometries have been determined and compared to those of 121SbH 3 and of 123SbD 3. Ab initio calculations at the coupled cluster CCSD(T) level with an energy-consistent large-core pseudopotential and large basis sets have been carried out to determine the equilibrium structure, the anharmonic force field, and the associated spectroscopic constants of 121-stibine. The theoretical constants and structural parameters are in good agreement with the experimental data.

  20. Gap between technically accurate information and socially appropriate information for structural health monitoring system installed into tall buildings

    NASA Astrophysics Data System (ADS)

    Mita, Akira

    2016-04-01

    The importance of the structural health monitoring system for tall buildings is now widely recognized by at least structural engineers and managers at large real estate companies to ensure the structural safety immediately after a large earthquake and appeal the quantitative safety of buildings to potential tenants. Some leading real estate companies decided to install the system into all tall buildings. Considering this tendency, a pilot project for the west area of Shinjuku Station supported by the Japan Science and Technology Agency was started by the author team to explore a possibility of using the system to provide safe spaces for commuters and residents. The system was installed into six tall buildings. From our experience, it turned out that viewing only from technological aspects was not sufficient for the system to be accepted and to be really useful. Safe spaces require not only the structural safety but also the soundness of key functions of the building. We need help from social scientists, medical doctors, city planners etc. to further improve the integrity of the system.

  1. A highly accurate protein structural class prediction approach using auto cross covariance transformation and recursive feature elimination.

    PubMed

    Li, Xiaowei; Liu, Taigang; Tao, Peiying; Wang, Chunhua; Chen, Lanming

    2015-12-01

    Structural class characterizes the overall folding type of a protein or its domain. Many methods have been proposed to improve the prediction accuracy of protein structural class in recent years, but it is still a challenge for the low-similarity sequences. In this study, we introduce a feature extraction technique based on auto cross covariance (ACC) transformation of position-specific score matrix (PSSM) to represent a protein sequence. Then support vector machine-recursive feature elimination (SVM-RFE) is adopted to select top K features according to their importance and these features are input to a support vector machine (SVM) to conduct the prediction. Performance evaluation of the proposed method is performed using the jackknife test on three low-similarity datasets, i.e., D640, 1189 and 25PDB. By means of this method, the overall accuracies of 97.2%, 96.2%, and 93.3% are achieved on these three datasets, which are higher than those of most existing methods. This suggests that the proposed method could serve as a very cost-effective tool for predicting protein structural class especially for low-similarity datasets. PMID:26460680

  2. Accurate modeling of spectral fine-structure in Earth radiance spectra measured with the Global Ozone Monitoring Experiment.

    PubMed

    van Deelen, Rutger; Hasekamp, Otto P; Landgraf, Jochen

    2007-01-10

    We present what we believe to be a novel approach to simulating the spectral fine structure (<1 nm) in measurements of spectrometers such as the Global Ozone Monitoring Experiment (GOME). GOME measures the Earth's radiance spectra and daily solar irradiance spectra from which a reflectivity spectrum is commonly extracted. The high-frequency structures contained in such a spectrum are, apart from atmospheric absorption, caused by Raman scattering and by a shift between the solar irradiance and the Earth's radiance spectrum. Normally, an a priori high-resolution solar spectrum is used to simulate these structures. We present an alternative method in which all the required information on the solar spectrum is retrieved from the GOME measurements. We investigate two approaches for the spectral range of 390-400 nm. First, a solar spectrum is reconstructed on a fine spectral grid from the GOME solar measurement. This approach leads to undersampling errors of up to 0.5% in the modeling of the Earth's radiance spectra. Second, a combination of the solar measurement and one of the Earth's radiance measurement is used to retrieve a solar spectrum. This approach effectively removes the undersampling error and results in residuals close to the GOME measurement noise of 0.1%. PMID:17268571

  3. Comparative study of exchange-correlation functionals for accurate predictions of structural and magnetic properties of multiferroic oxides

    NASA Astrophysics Data System (ADS)

    Chen, Hanghui; Millis, Andrew J.

    2016-05-01

    We systematically compare predictions of various exchange correlation functionals for the structural and magnetic properties of perovskite Sr1 -xBaxMnO3 (0 ≤x ≤1 )—a representative class of multiferroic oxides. The local spin density approximation (LSDA) and spin-dependent generalized gradient approximation with Perdew-Burke-Ernzerhof parametrization (sPBE) make substantial different predictions for ferroelectric atomic distortions, tetragonality, and ground state magnetic ordering. Neither approximation quantitatively reproduces all the measured structural and magnetic properties of perovskite Sr0.5Ba0.5MnO3 . The spin-dependent generalized gradient approximation with Perdew-Burke-Ernzerhof revised for solids parametrization (sPBEsol) and the charge-only Perdew-Burke-Ernzerhof parametrized generalized gradient approximation with Hubbard U and Hund's J extensions both provide overall better agreement with measured structural and magnetic properties of Sr0.5Ba0.5MnO3 , compared to LSDA and sPBE. Using these two methods, we find that different from previous predictions, perovskite BaMnO3 has large Mn off-center displacements and is close to a ferromagnetic-to-antiferromagnetic phase boundary, making it a promising candidate to induce effective giant magnetoelectric effects and to achieve cross-field control of polarization and magnetism.

  4. Development of an accurate and high-throughput methodology for structural comprehension of chlorophylls derivatives. (II) Dephytylated derivatives.

    PubMed

    Chen, Kewei; Ríos, José Julián; Roca, María; Pérez-Gálvez, Antonio

    2015-09-18

    Dephytylated chlorophylls (chlorophyllides and pheophorbides) are the starting point of the chlorophyll catabolism in green tissues, components of the chlorophyll pattern in storage/processed food vegetables, as well as the favoured structural arrangement for chlorophyll absorption. In addition, dephytylated native chlorophylls are prone to several modifications of their structure yielding pyro-, 13(2)-hydroxy- and 15(1)-hydroxy-lactone derivatives. Despite of these outstanding remarks only few of them have been analysed by MS(n). Besides new protocols for obtaining standards, we have developed a new high throughput methodology able to determine the fragmentation pathway of 16 dephytylated chlorophyll derivatives, elucidating the structures of the new product ions and new mechanisms of fragmentation. The new methodology combines, by first time, high resolution time-of-flight mass spectrometry and powerful post-processing software. Native chlorophyllides and pheophorbides mainly exhibit product ions that involve the fragmentation of D ring, as well as additional exclusive product ions. The introduction of an oxygenated function at E ring enhances the progress of fragmentation reactions through the β-keto ester group, developing also exclusive product ions for 13(2)-hydroxy derivatives and for 15(1)-hydroxy-lactone ones. Consequently, while MS(2)-based reactions of phytylated chlorophyll derivatives point to fragmentations at the phytyl and propionic chains, dephytylated chlorophyll derivatives behave different as the absence of phytyl makes β-keto ester group and E ring more prone to fragmentation. Proposals of the key reaction mechanisms underlying the origin of new product ions have been made. PMID:26277027

  5. A new methodology for non-contact accurate crack width measurement through photogrammetry for automated structural safety evaluation

    NASA Astrophysics Data System (ADS)

    Jahanshahi, Mohammad R.; Masri, Sami F.

    2013-03-01

    In mechanical, aerospace and civil structures, cracks are important defects that can cause catastrophes if neglected. Visual inspection is currently the predominant method for crack assessment. This approach is tedious, labor-intensive, subjective and highly qualitative. An inexpensive alternative to current monitoring methods is to use a robotic system that could perform autonomous crack detection and quantification. To reach this goal, several image-based crack detection approaches have been developed; however, the crack thickness quantification, which is an essential element for a reliable structural condition assessment, has not been sufficiently investigated. In this paper, a new contact-less crack quantification methodology, based on computer vision and image processing concepts, is introduced and evaluated against a crack quantification approach which was previously developed by the authors. The proposed approach in this study utilizes depth perception to quantify crack thickness and, as opposed to most previous studies, needs no scale attachment to the region under inspection, which makes this approach ideal for incorporation with autonomous or semi-autonomous mobile inspection systems. Validation tests are performed to evaluate the performance of the proposed approach, and the results show that the new proposed approach outperforms the previously developed one.

  6. Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.)

    PubMed Central

    Kim, Seungill; Kim, Myung-Shin; Kim, Yong-Min; Yeom, Seon-In; Cheong, Kyeongchae; Kim, Ki-Tae; Jeon, Jongbum; Kim, Sunggil; Kim, Do-Sun; Sohn, Seong-Han; Lee, Yong-Hwan; Choi, Doil

    2015-01-01

    The onion (Allium cepa L.) is one of the most widely cultivated and consumed vegetable crops in the world. Although a considerable amount of onion transcriptome data has been deposited into public databases, the sequences of the protein-coding genes are not accurate enough to be used, owing to non-coding sequences intermixed with the coding sequences. We generated a high-quality, annotated onion transcriptome from de novo sequence assembly and intensive structural annotation using the integrated structural gene annotation pipeline (ISGAP), which identified 54,165 protein-coding genes among 165,179 assembled transcripts totalling 203.0 Mb by eliminating the intron sequences. ISGAP performed reliable annotation, recognizing accurate gene structures based on reference proteins, and ab initio gene models of the assembled transcripts. Integrative functional annotation and gene-based SNP analysis revealed a whole biological repertoire of genes and transcriptomic variation in the onion. The method developed in this study provides a powerful tool for the construction of reference gene sets for organisms based solely on de novo transcriptome data. Furthermore, the reference genes and their variation described here for the onion represent essential tools for molecular breeding and gene cloning in Allium spp. PMID:25362073

  7. Development of an accurate and high-throughput methodology for structural comprehension of chlorophylls derivatives. (I) Phytylated derivatives.

    PubMed

    Chen, Kewei; Ríos, José Julián; Pérez-Gálvez, Antonio; Roca, María

    2015-08-01

    Phytylated chlorophyll derivatives undergo specific oxidative reactions through the natural metabolism or during food processing or storage, and consequently pyro-, 13(2)-hydroxy-, 15(1)-hydroxy-lactone chlorophylls, and pheophytins (a and b) are originated. New analytical procedures have been developed here to reproduce controlled oxidation reactions that specifically, and in reasonable amounts, produce those natural target standards. At the same time and under the same conditions, 16 natural chlorophyll derivatives have been analyzed by APCI-HPLC-hrMS(2) and most of them by the first time. The combination of the high-resolution MS mode with powerful post-processing software has allowed the identification of new fragmentation patterns, characterizing specific product ions for some particular standards. In addition, new hypotheses and reaction mechanisms for the established MS(2)-based reactions have been proposed. As a general rule, the main product ions involve the phytyl and the propionic chains but the introduction of oxygenated functional groups at the isocyclic ring produces new and specific productions and at the same time inhibits some particular fragmentations. It is noteworthy that all b derivatives, except 15(1)-hydroxy-lactone compounds, undergo specific CO losses. We propose a new reaction mechanism based in the structural configuration of a and b chlorophyll derivatives that explain the exclusive CO fragmentation in all b series except for 15(1)-hydroxy-lactone b and all a series compounds. PMID:26091781

  8. An accurately preorganized IRES RNA structure enables eIF4G capture for initiation of viral translation.

    PubMed

    Imai, Shunsuke; Kumar, Parimal; Hellen, Christopher U T; D'Souza, Victoria M; Wagner, Gerhard

    2016-09-01

    Many viruses bypass canonical cap-dependent translation in host cells by using internal ribosomal entry sites (IRESs) in their transcripts; IRESs hijack initiation factors for the assembly of initiation complexes. However, it is currently unknown how IRES RNAs recognize initiation factors that have no endogenous RNA binding partners; in a prominent example, the IRES of encephalomyocarditis virus (EMCV) interacts with the HEAT-1 domain of eukaryotic initiation factor 4G (eIF4G). Here we report the solution structure of the J-K region of this IRES and show that its stems are precisely organized to position protein-recognition bulges. This multisite interaction mechanism operates on an all-or-nothing principle in which all domains are required. This preorganization is accomplished by an 'adjuster module': a pentaloop motif that acts as a dual-sided docking station for base-pair receptors. Because subtle changes in the orientation abrogate protein capture, our study highlights how a viral RNA acquires affinity for a target protein. PMID:27525590

  9. Structural requirements of tetracycline-Tet repressor interaction: determination of equilibrium binding constants for tetracycline analogs with the Tet repressor.

    PubMed Central

    Degenkolb, J; Takahashi, M; Ellestad, G A; Hillen, W

    1991-01-01

    We used the Tn10-encoded Tet repressor, which has a highly specific binding capacity for tetracycline, to probe contacts between the drug and protein by chemical interference studies of the antibiotic. For that purpose, the equilibrium association constants of modified tetracyclines with the Tet repressor and Mg2+ cations were determined quantitatively. The results confirm the previous notion that Mg2+ probably binds with the oxygens at positions 11 and 12 and is absolutely required for protein-drug recognition. Modifications were introduced at positions seven, six, five, and four of the drug, and anhydrotetracycline was also studied. Substitutions or eliminations of functions at these positions influenced binding to the Tet repressor up to 35-fold. The introduction of an azido function at position seven in 7-azidotetracycline and epimerization of the substituents at position four in 4-epitetracycline lead to a 2- or 25-fold reduction, respectively, of Tet repressor affinity in those compounds. Anhydrotetracycline bound about 35-fold more strongly than tetracycline did, indicating that the oxygen at position 11 may be involved in Tet repressor recognition. This increased binding is in contrast to the lower antibiotic activity of anhydrotetracycline and indicates that the Tet repressor and ribosomes recognize the drug differently. PMID:1929330

  10. Equilibrium structure and Ti-catalyzed H2 desorption in NaAlH4 nanoparticles from density functional theory.

    PubMed

    Vegge, Tejs

    2006-11-14

    Improving the hydrogen ab- and desorption kinetics in complex hydrides is essential if these materials are to be used as reversible hydrogen storage media in the transport sector. Although reductions in particle size and the addition of titanium based compounds have been found to improve the kinetics significantly, the physical understanding remains elusive. Density functional theory is used to calculate the energy of the potential low energy surfaces of NaAlH(4) to establish the equilibrium particle shape, and furthermore to determine the deposition energy of Ti/TiH(2) and the substitutional energy for Ti@Al and Ti@Na-sites on the exposed facets. The substitutional processes are energetically preferred and the Na-vacancy formation energy is found to be strongly reduced in the presence of Ti. The barrier for H(2) desorption is found to depend significantly on surface morphology and in particular on the presence of Ti, where the activation energy for H(2) desorption on NaAlH(4){001} surfaces can drop to 0.98 eV--in good agreement with the experimentally observed activation energy for dehydrogenation. PMID:17066174

  11. ELAS: A general-purpose computer program for the equilibrium problems of linear structures. Volume 2: Documentation of the program. [subroutines and flow charts

    NASA Technical Reports Server (NTRS)

    Utku, S.

    1969-01-01

    A general purpose digital computer program for the in-core solution of linear equilibrium problems of structural mechanics is documented. The program requires minimum input for the description of the problem. The solution is obtained by means of the displacement method and the finite element technique. Almost any geometry and structure may be handled because of the availability of linear, triangular, quadrilateral, tetrahedral, hexahedral, conical, triangular torus, and quadrilateral torus elements. The assumption of piecewise linear deflection distribution insures monotonic convergence of the deflections from the stiffer side with decreasing mesh size. The stresses are provided by the best-fit strain tensors in the least squares at the mesh points where the deflections are given. The selection of local coordinate systems whenever necessary is automatic. The core memory is used by means of dynamic memory allocation, an optional mesh-point relabelling scheme and imposition of the boundary conditions during the assembly time.

  12. How to accurately bypass damage

    PubMed Central

    Broyde, Suse; Patel, Dinshaw J.

    2016-01-01

    Ultraviolet radiation can cause cancer through DNA damage — specifically, by linking adjacent thymine bases. Crystal structures show how the enzyme DNA polymerase η accurately bypasses such lesions, offering protection. PMID:20577203

  13. Quantum chemical study of the Fe(III)-desferrioxamine B siderophore complex—Electronic structure, vibrational frequencies, and equilibrium Fe-isotope fractionation

    NASA Astrophysics Data System (ADS)

    Domagal-Goldman, S. D.; Paul, K. W.; Sparks, D. L.; Kubicki, J. D.

    2009-01-01

    This study presents molecular orbital/density functional theory (MO/DFT) calculations of the electronic structure, vibrational frequencies, and equilibrium isotope fractionation factors for iron desferrioxamine B (Fe-DFO-B) complexes in aqueous solution. In general, there was good agreement between the predicted properties of Fe(III)-DFO-B and previously published experimental and theoretical results. The predicted fractionation factor for equilibrium between Fe(III)-DFO-B and Fe(III)-catecholate at 22 °C, 0.68 ± 0.25‰, was in good agreement with a previously measured isotopic difference between bacterial cells and solution during the bacterial-mediated dissolution of hornblende [Brantley S. L., Liermann L. and Bullen T. D. (2001) Fractionation of Fe isotopes by soil microbes and organic acids. Geology29, 535-538]. Conceptually, this agreement is consistent with the notion that Fe is first removed from mineral surfaces via complexation with small organic acids (e.g., oxalate), subsequently sequestered by DFO-B in solution, and ultimately delivered to bacterial cells by Fe(III)-DFO-B complexes. The ability of DFO-B to discriminate between Fe(III) and Fe(II)/Al(III) was investigated with Natural Bond Orbital (NBO) analysis and geometry calculations of each metal-DFO-B complex. The results indicated that higher affinity for Fe(III) is not strictly a function of bond length but also the degree of Fe-O covalent bonding.

  14. Investigation of internal magnetic structures and comparison with two-fluid equilibrium configurations in the multi-pulsing CHI on HIST

    NASA Astrophysics Data System (ADS)

    Nakayama, T.; Hanao, T.; Hirono, H.; Hyobu, T.; Ito, K.; Matsumoto, K.; Kikuchi, Y.; Fukumoto, N.; Nagata, M.; Kanki, T.

    2012-10-01

    Spherical torus (ST) plasmas have been successfully maintained by Muti-pulsing Coaxial Helicity Injection (M-CHI) on HIST. This research object is to clarify relations between plasma characteristics and magnetic flux amplifications, and to compare magnetic field structures measured in the plasma interior to a flowing equilibrium calculation. Two-dimensional magnetic probe array has been newly introduced nearby the gun muzzle. The initial result shows that the diverter configuration with a single X-point can be formed after a bubble burst process of the plasma. The closed magnetic flux is surrounded by the open magnetic field lines intersecting with the gun electrodes. To evaluate the sustained configurations, we use the two-fluid equilibrium code containing generalized Bernoulli and Grad-Shafranov equations which was developed by L.C. Steinhauer. The radial profiles of plasma flow, density and magnetic fields measured on the midplane of the FC are consistent to the calculation. We also found that the poloidal shear flow generation is attributed to ExB drift and ion diamagnetic drift. In addition, we will study temporal behaviors of impurity lines such as OV and OVI during the flux amplification by VUV spectroscopic measurements.

  15. Equilibrium Structure of Rotationally and Tidally Distorted Prasad Model Including the Effect of Mass Variation Inside the Star

    NASA Astrophysics Data System (ADS)

    Saini, Seema; Lal, A. K.; Kumar, Sunil

    2014-03-01

    In this paper we propose suitable modifications in the concept of Roche equipotentials to account for the effect of mass distribution inside the star on its equipotential surfaces and use this in conjunction with the approach of Kippenhahn and Thomas, in a manner earlier used by Prasad and Mohan, to incorporate the effects of rotational and tidal forces in the equations of stellar structure parameters. The proposed method has been used to compute the structure parameters of the rotationally and tidally distorted Prasad model of the star.

  16. How does your crystal grow? A commentary on Burton, Cabrera and Frank (1951) ‘The growth of crystals and the equilibrium structure of their surfaces’

    PubMed Central

    Woodruff, D. P.

    2015-01-01

    The key ideas presented in the classic paper ‘The growth of crystals and the equilibrium structure of their surfaces’ by W. K. Burton, N. Cabrera and F. C. Frank, published in Philosophical Transactions A in 1951, are summarized and put in the context of both the state of knowledge at the time of publication and the considerable amount of work since that time that has built on and developed these ideas. Many of these developments exploit the huge increase in the capabilities of computer modelling that complement the original analytic approach of the paper. The dearth of relevant experimental data at the time of the original publication has been transformed by the application of increasingly sophisticated modern methods of surface science. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society. PMID:25750141

  17. Accurate prediction of protein structural classes by incorporating predicted secondary structure information into the general form of Chou's pseudo amino acid composition.

    PubMed

    Kong, Liang; Zhang, Lichao; Lv, Jinfeng

    2014-03-01

    Extracting good representation from protein sequence is fundamental for protein structural classes prediction tasks. In this paper, we propose a novel and powerful method to predict protein structural classes based on the predicted secondary structure information. At the feature extraction stage, a 13-dimensional feature vector is extracted to characterize general contents and spatial arrangements of the secondary structural elements of a given protein sequence. Specially, four segment-level features are designed to elevate discriminative ability for proteins from the α/β and α+β classes. After the features are extracted, a multi-class non-linear support vector machine classifier is used to implement protein structural classes prediction. We report extensive experiments comparing the proposed method to the state-of-the-art in protein structural classes prediction on three widely used low-similarity benchmark datasets: FC699, 1189 and 640. Our method achieves competitive performance on prediction accuracies, especially for the overall prediction accuracies which have exceeded the best reported results on all of the three datasets. PMID:24316044

  18. Liquid-liquid phase equilibrium and core-shell structure formation in immiscible Al-Bi-Sn alloys

    NASA Astrophysics Data System (ADS)

    Li, Mingyang; Jia, Peng; Sun, Xiaofei; Geng, Haoran; Zuo, Min; Zhao, Degang

    2016-04-01

    In this paper, the liquid-phase separation of ternary immiscible Al45Bi19.8Sn35.2 and Al60Bi14.4Sn25.6 melts was studied with resistivity and thermal analysis methods at different temperature. The resistivity-temperature curves appear abrupt and anomalously change with rising temperature, corresponding to the anomalous and low peak of melting process in DSC curves, indicative of the occurrence of the liquid-phase separation. The anomalous behavior of the resistivity temperature dependence is attributable to concentration-concentration fluctuations. The effect of composition and melt temperature on the liquid-phase separation and core-shell structure formation in immiscible Al-Bi-Sn alloys was studied. The liquid-phase separation and formation of the core-shell structure in immiscible Al-Bi-Sn alloys are readily acquired when the alloy compositions fall into liquid miscibility gap. What's more, the cross-sectional structure changes from irregular, dispersed to core-type shapes under the actions of Marangoni motion with increasing melt temperature. This study provides some clues for the preparation of core-shell microspheres of immiscible Al-Bi-Sn alloys via liquid-phase separation.

  19. Under proper control, oxidation of proteins with known chemical structure provides an accurate and absolute method for the determination of their molar concentration.

    PubMed

    Guermant, C; Azarkan, M; Smolders, N; Baeyens-Volant, D; Nijs, M; Paul, C; Brygier, J; Vincentelli, J; Looze, Y

    2000-01-01

    Oxidation at 120 degrees C of inorganic and organic (including amino acids, di- and tripeptides) model compounds by K(2)Cr(2)O(7) in the presence of H(2)SO(4) (mass fraction: 0.572), Ag(2)SO(4) (catalyst), and HgSO(4) results in the quantitative conversion of their C-atoms into CO(2) within 24 h or less. Under these stressed, well-defined conditions, the S-atoms present in cysteine and cystine residues are oxidized into SO(3) while, interestingly, the oxidation states of all the other (including the N-) atoms normally present in a protein do remain quite unchanged. When the chemical structure of a given protein is available, the total number of electrons the protein is able to transfer to K(2)Cr(2)O(7) and thereof, the total number of moles of Cr(3+) ions which the protein is able to generate upon oxidation can be accurately calculated. In such cases, unknown protein molar concentrations can thus be determined through straightforward spectrophotometric measurements of Cr(3+) concentrations. The values of molar absorption coefficients for several well-characterized proteins have been redetermined on this basis and observed to be in excellent agreement with the most precise values reported in the literature, which fully assesses the validity of the method. When applied to highly purified proteins of known chemical structure (more generally of known atomic composition), this method is absolute and accurate (+/-1%). Furthermore, it is well adapted to series measurements since available commercial kits for chemical oxygen demand (COD) measurements can readily be adapted to work under the experimental conditions recommended here for the protein assay. PMID:10610688

  20. Shape characteristics of equilibrium and non-equilibrium fractal clusters

    NASA Astrophysics Data System (ADS)

    Mansfield, Marc L.; Douglas, Jack F.

    2013-07-01

    It is often difficult in practice to discriminate between equilibrium and non-equilibrium nanoparticle or colloidal-particle clusters that form through aggregation in gas or solution phases. Scattering studies often permit the determination of an apparent fractal dimension, but both equilibrium and non-equilibrium clusters in three dimensions frequently have fractal dimensions near 2, so that it is often not possible to discriminate on the basis of this geometrical property. A survey of the anisotropy of a wide variety of polymeric structures (linear and ring random and self-avoiding random walks, percolation clusters, lattice animals, diffusion-limited aggregates, and Eden clusters) based on the principal components of both the radius of gyration and electric polarizability tensor indicates, perhaps counter-intuitively, that self-similar equilibrium clusters tend to be intrinsically anisotropic at all sizes, while non-equilibrium processes such as diffusion-limited aggregation or Eden growth tend to be isotropic in the large-mass limit, providing a potential means of discriminating these clusters experimentally if anisotropy could be determined along with the fractal dimension. Equilibrium polymer structures, such as flexible polymer chains, are normally self-similar due to the existence of only a single relevant length scale, and are thus anisotropic at all length scales, while non-equilibrium polymer structures that grow irreversibly in time eventually become isotropic if there is no difference in the average growth rates in different directions. There is apparently no proof of these general trends and little theoretical insight into what controls the universal anisotropy in equilibrium polymer structures of various kinds. This is an obvious topic of theoretical investigation, as well as a matter of practical interest. To address this general problem, we consider two experimentally accessible ratios, one between the hydrodynamic and gyration radii, the other

  1. Shape characteristics of equilibrium and non-equilibrium fractal clusters.

    PubMed

    Mansfield, Marc L; Douglas, Jack F

    2013-07-28

    It is often difficult in practice to discriminate between equilibrium and non-equilibrium nanoparticle or colloidal-particle clusters that form through aggregation in gas or solution phases. Scattering studies often permit the determination of an apparent fractal dimension, but both equilibrium and non-equilibrium clusters in three dimensions frequently have fractal dimensions near 2, so that it is often not possible to discriminate on the basis of this geometrical property. A survey of the anisotropy of a wide variety of polymeric structures (linear and ring random and self-avoiding random walks, percolation clusters, lattice animals, diffusion-limited aggregates, and Eden clusters) based on the principal components of both the radius of gyration and electric polarizability tensor indicates, perhaps counter-intuitively, that self-similar equilibrium clusters tend to be intrinsically anisotropic at all sizes, while non-equilibrium processes such as diffusion-limited aggregation or Eden growth tend to be isotropic in the large-mass limit, providing a potential means of discriminating these clusters experimentally if anisotropy could be determined along with the fractal dimension. Equilibrium polymer structures, such as flexible polymer chains, are normally self-similar due to the existence of only a single relevant length scale, and are thus anisotropic at all length scales, while non-equilibrium polymer structures that grow irreversibly in time eventually become isotropic if there is no difference in the average growth rates in different directions. There is apparently no proof of these general trends and little theoretical insight into what controls the universal anisotropy in equilibrium polymer structures of various kinds. This is an obvious topic of theoretical investigation, as well as a matter of practical interest. To address this general problem, we consider two experimentally accessible ratios, one between the hydrodynamic and gyration radii, the other

  2. Structural and functional screening in human induced-pluripotent stem cell-derived cardiomyocytes accurately identifies cardiotoxicity of multiple drug types

    SciTech Connect

    Doherty, Kimberly R. Talbert, Dominique R.; Trusk, Patricia B.; Moran, Diarmuid M.; Shell, Scott A.; Bacus, Sarah

    2015-05-15

    Safety pharmacology studies that evaluate new drug entities for potential cardiac liability remain a critical component of drug development. Current studies have shown that in vitro tests utilizing human induced pluripotent stem cell-derived cardiomyocytes (hiPS-CM) may be beneficial for preclinical risk evaluation. We recently demonstrated that an in vitro multi-parameter test panel assessing overall cardiac health and function could accurately reflect the associated clinical cardiotoxicity of 4 FDA-approved targeted oncology agents using hiPS-CM. The present studies expand upon this initial observation to assess whether this in vitro screen could detect cardiotoxicity across multiple drug classes with known clinical cardiac risks. Thus, 24 drugs were examined for their effect on both structural (viability, reactive oxygen species generation, lipid formation, troponin secretion) and functional (beating activity) endpoints in hiPS-CM. Using this screen, the cardiac-safe drugs showed no effects on any of the tests in our panel. However, 16 of 18 compounds with known clinical cardiac risk showed drug-induced changes in hiPS-CM by at least one method. Moreover, when taking into account the Cmax values, these 16 compounds could be further classified depending on whether the effects were structural, functional, or both. Overall, the most sensitive test assessed cardiac beating using the xCELLigence platform (88.9%) while the structural endpoints provided additional insight into the mechanism of cardiotoxicity for several drugs. These studies show that a multi-parameter approach examining both cardiac cell health and function in hiPS-CM provides a comprehensive and robust assessment that can aid in the determination of potential cardiac liability. - Highlights: • 24 drugs were tested for cardiac liability using an in vitro multi-parameter screen. • Changes in beating activity were the most sensitive in predicting cardiac risk. • Structural effects add in

  3. Equilibrium state of anatase to rutile transformation for nano-structured Titanium Dioxide powder using polymer template method.

    NASA Astrophysics Data System (ADS)

    Dam, Tapabrata; Jena, Sidhartha S.; Pradhan, Dillip K.

    2016-02-01

    In this work we report the novel synthesis procedure of phase-pure nano-structured titania in anatase phase using polyacrylamide gel based polymer template method. The evolution of rutile phased titania with increasing temperature has also been investigated. The synthesized nano-materials are characterized using X-ray diffraction, Brunauer - Emmett - Teller surface analysis technique and Scanning electron microscopy. We have used dual phase Rietveld refinement method to analyse the X-Ray diffraction data to get clear picture of crystallographic information of the prepared samples.

  4. Accurate quantum chemical calculations

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1989-01-01

    An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

  5. The crystal structure of the global anaerobic transcriptional regulator FNR explains its extremely fine-tuned monomer-dimer equilibrium.

    PubMed

    Volbeda, Anne; Darnault, Claudine; Renoux, Oriane; Nicolet, Yvain; Fontecilla-Camps, Juan C

    2015-12-01

    The structure of the dimeric holo-fumarate and nitrate reduction regulator (FNR) from Aliivibrio fischeri has been solved at 2.65 Å resolution. FNR globally controls the transition between anaerobic and aerobic respiration in facultative anaerobes through the assembly/degradation of its oxygen-sensitive [4Fe-4S] cluster. In the absence of O2, FNR forms a dimer and specifically binds to DNA, whereas in its presence, the cluster is degraded causing FNR monomerization and DNA dissociation. We have used our crystal structure and the information previously gathered from numerous FNR variants to propose that this process is governed by extremely fine-tuned interactions, mediated by two salt bridges near the amino-terminal cluster-binding domain and an "imperfect" coiled-coil dimer interface. [4Fe-4S] to [2Fe-2S] cluster degradation propagates a conformational signal that indirectly causes monomerization by disrupting the first of these interactions and unleashing the "unzipping" of the FNR dimer in the direction of the carboxyl-terminal DNA binding domain. PMID:26665177

  6. The crystal structure of the global anaerobic transcriptional regulator FNR explains its extremely fine-tuned monomer-dimer equilibrium

    PubMed Central

    Volbeda, Anne; Darnault, Claudine; Renoux, Oriane; Nicolet, Yvain; Fontecilla-Camps, Juan C.

    2015-01-01

    The structure of the dimeric holo–fumarate and nitrate reduction regulator (FNR) from Aliivibrio fischeri has been solved at 2.65 Å resolution. FNR globally controls the transition between anaerobic and aerobic respiration in facultative anaerobes through the assembly/degradation of its oxygen-sensitive [4Fe-4S] cluster. In the absence of O2, FNR forms a dimer and specifically binds to DNA, whereas in its presence, the cluster is degraded causing FNR monomerization and DNA dissociation. We have used our crystal structure and the information previously gathered from numerous FNR variants to propose that this process is governed by extremely fine-tuned interactions, mediated by two salt bridges near the amino-terminal cluster-binding domain and an “imperfect” coiled-coil dimer interface. [4Fe-4S] to [2Fe-2S] cluster degradation propagates a conformational signal that indirectly causes monomerization by disrupting the first of these interactions and unleashing the “unzipping” of the FNR dimer in the direction of the carboxyl-terminal DNA binding domain. PMID:26665177

  7. Determination of the structure of {gamma}-alumina from interatomic potential and first-principles calculations: The requirement of significant numbers of nonspinel positions to achieve an accurate structural model

    SciTech Connect

    Paglia, Gianluca; Rohl, Andrew L.; Gale, Julian D.; Buckley, Craig E.

    2005-06-01

    We have performed an extensive computational study of {gamma}-Al{sub 2}O{sub 3}, beginning with the geometric analysis of approximately 1.47 billion spinel-based structural candidates, followed by derivative method energy minimization calculations of approximately 122 000 structures. Optimization of the spinel-based structural models demonstrated that structures exhibiting nonspinel site occupancy after simulation were more energetically favorable, as suggested in other computational studies. More importantly, none of the spinel structures exhibited simulated diffraction patterns that were characteristic of {gamma}-Al{sub 2}O{sub 3}. This suggests that cations of {gamma}-Al{sub 2}O{sub 3} are not exclusively held in spinel positions, that the spinel model of {gamma}-Al{sub 2}O{sub 3} does not accurately reflect its structure, and that a representative structure cannot be achieved from molecular modeling when the spinel representation is used as the starting structure. The latter two of these three findings are extremely important when trying to accurately model the structure. A second set of starting models were generated with a large number of cations occupying c symmetry positions, based on the findings from recent experiments. Optimization of the new c symmetry-based structural models resulted in simulated diffraction patterns that were characteristic of {gamma}-Al{sub 2}O{sub 3}. The modeling, conducted using supercells, yields a more accurate and complete determination of the defect structure of {gamma}-Al{sub 2}O{sub 3} than can be achieved with current experimental techniques. The results show that on average over 40% of the cations in the structure occupy nonspinel positions, and approximately two-thirds of these occupy c symmetry positions. The structures exhibit variable occupancy in the site positions that follow local symmetry exclusion rules. This variation was predominantly represented by a migration of cations away from a symmetry positions to other

  8. Determination of the structure of γ -alumina from interatomic potential and first-principles calculations: The requirement of significant numbers of nonspinel positions to achieve an accurate structural model

    NASA Astrophysics Data System (ADS)

    Paglia, Gianluca; Rohl, Andrew L.; Buckley, Craig E.; Gale, Julian D.

    2005-06-01

    We have performed an extensive computational study of γ-Al2O3 , beginning with the geometric analysis of approximately 1.47 billion spinel-based structural candidates, followed by derivative method energy minimization calculations of approximately 122 000 structures. Optimization of the spinel-based structural models demonstrated that structures exhibiting nonspinel site occupancy after simulation were more energetically favorable, as suggested in other computational studies. More importantly, none of the spinel structures exhibited simulated diffraction patterns that were characteristic of γ-Al2O3 . This suggests that cations of γ-Al2O3 are not exclusively held in spinel positions, that the spinel model of γ-Al2O3 does not accurately reflect its structure, and that a representative structure cannot be achieved from molecular modeling when the spinel representation is used as the starting structure. The latter two of these three findings are extremely important when trying to accurately model the structure. A second set of starting models were generated with a large number of cations occupying c symmetry positions, based on the findings from recent experiments. Optimization of the new c symmetry-based structural models resulted in simulated diffraction patterns that were characteristic of γ-Al2O3 . The modeling, conducted using supercells, yields a more accurate and complete determination of the defect structure of γ-Al2O3 than can be achieved with current experimental techniques. The results show that on average over 40% of the cations in the structure occupy nonspinel positions, and approximately two-thirds of these occupy c symmetry positions. The structures exhibit variable occupancy in the site positions that follow local symmetry exclusion rules. This variation was predominantly represented by a migration of cations away from a symmetry positions to other tetrahedral site positions during optimization which were found not to affect the diffraction

  9. EASI - EQUILIBRIUM AIR SHOCK INTERFERENCE

    NASA Technical Reports Server (NTRS)

    Glass, C. E.

    1994-01-01

    New research on hypersonic vehicles, such as the National Aero-Space Plane (NASP), has raised concerns about the effects of shock-wave interference on various structural components of the craft. State-of-the-art aerothermal analysis software is inadequate to predict local flow and heat flux in areas of extremely high heat transfer, such as the surface impingement of an Edney-type supersonic jet. EASI revives and updates older computational methods for calculating inviscid flow field and maximum heating from shock wave interference. The program expands these methods to solve problems involving the six shock-wave interference patterns on a two-dimensional cylindrical leading edge with an equilibrium chemically reacting gas mixture (representing, for example, the scramjet cowl of the NASP). The inclusion of gas chemistry allows for a more accurate prediction of the maximum pressure and heating loads by accounting for the effects of high temperature on the air mixture. Caloric imperfections and specie dissociation of high-temperature air cause shock-wave angles, flow deflection angles, and thermodynamic properties to differ from those calculated by a calorically perfect gas model. EASI contains pressure- and temperature-dependent thermodynamic and transport properties to determine heating rates, and uses either a calorically perfect air model or an 11-specie, 7-reaction reacting air model at equilibrium with temperatures up to 15,000 K for the inviscid flowfield calculations. EASI solves the flow field and the associated maximum surface pressure and heat flux for the six common types of shock wave interference. Depending on the type of interference, the program solves for shock-wave/boundary-layer interaction, expansion-fan/boundary-layer interaction, attaching shear layer or supersonic jet impingement. Heat flux predictions require a knowledge (from experimental data or relevant calculations) of a pertinent length scale of the interaction. Output files contain flow

  10. The Theory of Variances in Equilibrium Reconstruction

    SciTech Connect

    Zakharov, Leonid E.; Lewandowski, Jerome; Foley, Elizabeth L.; Levinton, Fred M.; Yuh, Howard Y.; Drozdov, Vladimir; McDonald, Darren

    2008-01-14

    The theory of variances of equilibrium reconstruction is presented. It complements existing practices with information regarding what kind of plasma profiles can be reconstructed, how accurately, and what remains beyond the abilities of diagnostic systems. The σ-curves, introduced by the present theory, give a quantitative assessment of quality of effectiveness of diagnostic systems in constraining equilibrium reconstructions. The theory also suggests a method for aligning the accuracy of measurements of different physical nature.

  11. Analysis of the Rotational Structure in the High-Resolution Infrared Spectrum of trans-Hexatriene-1-13C1; a Semiexperimental Equilibrium Structure for the C6 Backbone for trans-Hexatriene

    SciTech Connect

    Craig, Norman C.; Tian, Hengfeng; Blake, Thomas A.

    2012-03-29

    trans-Hexatriene-1-13C1 (tHTE-1-13C1) has been synthesized, and its high-resolution (0.0015 cm-1) infrared spectrum has been recorded. The rotational structure in the C-type bands for v26 at 1011 cm-1 and v30 at 894 cm-1 has been analyzed. To the 1458 ground state combination differences from these bands, ground state rotational constants were fitted to a Watson-type Hamiltonian to give A0 = 0.8728202(9), B0 = 0.0435868(4), and C0 = 0.0415314(2) cm-1. Upper state rotational constants for the v30 band were also fitted. Predictions of the ground state rotational constants for t-HTE-1-13C1 from a B3LYP/cc-pVTZ model with scale factors based on the normal species were in excellent agreement with observations. Similar good agreement was found between predicted and observed ground state rotational constants for the three 13C1 isotopologues of cis-hexatriene (cHTE), as determined from microwave spectroscopy. Equilibrium rotational constants for tHTE and its three 13C1 isotopologues, of which two were predicted, were used to find a semiexperimental equilibrium structure for the C6 backbone of tHTE. This structure shows increased structural effects of pi-electron delocalization in comparison with butadiene.

  12. Towards accurate structural characterization of metal centres in protein crystals: the structures of Ni and Cu T{sub 6} bovine insulin derivatives

    SciTech Connect

    Frankaer, Christian Grundahl; Mossin, Susanne; Ståhl, Kenny; Harris, Pernille

    2014-01-01

    The level of structural detail around the metal sites in Ni{sup 2+} and Cu{sup 2+} T{sub 6} insulin derivatives was significantly improved by using a combination of single-crystal X-ray crystallography and X-ray absorption spectroscopy. Photoreduction and subsequent radiation damage of the Cu{sup 2+} sites in Cu insulin was followed by XANES spectroscopy. Using synchrotron radiation (SR), the crystal structures of T{sub 6} bovine insulin complexed with Ni{sup 2+} and Cu{sup 2+} were solved to 1.50 and 1.45 Å resolution, respectively. The level of detail around the metal centres in these structures was highly limited, and the coordination of water in Cu site II of the copper insulin derivative was deteriorated as a consequence of radiation damage. To provide more detail, X-ray absorption spectroscopy (XAS) was used to improve the information level about metal coordination in each derivative. The nickel derivative contains hexacoordinated Ni{sup 2+} with trigonal symmetry, whereas the copper derivative contains tetragonally distorted hexacoordinated Cu{sup 2+} as a result of the Jahn–Teller effect, with a significantly longer coordination distance for one of the three water molecules in the coordination sphere. That the copper centre is of type II was further confirmed by electron paramagnetic resonance (EPR). The coordination distances were refined from EXAFS with standard deviations within 0.01 Å. The insulin derivative containing Cu{sup 2+} is sensitive towards photoreduction when exposed to SR. During the reduction of Cu{sup 2+} to Cu{sup +}, the coordination geometry of copper changes towards lower coordination numbers. Primary damage, i.e. photoreduction, was followed directly by XANES as a function of radiation dose, while secondary damage in the form of structural changes around the Cu atoms after exposure to different radiation doses was studied by crystallography using a laboratory diffractometer. Protection against photoreduction and subsequent

  13. Synthesis of Vertically-Aligned Single-Walled Carbon Nanotubes in Micro Structure of Atmospheric Pressure Non-Equilibrium Plasma

    NASA Astrophysics Data System (ADS)

    Ohnishi, Kuma; Nozaki, Tomohiro; Okazaki, Ken; Heberlein, Joachim; Kortshagen, Uwe

    Plasma enhanced chemical vapor deposition (PECVD) is recognized as one of the viable fabrication techniques of carbon nanotubes. The outstanding advantage of PECVD is that free-standing, vertically-aligned carbon nanotubes (VA-CNTs) are synthesized due to the electric field normal to the substrate. This feature draws intense attention for the fabrication of nanoelectronic devices such as high-resolution scanning nanoprobes, interconnects, and field emission devices. However, carbon nanotubes synthesized in PECVD are overwhelmingly carbon nanofibers (CNFs) or multi-walled carbon nanotubes (MWNTs) with measurable structural defects. Tremendous interest in the preparation and characterization of vertically-aligned single-walled carbon nanotubes (VA-SWNTs) and related applications had not been realized in the scope of PECVD until recently. Here we present a fabrication technique of high-purity vertically-aligned single-walled carbon nanotubes using atmospheric pressure plasma enhanced chemical vapor deposition. By now, we have developed the atmospheric pressure radio-frequency discharge (APRFD) for this purpose. Although densely mono-dispersed Fe-Co catalysts of a few nanometers is primarily responsible for VA-SWNT growth, carbon precipitation was virtually absent in the thermal CVD regime at 700°C. On the other hand, high-yield VA-SWNTs were grown at 4 μm min-1 by applying the atmospheric pressure radio-frequency discharge. The results proved that cathodic ion sheath adjacent to the substrates, where a large potential drop exists, also plays an essential role for the controlled growth of SWNTs, while ion damage to the VA-SWNTs is inherently avoided due to high collision frequency among molecules in atmospheric pressure. In this paper, operation regime of APRFD and tentative reaction mechanisms for VA-SWNT growth are discussed along with optical imaging of near substrate region of APRFD.

  14. Ab-initio structure, energy and stable Fe isotope equilibrium fractionation of some geochemically relevant H-O-Fe complexes

    NASA Astrophysics Data System (ADS)

    Ottonello, Giulio; Zuccolini, Marino Vetuschi

    2009-11-01

    The hexa-aqua complexes [Fe(H 2O) 6-m-n(OH) n] (2-n)+n = 0 → 3, m = 0 → 6 - n; [Fe(H 2O) 6-m-n(OH) n] (3-n)+n = 0 → 4, m = 0 → 6 - n were investigated by ab-initio methods with the aim of determining their ground-state geometries, total energies and vibrational properties by treating their inner solvation shell as part of their gaseous precursor (or " hybrid approach"). After a gas-phase energy optimization within the Density Functional Theory (DFT), the molecules were surrounded by a dielectric representing the Reaction Field through an implicit Polarized Continuum Model (PCM). The exploration of several structural ligand arrangements allowed us to quantify the relative stabilities of the various ionic species and the role of the various forms of energy (solute-solvent electronic interaction, cavitation, dispersion, repulsion, liberation free energy) that contribute to stabilize the aqueous complexes. A comparison with experimental thermochemistries showed that ab-initio gas-phase + solvation energies are quite consistent with experimental evidence and allow the depiction of the most stable form in solution and the eventual configurational disorder of water/hydroxyl species around central cations. A vibrational analysis performed on the 54Fe, 56Fe, 57Fe and 58Fe isotopomers indicated important separative effects systematically affected by the extent of deprotonation. The role of the system's redox state (fO 2) and acidity (pH) on the isotopic imprinting of the aqueous species in solution was investigated by coupling the separative effects with speciation calculations. The observed systematics provided a tool of general utility in the interpretation of the iron isotopic signature of natural waters. Applications to the interpretation of isotopic fractionation in solution dictated by redox equilibria and to the significance of the Fe-isotopic imprinting of Banded Iron Formations are given. With "gaseous precursor" it is intended here the isolated gaseous

  15. Statistical physics ""Beyond equilibrium

    SciTech Connect

    Ecke, Robert E

    2009-01-01

    The scientific challenges of the 21st century will increasingly involve competing interactions, geometric frustration, spatial and temporal intrinsic inhomogeneity, nanoscale structures, and interactions spanning many scales. We will focus on a broad class of emerging problems that will require new tools in non-equilibrium statistical physics and that will find application in new material functionality, in predicting complex spatial dynamics, and in understanding novel states of matter. Our work will encompass materials under extreme conditions involving elastic/plastic deformation, competing interactions, intrinsic inhomogeneity, frustration in condensed matter systems, scaling phenomena in disordered materials from glasses to granular matter, quantum chemistry applied to nano-scale materials, soft-matter materials, and spatio-temporal properties of both ordinary and complex fluids.

  16. Adiabatic evolution of plasma equilibrium

    PubMed Central

    Grad, H.; Hu, P. N.; Stevens, D. C.

    1975-01-01

    A new theory of plasma equilibrium is introduced in which adiabatic constraints are specified. This leads to a mathematically nonstandard structure, as compared to the usual equilibrium theory, in which prescription of pressure and current profiles leads to an elliptic partial differential equation. Topologically complex configurations require further generalization of the concept of adiabaticity to allow irreversible mixing of plasma and magnetic flux among islands. Matching conditions across a boundary layer at the separatrix are obtained from appropriate conservation laws. Applications are made to configurations with planned islands (as in Doublet) and accidental islands (as in Tokamaks). Two-dimensional, axially symmetric, helically symmetric, and closed line equilibria are included. PMID:16578729

  17. Lead-free piezoelectric system (Na0.5Bi0.5)TiO3-BaTiO3: Equilibrium structures and irreversible structural transformations driven by electric field and mechanical impact

    NASA Astrophysics Data System (ADS)

    Garg, Rohini; Rao, Badari Narayana; Senyshyn, Anatoliy; Krishna, P. S. R.; Ranjan, Rajeev

    2013-07-01

    The structure-property correlation in the lead-free piezoelectric (1-x)(Na0.5Bi0.5)TiO3-(x)BaTiO3 has been systematically investigated in detail as a function of composition (0structural features in the equilibrium state at room temperature: (i) monoclinic (Cc)+rhombohedral (R3c) for the precritical compositions, 0≤x≤0.05, (ii) cubiclike for 0.06≤x≤0.0675, and (iii) morphotropic phase boundary (MPB) like for 0.07≤x<0.10, Raman and neutron powder diffraction studies revealed identical symmetry for the cubiclike and the MPB compositions. The cubiclike structure undergoes irreversible phase separation by electric poling as well as by pure mechanical impact. This cubiclike phase exhibits relaxor ferroelectricity in its equilibrium state. The short coherence length (˜50 Å) of the out-of-phase octahedral tilts does not allow the normal ferroelectric state to develop below the dipolar freezing temperature, forcing the system to remain in a dipolar glass state at room temperature. Electric poling helps the dipolar glass state to transform to a normal ferroelectric state with a concomitant enhancement in the correlation length of the out-of-phase octahedral tilt.

  18. Picosecond spectroscopic studies of equilibrium structural fluctuations of native and partially unfolded states of Zinc II-substituted and metal-free cytochromes C

    NASA Astrophysics Data System (ADS)

    Tripathy, Jagnyaseni

    Picosecond time-resolved fluorescence spectroscopy was employed to characterize the equilibrium and non-equilibrium protein structural fluctuations in Zn II-substituted (ZnCytc) and metal-free (fbCytc) cytochromes c using dynamic fluorescence Stokes shift (FSS) and fluorescence anisotropy (FA) measurements. The intrinsic porphyrin chromophore is used as the probe for the structural fluctuations of the surrounding protein and solvent. The FSS experiments examine how the time scales detected from the dynamic solvation of a chromoprotein report changes in the character of motion. ZnCytc and fbCytc serve as limited, single-chromophore models for photosynthetic reaction center and light-harvesting proteins. The dynamic solvation of redox and light-harvesting chromophores in photosynthesis plays an important role in the quantum efficiency of electron transfer and energy transfer performed by these systems, respectively. The FSS response function of fbCytc in water is biexponential over the 100-ps--50-ns regime and the two time constants are 1.4 ns and 9.1 ns. ZnCytc under similar solution conditions shows a biexponential FSS response but with time constants of 0.2 ns and 1.5 ns. The two correlation times from the FSS response function correspond to motions of the hydrophobic core and the solvent-contact layer, respectively. Both FSS correlation times were lengthened and the solvation reorganization energy was reduced from 43 cm-1 to 33 cm-1 in the presence of 50% (v/v) glycerol. A Brownian diffusion model with thermally activated barrier crossings on the protein-folding energy landscape is used to interpret these results. The conclusion is that the mean-squared deviations of the fluctuations exhibited by fbCytc are perhaps a factor of ten larger than those in ZnCytc, which is consistent with the suggestion that fbCytc assumes a dynamic, partially unfolded structure with some of the characteristics of a molten globule. The nature of the motion associated with the

  19. Molecular dynamics simulation study of P (VP-co-HEMA) hydrogels: effect of water content on equilibrium structures and mechanical properties.

    PubMed

    Lee, Seung G; Brunello, Giuseppe F; Jang, Seung S; Bucknall, David G

    2009-10-01

    Poly (N-vinyl-2-pyrrolidone-co-2-hydroxyethyl methacrylate) (P(VP-co-HEMA)) hydrogel system with a composition of VP:HEMA=37:13 was studied using molecular dynamics simulations in order to investigate the effect of the water content on the equilibrium structures and the mechanical properties. The degree of randomness of the monomer sequence for the random and the blocky copolymers, were 1.170 and 0.104, respectively, and the degree of polymerization was fixed at 50. The equilibrated density of the hydrogel was found to be larger for the random sequence than for the blocky sequence at low water contents (<40 wt%), but this density difference decreased with increasing water content. The pair correlation function analysis shows that VP is more hydrophilic than HEMA and that the random sequence hydrogel is solvated more than the blocky sequence hydrogel at low water content, which disappears with increasing water content. Correspondingly, the water structure is more disrupted by the random sequence hydrogel at low water content but eventually develops the expected bulk water-like structure with increasing water content. From mechanical deformation simulations, stress-strain analysis showed that the VP is found to relax more efficiently, especially in the blocky sequence, so that the blocky sequence hydrogel shows less stress levels compared to the random sequence hydrogel. As the water content increases, the stress level becomes identical for both sequences. The elastic moduli of the hydrogels calculated from the constant strain energy minimization show the same trend with the stress-strain analysis. PMID:19656562

  20. Observed and expected frequencies of structural hemoglobin variants in newborn screening surveys in Africa and the Middle East: Deviations from Hardy-Weinberg equilibrium

    PubMed Central

    Piel, Frédéric B.; Adamkiewicz, Thomas V.; Amendah, Djesika; Williams, Thomas N.; Gupta, Sunetra; Grosse, Scott D.

    2015-01-01

    Purpose Our objective was to compare observed and expected genotype proportions from newborn screening surveys of structural hemoglobin variants. Methods We conducted a systematic review of newborn screening surveys of hemoglobins S and C in Africa and the Middle-East. We compared observed frequencies to those expected assuming Hardy-Weinberg equilibrium (HWE). Significant deviations were identified by an exact test. The fixation index FIS was calculated to assess excess homozygosity. We compared newborn estimates corrected and uncorrected for HWE deviations using demographic data. Results Sixty samples reported genotype counts for hemoglobin variants in Africa and the Middle-East. Observed and expected counts matched in 27%. The observed number of sickle-cell anemia (SCA) individuals was higher than expected in 42 samples, reaching significance (p<0.05) in 24. High FIS were common across the study regions. The estimated total number of newborns with SCA, corrected based on FIS, were 33,261 annual births instead of 24,958 for the 38 samples across sub-Saharan Africa and 1,109 annual births instead of 578 for 12 samples from the Middle East. Conclusion Differences between observed and expected genotype frequencies are common in surveys of hemoglobin variants in the study regions. Further research is required to identify and quantify factors responsible for such deviations. Estimates based on HWE might substantially underestimate the annual number of SCA affected newborns (up to one third in sub-Saharan Africa and one half in the Middle East). PMID:26633548

  1. Phase equilibrium and structural properties in the Ca-Al-Si-O system up to the P,T conditions of the Earth's lowermost transition zone.

    NASA Astrophysics Data System (ADS)

    Gréaux, S.; Nishiyama, N.; Kono, Y.; Shinmei, T.; Irifune, T.

    2008-12-01

    Ca- and Al-bearing silicates have been extensively investigated for their importance into the mantle processes. In the transition zone, majorite garnet and Ca-perovskite are reported to be the major hosts of Ca as well as deposits of Al [1]. At higher P, Ca gets completely exsolved from the majorite to the Ca-pv. It is observed that Al plays a significant role in the Ca-Si-O system by inducing new phase equilibriums [2,3,4], and influencing the physical properties of the Ca-pv [5]. It is then suggested that phase transitions and chemical reactions involving Ca- and Al-bearing silicates could conciliate mineralogical results and seismological observations in the region of the transition zone [3,6]. We studied the phase equilibrium at HP-HT in the grossular and anorthite systems using a Kawai-type multi- anvil apparatus up to 25 GPa and 2000 K. Grossular garnet is reported to decompose into a mix of corundum and Ca-pv [3] or to transform into a perovskite of grossular composition [7]. Our study shows that grossular mainly decomposes into a mix of Al-Ca-pv and CAS phase in the same P range and higher T. Anorthite is also found to mainly decompose into a mix of Al-Ca-pv and CAS phase. Despite some Al-content in the Ca-pv, the CAS phase is the major host of Al, which suggests according to previous studies [3,5], a lower solubility of Al into the perovskite structure at high T. The Al-content of the Ca-pv as well as the presence of another Al-rich Ca-bearing silicate in zone of variable temperatures and composition as subducting slabs are discussed for their possible implication into the transition zone processes. [1] T. Irifune, 1994. Nature 370, 131-133 [2] L. Gautron et al., 1996. Phys. Earth Planet. Int. 94, 71-81 [3] N. Takafuji et al., 2002. Phys. Chem. Mineral 29, 532-537 [4] S. Zhai and E. Ito, 2008. Phys. Earth Planet. Int. In press [5] T. Kurashina et al., 2004. Phys. Earth Planet. Int. 145, 67-7 [6] L. Stixrude et al., 1996. Am. Mineral. 81, 1293-1296 [7] H

  2. Non-Equilibrium Properties from Equilibrium Free Energy Calculations

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; Wilson, Michael A.

    2012-01-01

    Calculating free energy in computer simulations is of central importance in statistical mechanics of condensed media and its applications to chemistry and biology not only because it is the most comprehensive and informative quantity that characterizes the eqUilibrium state, but also because it often provides an efficient route to access dynamic and kinetic properties of a system. Most of applications of equilibrium free energy calculations to non-equilibrium processes rely on a description in which a molecule or an ion diffuses in the potential of mean force. In general case this description is a simplification, but it might be satisfactorily accurate in many instances of practical interest. This hypothesis has been tested in the example of the electrodiffusion equation . Conductance of model ion channels has been calculated directly through counting the number of ion crossing events observed during long molecular dynamics simulations and has been compared with the conductance obtained from solving the generalized Nernst-Plank equation. It has been shown that under relatively modest conditions the agreement between these two approaches is excellent, thus demonstrating the assumptions underlying the diffusion equation are fulfilled. Under these conditions the electrodiffusion equation provides an efficient approach to calculating the full voltage-current dependence routinely measured in electrophysiological experiments.

  3. Calculating Shocks In Flows At Chemical Equilibrium

    NASA Technical Reports Server (NTRS)

    Eberhardt, Scott; Palmer, Grant

    1988-01-01

    Boundary conditions prove critical. Conference paper describes algorithm for calculation of shocks in hypersonic flows of gases at chemical equilibrium. Although algorithm represents intermediate stage in development of reliable, accurate computer code for two-dimensional flow, research leading up to it contributes to understanding of what is needed to complete task.

  4. Effect of chemical fixatives on accurate preservation of Escherichia coli and Bacillus subtilis structure in cells prepared by freeze-substitution

    SciTech Connect

    Graham, L.L.; Beveridge, T.J. )

    1990-04-01

    Five chemical fixatives were evaluated for their ability to accurately preserve bacterial ultrastructure during freeze-substitution of select Escherichia coli and Bacillus subtilis strains. Radioisotopes were specifically incorporated into the peptidoglycan, lipopolysaccharide, and nucleic acids of E. coli SFK11 and W7 and into the peptidoglycan and RNA of B. subtilis 168 and W23. The ease of extraction of radiolabels, as assessed by liquid scintillation counting during all stages of processing for freeze-substitution, was used as an indicator of cell structural integrity and retention of cellular chemical composition. Subsequent visual examination by electron microscopy was used to confirm ultrastructural conformation. The fixatives used were: 2% (wt/vol) osmium tetroxide and 2% (wt/vol) uranyl acetate; 2% (vol/vol) glutaraldehyde and 2% (wt/vol) uranyl acetate; 2% (vol/vol) acrolein and 2% (wt/vol) uranyl acetate; 2% (wt/vol) gallic acid; and 2% (wt/vol) uranyl acetate. All fixatives were prepared in a substitution solvent of anhydrous acetone. Extraction of cellular constituents depended on the chemical fixative used. A combination of 2% osmium tetroxide-2% uranyl acetate or 2% gallic acid alone resulted in optimum fixation as ascertained by least extraction of radiolabels. In both gram-positive and gram-negative organisms, high levels of radiolabel were detected in the processing fluids in which 2% acrolein-2% uranyl acetate, 2% glutaraldehyde-2% uranyl acetate, or 2% uranyl acetate alone were used as fixatives. Ultrastructural variations were observed in cells freeze-substituted in the presence of different chemical fixatives. We recommend the use of osmium tetroxide and uranyl acetate in acetone for routine freeze-substitution of eubacteria, while gallic acid is recommended for use when microanalytical processing necessitates the omission of osmium.

  5. Getting Freshman in Equilibrium.

    ERIC Educational Resources Information Center

    Journal of Chemical Education, 1983

    1983-01-01

    Various aspects of chemical equilibrium were discussed in six papers presented at the Seventh Biennial Conference on Chemical Education (Stillwater, Oklahoma 1982). These include student problems in understanding hydrolysis, helping students discover/uncover topics, equilibrium demonstrations, instructional strategies, and flaws to kinetic…

  6. Local Nash Equilibrium in Social Networks

    PubMed Central

    Zhang, Yichao; Aziz-Alaoui, M. A.; Bertelle, Cyrille; Guan, Jihong

    2014-01-01

    Nash equilibrium is widely present in various social disputes. As of now, in structured static populations, such as social networks, regular, and random graphs, the discussions on Nash equilibrium are quite limited. In a relatively stable static gaming network, a rational individual has to comprehensively consider all his/her opponents' strategies before they adopt a unified strategy. In this scenario, a new strategy equilibrium emerges in the system. We define this equilibrium as a local Nash equilibrium. In this paper, we present an explicit definition of the local Nash equilibrium for the two-strategy games in structured populations. Based on the definition, we investigate the condition that a system reaches the evolutionary stable state when the individuals play the Prisoner's dilemma and snow-drift game. The local Nash equilibrium provides a way to judge whether a gaming structured population reaches the evolutionary stable state on one hand. On the other hand, it can be used to predict whether cooperators can survive in a system long before the system reaches its evolutionary stable state for the Prisoner's dilemma game. Our work therefore provides a theoretical framework for understanding the evolutionary stable state in the gaming populations with static structures. PMID:25169150

  7. Chemical Principles Revisited: Chemical Equilibrium.

    ERIC Educational Resources Information Center

    Mickey, Charles D.

    1980-01-01

    Describes: (1) Law of Mass Action; (2) equilibrium constant and ideal behavior; (3) general form of the equilibrium constant; (4) forward and reverse reactions; (5) factors influencing equilibrium; (6) Le Chatelier's principle; (7) effects of temperature, changing concentration, and pressure on equilibrium; and (8) catalysts and equilibrium. (JN)

  8. Computing Equilibrium Chemical Compositions

    NASA Technical Reports Server (NTRS)

    Mcbride, Bonnie J.; Gordon, Sanford

    1995-01-01

    Chemical Equilibrium With Transport Properties, 1993 (CET93) computer program provides data on chemical-equilibrium compositions. Aids calculation of thermodynamic properties of chemical systems. Information essential in design and analysis of such equipment as compressors, turbines, nozzles, engines, shock tubes, heat exchangers, and chemical-processing equipment. CET93/PC is version of CET93 specifically designed to run within 640K memory limit of MS-DOS operating system. CET93/PC written in FORTRAN.

  9. Grading More Accurately

    ERIC Educational Resources Information Center

    Rom, Mark Carl

    2011-01-01

    Grades matter. College grading systems, however, are often ad hoc and prone to mistakes. This essay focuses on one factor that contributes to high-quality grading systems: grading accuracy (or "efficiency"). I proceed in several steps. First, I discuss the elements of "efficient" (i.e., accurate) grading. Next, I present analytical results…

  10. Equilibrium games in networks

    NASA Astrophysics Data System (ADS)

    Li, Angsheng; Zhang, Xiaohui; Pan, Yicheng; Peng, Pan

    2014-12-01

    It seems a universal phenomenon of networks that the attacks on a small number of nodes by an adversary player Alice may generate a global cascading failure of the networks. It has been shown (Li et al., 2013) that classic scale-free networks (Barabási and Albert, 1999, Barabási, 2009) are insecure against attacks of as small as O(logn) many nodes. This poses a natural and fundamental question: Can we introduce a second player Bob to prevent Alice from global cascading failure of the networks? We proposed a game in networks. We say that a network has an equilibrium game if the second player Bob has a strategy to balance the cascading influence of attacks by the adversary player Alice. It was shown that networks of the preferential attachment model (Barabási and Albert, 1999) fail to have equilibrium games, that random graphs of the Erdös-Rényi model (Erdös and Rényi, 1959, Erdös and Rényi, 1960) have, for which randomness is the mechanism, and that homophyly networks (Li et al., 2013) have equilibrium games, for which homophyly and preferential attachment are the underlying mechanisms. We found that some real networks have equilibrium games, but most real networks fail to have. We anticipate that our results lead to an interesting new direction of network theory, that is, equilibrium games in networks.

  11. Analytic prediction of airplane equilibrium spin characteristics

    NASA Technical Reports Server (NTRS)

    Adams, W. M., Jr.

    1972-01-01

    The nonlinear equations of motion are solved algebraically for conditions for which an airplane is in an equilibrium spin. Constrained minimization techniques are employed in obtaining the solution. Linear characteristics of the airplane about the equilibrium points are also presented and their significance in identifying the stability characteristics of the equilibrium points is discussed. Computer time requirements are small making the method appear potentially applicable in airplane design. Results are obtained for several configurations and are compared with other analytic-numerical methods employed in spin prediction. Correlation with experimental results is discussed for one configuration for which a rather extensive data base was available. A need is indicated for higher Reynolds number data taken under conditions which more accurately simulate a spin.

  12. Accurate interlaminar stress recovery from finite element analysis

    NASA Technical Reports Server (NTRS)

    Tessler, Alexander; Riggs, H. Ronald

    1994-01-01

    The accuracy and robustness of a two-dimensional smoothing methodology is examined for the problem of recovering accurate interlaminar shear stress distributions in laminated composite and sandwich plates. The smoothing methodology is based on a variational formulation which combines discrete least-squares and penalty-constraint functionals in a single variational form. The smoothing analysis utilizes optimal strains computed at discrete locations in a finite element analysis. These discrete strain data are smoothed with a smoothing element discretization, producing superior accuracy strains and their first gradients. The approach enables the resulting smooth strain field to be practically C1-continuous throughout the domain of smoothing, exhibiting superconvergent properties of the smoothed quantity. The continuous strain gradients are also obtained directly from the solution. The recovered strain gradients are subsequently employed in the integration o equilibrium equations to obtain accurate interlaminar shear stresses. The problem is a simply-supported rectangular plate under a doubly sinusoidal load. The problem has an exact analytic solution which serves as a measure of goodness of the recovered interlaminar shear stresses. The method has the versatility of being applicable to the analysis of rather general and complex structures built of distinct components and materials, such as found in aircraft design. For these types of structures, the smoothing is achieved with 'patches', each patch covering the domain in which the smoothed quantity is physically continuous.

  13. Accurate monotone cubic interpolation

    NASA Technical Reports Server (NTRS)

    Huynh, Hung T.

    1991-01-01

    Monotone piecewise cubic interpolants are simple and effective. They are generally third-order accurate, except near strict local extrema where accuracy degenerates to second-order due to the monotonicity constraint. Algorithms for piecewise cubic interpolants, which preserve monotonicity as well as uniform third and fourth-order accuracy are presented. The gain of accuracy is obtained by relaxing the monotonicity constraint in a geometric framework in which the median function plays a crucial role.

  14. Accurate Finite Difference Algorithms

    NASA Technical Reports Server (NTRS)

    Goodrich, John W.

    1996-01-01

    Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.

  15. Conformations of Proteins in Equilibrium

    NASA Astrophysics Data System (ADS)

    Micheletti, Cristian; Banavar, Jayanth R.; Maritan, Amos

    2001-08-01

    We introduce a simple theoretical approach for an equilibrium study of proteins with known native-state structures. We test our approach with results on well-studied globular proteins, chymotrypsin inhibitor (2ci2), barnase, and the alpha spectrin SH3 domain, and present evidence for a hierarchical onset of order on lowering the temperature with significant organization at the local level even at high temperatures. A further application to the folding process of HIV-1 protease shows that the model can be reliably used to identify key folding sites that are responsible for the development of drug resistance.

  16. An Updated Equilibrium Machine

    ERIC Educational Resources Information Center

    Schultz, Emeric

    2008-01-01

    A device that can demonstrate equilibrium, kinetic, and thermodynamic concepts is described. The device consists of a leaf blower attached to a plastic container divided into two chambers by a barrier of variable size and form. Styrofoam balls can be exchanged across the barrier when the leaf blower is turned on and various air pressures are…

  17. Quantitative Assessment of Protein Structural Models by Comparison of H/D Exchange MS Data with Exchange Behavior Accurately Predicted by DXCOREX

    NASA Astrophysics Data System (ADS)

    Liu, Tong; Pantazatos, Dennis; Li, Sheng; Hamuro, Yoshitomo; Hilser, Vincent J.; Woods, Virgil L.

    2012-01-01

    Peptide amide hydrogen/deuterium exchange mass spectrometry (DXMS) data are often used to qualitatively support models for protein structure. We have developed and validated a method (DXCOREX) by which exchange data can be used to quantitatively assess the accuracy of three-dimensional (3-D) models of protein structure. The method utilizes the COREX algorithm to predict a protein's amide hydrogen exchange rates by reference to a hypothesized structure, and these values are used to generate a virtual data set (deuteron incorporation per peptide) that can be quantitatively compared with the deuteration level of the peptide probes measured by hydrogen exchange experimentation. The accuracy of DXCOREX was established in studies performed with 13 proteins for which both high-resolution structures and experimental data were available. The DXCOREX-calculated and experimental data for each protein was highly correlated. We then employed correlation analysis of DXCOREX-calculated versus DXMS experimental data to assess the accuracy of a recently proposed structural model for the catalytic domain of a Ca2+-independent phospholipase A2. The model's calculated exchange behavior was highly correlated with the experimental exchange results available for the protein, supporting the accuracy of the proposed model. This method of analysis will substantially increase the precision with which experimental hydrogen exchange data can help decipher challenging questions regarding protein structure and dynamics.

  18. Formation of bcc non-equilibrium La, Gd, and Dy alloys and the magnetic structure of Mg-stabilized. beta. Gd and. beta. Dy

    SciTech Connect

    Herchenroeder, J.W.

    1988-01-01

    The high temperature bcc allotrope of a rare earth metal has the potential for substantially different magnetic properties than the room temperature hexagonal (hcp or dcp) counterpart because of its more symmetrical crystal field. The stabilization by alloying and quenching of this bcc phase was studied for La-M alloys where M is a non-rare earth metal from Group II or III. The factors influencing the stabilization, such as size of M and quench rate, are discussed. {gamma}La (bcc) could be retained over a composition range around the eutectoid composition by Mg or Cd alloying. A comparison of T{sub o} curves of the various alloy systems suggest that the eutectoid temperature of the La-M system must be approximately equal to or less than a critical T{sub o} temperature of 515{degree}C if the bcc phase is to be retained by quenching. The thermal stability of {beta}Gd (bcc) was investigated by DTA and isothermal annealing. It was found to transform to an intermediate phase before reverting to the equilibrium phases in contrast to {gamma}La alloys which decompose directly on heating to the equilibrium phases. Bcc {beta}Gd and {beta}Dy stabilized by Mg additions exhibit spin glass-like behavior. Both systems show field cooling effects in the magnetic susceptibility which is indicative of spin freezing reactions.

  19. Formation of bcc non-equilibrium La, Gd and Dy alloys and the magnetic structure of Mg-stabilized. beta. Gd and. beta. Dy

    SciTech Connect

    Herchenroeder, J.W.

    1989-02-01

    The high temperature bcc allotrope of a rare earth metal has the potential for substantially different magnetic properties than the room temperature hexagonal (hcp or dhcp) counterpart because of its more symmetrical crystal field. The stabilization by alloying and quenching of this bcc phase was studied for La-M alloys where M is an non-rare earth metal from Group II or III. The factors influencing the stabilization, such as size of M and quench rate, are discussed. ..gamma..La (bcc) could be retained over a composition range around the eutectoid composition by Mg or Cd alloying. A comparison of T/sub o/ curves of the various alloy systems suggest that the eutectoid temperature of the La-M system must be approximately equal to or less than a critical T/sub o/ temperature of 515/degree/C if the bcc phase is to be retained by quenching. The thermal stability of ..beta..Gd (bcc) was investigated by DTA and isothermal annealing. It was found to transform to an intermediate phase before reverting to the equilibrium phases in contrast to ..gamma..La alloys which decompose directly on heating to the equilibrium phases. 71 refs., 52 figs., 7 tabs.

  20. An Updated Equilibrium Machine

    NASA Astrophysics Data System (ADS)

    Schultz, Emeric

    2008-08-01

    A device that can demonstrate equilibrium, kinetic, and thermodynamic concepts is described. The device consists of a leaf blower attached to a plastic container divided into two chambers by a barrier of variable size and form. Styrofoam balls can be exchanged across the barrier when the leaf blower is turned on and various air pressures are applied. Equilibrium can be approached from different distributions of balls in the container under different conditions. The Le Châtelier principle can be demonstrated. Kinetic concepts can be demonstrated by changing the nature of the barrier, either changing the height or by having various sized holes in the barrier. Thermodynamic concepts can be demonstrated by taping over some or all of the openings and restricting air flow into container on either side of the barrier.

  1. Absolute Equilibrium Entropy

    NASA Technical Reports Server (NTRS)

    Shebalin, John V.

    1997-01-01

    The entropy associated with absolute equilibrium ensemble theories of ideal, homogeneous, fluid and magneto-fluid turbulence is discussed and the three-dimensional fluid case is examined in detail. A sigma-function is defined, whose minimum value with respect to global parameters is the entropy. A comparison is made between the use of global functions sigma and phase functions H (associated with the development of various H-theorems of ideal turbulence). It is shown that the two approaches are complimentary though conceptually different: H-theorems show that an isolated system tends to equilibrium while sigma-functions allow the demonstration that entropy never decreases when two previously isolated systems are combined. This provides a more complete picture of entropy in the statistical mechanics of ideal fluids.

  2. The equilibrium dayside magnetosphere

    NASA Technical Reports Server (NTRS)

    Zavriyev, Anton; Hasegawa, Akira

    1989-01-01

    A method is presented of computing the dayside global earth magnetic field which is in equilibrium with the plasma pressure, based on satellite observations at a local region of the magnetosphere. The method, which utilizes a perturbation around a dipole magnetic field, involves computation of the global plasma pressure profile based on the equatorial (anisotropic) pressure data, derivation of the current profile which satisfies the equilibrium condition, and computation of the magnetic field using the current profile and the boundary current produced by the solar wind. The method is applied for the Active Magnetospheric Particle Tracer Explorers data, and the result of the computation is found to compare reasonably well with the observed magnetic field profile near the geomagnetic equator.

  3. Accurate measurement of time

    NASA Astrophysics Data System (ADS)

    Itano, Wayne M.; Ramsey, Norman F.

    1993-07-01

    The paper discusses current methods for accurate measurements of time by conventional atomic clocks, with particular attention given to the principles of operation of atomic-beam frequency standards, atomic hydrogen masers, and atomic fountain and to the potential use of strings of trapped mercury ions as a time device more stable than conventional atomic clocks. The areas of application of the ultraprecise and ultrastable time-measuring devices that tax the capacity of modern atomic clocks include radio astronomy and tests of relativity. The paper also discusses practical applications of ultraprecise clocks, such as navigation of space vehicles and pinpointing the exact position of ships and other objects on earth using the GPS.

  4. FILMPAR: A parallel algorithm designed for the efficient and accurate computation of thin film flow on functional surfaces containing micro-structure

    NASA Astrophysics Data System (ADS)

    Lee, Y. C.; Thompson, H. M.; Gaskell, P. H.

    2009-12-01

    , industrial and physical applications. However, despite recent modelling advances, the accurate numerical solution of the equations governing such problems is still at a relatively early stage. Indeed, recent studies employing a simplifying long-wave approximation have shown that highly efficient numerical methods are necessary to solve the resulting lubrication equations in order to achieve the level of grid resolution required to accurately capture the effects of micro- and nano-scale topographical features. Solution method: A portable parallel multigrid algorithm has been developed for the above purpose, for the particular case of flow over submerged topographical features. Within the multigrid framework adopted, a W-cycle is used to accelerate convergence in respect of the time dependent nature of the problem, with relaxation sweeps performed using a fixed number of pre- and post-Red-Black Gauss-Seidel Newton iterations. In addition, the algorithm incorporates automatic adaptive time-stepping to avoid the computational expense associated with repeated time-step failure. Running time: 1.31 minutes using 128 processors on BlueGene/P with a problem size of over 16.7 million mesh points.

  5. Solids Far from Equilibrium

    NASA Astrophysics Data System (ADS)

    Godrèche, C.

    2011-03-01

    Preface; 1. Shape and growth of crystals P. Nozières; 2. Instabilities of planar solidification fronts B. Caroli, C. Caroli and B. Roulet; 3. An introduction to the kinetics of first-order phase transition J. S. Langer; 4. Dendritic growth and related topics Y. Pomeau and M. Ben Amar; 5. Growth and aggregation far from equilibrium L. M. Sander; 6. Kinetic roughening of growing surfaces J. Krug and H. Spohn; Acknowledgements; References; Index.

  6. Exoplanet Equilibrium Chemistry Calculations

    NASA Astrophysics Data System (ADS)

    Blumenthal, Sarah; Harrington, J.; Bowman, M.; Blecic, J.

    2013-10-01

    Recently, Agundez et al. (2012, A&A 548, A73) used a chemical kinetics code to study a model HD 209458b (equilibrium temperature of 1450 K, assuming full redistribution and 0 albedo). They found that thermochemistry dominates most of the dayside, but that significant compositional gradients may exist across the dayside. We calculate equilibrium-chemistry molecular abundances for several model exoplanets, using NASA's open-source Chemical Equilibrium Abundances code (McBride and Gordon 1996). We vary the degree of radiation redistribution to the dark side, ranging from total redistribution to instantaneous reradiation. Atomically, both the solar abundance multiple and the carbon fraction vary. Planet substellar temperatures range from just above 1200 K, where photochemistry should no longer be important, to those of hot planets (3000 K). We present synthetic abundance images for the key spectroscopic molecules CO, CH4, and H2O for several hot-Jupiter model planets. This work was supported by the NASA Planetary Atmospheres grant NNX12AI69G.

  7. Equilibrium Electroconvective Instability

    NASA Astrophysics Data System (ADS)

    Rubinstein, I.; Zaltzman, B.

    2015-03-01

    Since its prediction 15 years ago, hydrodynamic instability in concentration polarization at a charge-selective interface has been attributed to nonequilibrium electro-osmosis related to the extended space charge which develops at the limiting current. This attribution had a double basis. On the one hand, it has been recognized that neither equilibrium electro-osmosis nor bulk electroconvection can yield instability for a perfectly charge-selective solid. On the other hand, it has been shown that nonequilibrium electro-osmosis can. The first theoretical studies in which electro-osmotic instability was predicted and analyzed employed the assumption of perfect charge selectivity for the sake of simplicity and so did the subsequent studies of various time-dependent and nonlinear features of electro-osmotic instability. In this Letter, we show that relaxing the assumption of perfect charge selectivity (tantamount to fixing the electrochemical potential of counterions in the solid) allows for the equilibrium electroconvective instability. In addition, we suggest a simple experimental test for determining the true, either equilibrium or nonequilibrium, origin of instability in concentration polarization.

  8. Interaction between wheat alpha-amylase/trypsin bi-functional inhibitor and mammalian digestive enzymes: Kinetic, equilibrium and structural characterization of binding.

    PubMed

    Cuccioloni, Massimiliano; Mozzicafreddo, Matteo; Ali, Ishtiaq; Bonfili, Laura; Cecarini, Valentina; Eleuteri, Anna Maria; Angeletti, Mauro

    2016-12-15

    Alpha-amylase/trypsin bi-functional inhibitors (ATIs) are non-gluten protein components of wheat and other cereals that can hypersensitise the human gastrointestinal tract, eventually causing enteropathies in predisposed individuals. These inhibitory proteins can act both directly by targeting specific pro-inflammatory receptors, and indirectly by impairing the activity of digestive enzymes, the latter event causing the accumulation of undigested peptides with potential immunogenic properties. Herein, according to a concerted approach based on in vitro and in silico methods we characterized kinetics, equilibrium parameters and modes of binding of the complexes formed between wheat ATI and two representative mammalian digestive enzymes, namely trypsin and alpha-amylase. Interestingly, we demonstrated ATI to target both enzymes with independent binding sites and with moderately high affinity. PMID:27451220

  9. Non-equilibrium Green's function calculation of AlGaAs-well-based and GaSb-based terahertz quantum cascade laser structures

    SciTech Connect

    Yasuda, H. Hosako, I.

    2015-03-16

    We investigate the performance of terahertz quantum cascade lasers (THz-QCLs) based on Al{sub x}Ga{sub 1−x}As/Al{sub y}Ga{sub 1−y}As and GaSb/AlGaSb material systems to realize higher-temperature operation. Calculations with the non-equilibrium Green's function method reveal that the AlGaAs-well-based THz-QCLs do not show improved performance, mainly because of alloy scattering in the ternary compound semiconductor. The GaSb-based THz-QCLs offer clear advantages over GaAs-based THz-QCLs. Weaker longitudinal optical phonon–electron interaction in GaSb produces higher peaks in the spectral functions of the lasing levels, which enables more electrons to be accumulated in the upper lasing level.

  10. Hierarchical condensation near phase equilibrium

    NASA Astrophysics Data System (ADS)

    Olemskoi, A. I.; Yushchenko, O. V.; Borisyuk, V. N.; Zhilenko, T. I.; Kosminska, Yu. O.; Perekrestov, V. I.

    2012-06-01

    A novel mechanism of new phase formation is studied both experimentally and theoretically in the example of quasi-equilibrium stationary condensation in an ion-plasma sputterer. Copper condensates are obtained to demonstrate that a specific network structure is formed as a result of self-assembly in the course of deposition. The fractal pattern related is inherent in the phenomena of diffusion limited aggregation. Condensate nuclei are shown to form statistical ensemble of hierarchically subordinated objects distributed in ultrametric space. The Langevin equation and the Fokker-Planck equation related are found to describe stationary distribution of thermodynamic potential variations at condensation. Time dependence of the formation probability of branching structures is found to clarify the experimental situation.

  11. Synthesis, structure and study of azo-hydrazone tautomeric equilibrium of 1,3-dimethyl-5-(arylazo)-6-amino-uracil derivatives

    NASA Astrophysics Data System (ADS)

    Debnath, Diptanu; Roy, Subhadip; Li, Bing-Han; Lin, Chia-Her; Misra, Tarun Kumar

    2015-04-01

    Azo dyes, 1,3-dimethyl-5-(arylazo)-6-aminouracil (aryl = -C6H5 (1), -p-CH3C6H4 (2), -p-ClC6H4 (3), -p-NO2C6H4 (4)) were prepared and characterized by UV-vis, FT-IR, 1H NMR, 13C NMR spectroscopic techniques and single crystal X-ray crystallographic analysis. In the light of spectroscopic analysis it evidences that of the tautomeric forms, the azo-enamine-keto (A) form is the predominant form in the solid state whereas in different solvents it is the hydrazone-imine-keto (B) form. The study also reveals that the hydrazone-imine-keto (B) form exists in an equilibrium mixture with its anionic form in various organic solvents. The solvatochromic and photophysical properties of the dyes in various solvents with different hydrogen bonding parameter were investigated. The dyes exhibit positive solvatochromic property on moving from polar protic to polar aprotic solvents. They are fluorescent active molecules and exhibit high intense fluorescent peak in some solvents like DMSO and DMF. It has been demonstrated that the anionic form of the hydrazone-imine form is responsible for the high intense fluorescent peak. In addition, the acid-base equilibrium in between neutral and anionic form of hydrazone-imine form in buffer solution of varying pH was investigated and evaluated the pKa values of the dyes by making the use of UV-vis spectroscopic methods. The determined acid dissociation constant (pKa) values increase according to the sequence of 2 > 1 > 3 > 4.

  12. Accurate electron affinity of Co and fine-structure splittings of C o- via slow-electron velocity-map imaging

    NASA Astrophysics Data System (ADS)

    Chen, Xiaolin; Ning, Chuangang

    2016-05-01

    The high-resolution photoelectron spectra of C o- were obtained via the slow-electron velocity-map imaging method. The electron affinity of cobalt element was determined to be 5341.45 (37 ) c m-1 or 662.256(46) meV. The fine structure of C o- was well resolved. The fine-structure intervals C o-(F34) -C o-(F33) and C o-(F34) -C o-(F32) were found to be 920.9 (6 ) c m-1 and 1550.3 (9 ) c m-1 , respectively. The accuracy was improved by a factor of more than ten with respect to the previous laser photodetachment threshold measurement.

  13. Scaling up the Single Transducer Thickness-Independent Ultrasonic Imaging Method for Accurate Characterization of Microstructural Gradients in Monolithic and Composite Tubular Structures

    NASA Technical Reports Server (NTRS)

    Roth, Don J.; Carney, Dorothy V.; Baaklini, George Y.; Bodis, James R.; Rauser, Richard W.

    1998-01-01

    Ultrasonic velocity/time-of-flight imaging that uses back surface reflections to gauge volumetric material quality is highly suited for quantitative characterization of microstructural gradients including those due to pore fraction, density, fiber fraction, and chemical composition variations. However, a weakness of conventional pulse-echo ultrasonic velocity/time-of-flight imaging is that the image shows the effects of thickness as well as microstructural variations unless the part is uniformly thick. This limits this imaging method's usefulness in practical applications. Prior studies have described a pulse-echo time-of-flight-based ultrasonic imaging method that requires using a single transducer in combination with a reflector plate placed behind samples that eliminates the effect of thickness variation in the image. In those studies, this method was successful at isolating ultrasonic variations due to material microstructure in plate-like samples of silicon nitride, metal matrix composite, and polymer matrix composite. In this study, the method is engineered for inspection of more complex-shaped structures-those having (hollow) tubular/curved geometry. The experimental inspection technique and results are described as applied to (1) monolithic mullite ceramic and polymer matrix composite 'proof-of-concept' tubular structures that contain machined patches of various depths and (2) as-manufactured monolithic silicon nitride ceramic and silicon carbide/silicon carbide composite tubular structures that might be used in 'real world' applications.

  14. Insights in the electronic structure and redox reaction energy in LiFePO{sub 4} battery material from an accurate Tran-Blaha modified Becke Johnson potential

    SciTech Connect

    Araujo, Rafael B.; Almeida, J. de S; Ferreira da Silva, A.; Ahuja, Rajeev

    2015-09-28

    The main goals of this paper are to investigate the accuracy of the Tran-Blaha modified Becke Johnson (TB-mBJ) potential to predict the electronic structure of lithium iron phosphate and the related redox reaction energy with the lithium deintercalation process. The computed electronic structures show that the TB-mBJ method is able to partially localize Fe-3d electrons in LiFePO{sub 4} and FePO{sub 4} which usually is a problem for the generalized gradient approximation (GGA) due to the self interaction error. The energy band gap is also improved by the TB-mBJ calculations in comparison with the GGA results. It turned out, however, that the redox reaction energy evaluated by the TB-mBJ technique is not in good agreement with the measured one. It is speculated that this disagreement in the computed redox energy and the experimental value is due to the lack of a formal expression to evaluate the exchange and correlation energy. Therefore, the TB-mBJ is an efficient method to improve the prediction of the electronic structures coming form the standard GGA functional in LiFePO{sub 4} and FePO{sub 4}. However, it does not appear to have the same efficiency for evaluating the redox reaction energies for the investigated system.

  15. Insights in the electronic structure and redox reaction energy in LiFePO4 battery material from an accurate Tran-Blaha modified Becke Johnson potential

    NASA Astrophysics Data System (ADS)

    B. Araujo, Rafael; S. de Almeida, J.; Ferreira da Silva, A.; Ahuja, Rajeev

    2015-09-01

    The main goals of this paper are to investigate the accuracy of the Tran-Blaha modified Becke Johnson (TB-mBJ) potential to predict the electronic structure of lithium iron phosphate and the related redox reaction energy with the lithium deintercalation process. The computed electronic structures show that the TB-mBJ method is able to partially localize Fe-3d electrons in LiFePO4 and FePO4 which usually is a problem for the generalized gradient approximation (GGA) due to the self interaction error. The energy band gap is also improved by the TB-mBJ calculations in comparison with the GGA results. It turned out, however, that the redox reaction energy evaluated by the TB-mBJ technique is not in good agreement with the measured one. It is speculated that this disagreement in the computed redox energy and the experimental value is due to the lack of a formal expression to evaluate the exchange and correlation energy. Therefore, the TB-mBJ is an efficient method to improve the prediction of the electronic structures coming form the standard GGA functional in LiFePO4 and FePO4. However, it does not appear to have the same efficiency for evaluating the redox reaction energies for the investigated system.

  16. A Computationally Efficient Algorithm for Aerosol Phase Equilibrium

    SciTech Connect

    Zaveri, Rahul A.; Easter, Richard C.; Peters, Len K.; Wexler, Anthony S.

    2004-10-04

    Three-dimensional models of atmospheric inorganic aerosols need an accurate yet computationally efficient thermodynamic module that is repeatedly used to compute internal aerosol phase state equilibrium. In this paper, we describe the development and evaluation of a computationally efficient numerical solver called MESA (Multicomponent Equilibrium Solver for Aerosols). The unique formulation of MESA allows iteration of all the equilibrium equations simultaneously while maintaining overall mass conservation and electroneutrality in both the solid and liquid phases. MESA is unconditionally stable, shows robust convergence, and typically requires only 10 to 20 single-level iterations (where all activity coefficients and aerosol water content are updated) per internal aerosol phase equilibrium calculation. Accuracy of MESA is comparable to that of the highly accurate Aerosol Inorganics Model (AIM), which uses a rigorous Gibbs free energy minimization approach. Performance evaluation will be presented for a number of complex multicomponent mixtures commonly found in urban and marine tropospheric aerosols.

  17. Accurate prediction of higher-level electronic structure energies for large databases using neural networks, Hartree-Fock energies, and small subsets of the database

    NASA Astrophysics Data System (ADS)

    Malshe, M.; Pukrittayakamee, A.; Raff, L. M.; Hagan, M.; Bukkapatnam, S.; Komanduri, R.

    2009-09-01

    A novel method is presented that significantly reduces the computational bottleneck of executing high-level, electronic structure calculations of the energies and their gradients for a large database that adequately samples the configuration space of importance for systems containing more than four atoms that are undergoing multiple, simultaneous reactions in several energetically open channels. The basis of the method is the high-degree of correlation that generally exists between the Hartree-Fock (HF) and higher-level electronic structure energies. It is shown that if the input vector to a neural network (NN) includes both the configuration coordinates and the HF energies of a small subset of the database, MP4(SDQ) energies with the same basis set can be predicted for the entire database using only the HF and MP4(SDQ) energies for the small subset and the HF energies for the remainder of the database. The predictive error is shown to be less than or equal to the NN fitting error if a NN is fitted to the entire database of higher-level electronic structure energies. The general method is applied to the computation of MP4(SDQ) energies of 68 308 configurations that comprise the database for the simultaneous, unimolecular decomposition of vinyl bromide into six different reaction channels. The predictive accuracy of the method is investigated by employing successively smaller subsets of the database to train the NN to predict the MP4(SDQ) energies of the remaining configurations of the database. The results indicate that for this system, the subset can be as small as 8% of the total number of configurations in the database without loss of accuracy beyond that expected if a NN is employed to fit the higher-level energies for the entire database. The utilization of this procedure is shown to save about 78% of the total computational time required for the execution of the MP4(SDQ) calculations. The sampling error involved with selection of the subset is shown to be

  18. A new 3D grid method for accurate electronic structure calculation of polyatomic molecules: The Voronoi-cell finite difference method

    NASA Astrophysics Data System (ADS)

    Son, Sang-Kil; Chu, Shih-I.

    2008-05-01

    We introduce a new computational method on unstructured grids in the three-dimensional (3D) spaces to investigate the electronic structure of polyatomic molecules. The Voronoi-cell finite difference (VFD) method realizes a simple discrete Laplacian operator on unstructured grids based on Voronoi cells and their natural neighbors. The feature of unstructured grids enables us to choose intuitive pictures for an optimal molecular grid system. The new VFD method achieves highly adaptability by the Voronoi-cell diagram and yet simplicity by the finite difference scheme. It has no limitation in local refinement of grids in the vicinity of nuclear positions and provides an explicit expression at each grid without any integration. This method augmented by unstructured molecular grids is suitable for solving the Schr"odinger equation with the realistic 3D Coulomb potentials regardless of symmetry of molecules. For numerical examples, we test accuracies for electronic structures of one-electron polyatomic systems: linear H2^+ and triangular H3^++. We also extend VFD to the density functional theory (DFT) for many-electron polyatomic molecules.

  19. Precise and Accurate Density Determination of Explosives Using Hydrostatic Weighing

    SciTech Connect

    B. Olinger

    2005-07-01

    Precise and accurate density determination requires weight measurements in air and water using sufficiently precise analytical balances, knowledge of the densities of air and water, knowledge of thermal expansions, availability of a density standard, and a method to estimate the time to achieve thermal equilibrium with water. Density distributions in pressed explosives are inferred from the densities of elements from a central slice.

  20. Non-equilibrium phase transitions

    SciTech Connect

    Mottola, E.; Cooper, F.M.; Bishop, A.R.; Habib, S.; Kluger, Y.; Jensen, N.G.

    1998-12-31

    This is the final report of a one-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). Non-equilibrium phase transitions play a central role in a very broad range of scientific areas, ranging from nuclear, particle, and astrophysics to condensed matter physics and the material and biological sciences. The aim of this project was to explore the path to a deeper and more fundamental understanding of the common physical principles underlying the complex real time dynamics of phase transitions. The main emphasis was on the development of general theoretical tools to deal with non-equilibrium processes, and of numerical methods robust enough to capture the time-evolving structures that occur in actual experimental situations. Specific applications to Laboratory multidivisional efforts in relativistic heavy-ion physics (transition to a new phase of nuclear matter consisting of a quark-gluon plasma) and layered high-temperature superconductors (critical currents and flux flow at the National High Magnetic Field Laboratory) were undertaken.

  1. A more accurate relocation of the 2013 M s7.0 Lushan, Sichuan, China, earthquake sequence, and the seismogenic structure analysis

    NASA Astrophysics Data System (ADS)

    Long, F.; Wen, X. Z.; Ruan, X.; Zhao, M.; Yi, G. X.

    2015-07-01

    We use a combined earthquake location technique to relocate the M s7.0 Lushan, Sichuan, China, earthquake sequence of April 20, 2013. A stepwise approach, employing three existing location methods (the HYPOINVERSE method, the Minimum 1-D model, and the Double Difference method), is used to improve location precision by iteratively revising the velocity model station corrections, and hypocenter relocations throughout the process. Our stepwise approach has significantly improved the location precision of the Lushan earthquake sequence, yielding hypocenter locations with final errors of 359, 309, and 605 m in the E-W, N-S, and vertical directions, respectively, with average travel time residuals of 0.12 s. Furthermore, we analyzed the seismogenic structure surrounding the Lushan earthquake sequence by combining the results of the relocated hypocenter distribution with new focal mechanism solutions and information from regional geological and geophysical investigations. From our analysis, we conclude that the vast majority of the aftershocks of the Lushan earthquake sequence occurred at depths of 6-9 km, near the front of the southwestern segment of the NE-trending Longmenshan fault zone. Densely aligned hypocenters clearly suggest that the seismogenic structure of the mainshock consists of a set of basal thrust faults dipping to the NW at 40-50°, at a ramp of the deep basal décollement-thrust system at depths of 7-18 km. Focal mechanism solutions suggest that the seismogenic faults have produced almost pure thrusting. At least one SE-dipping back-thrust is also observed within the basement, as indicated by the hypocenter relocations, which points to either a secondary rupture plane during the mainshock or a plane of aftershock slips. A small number of minor events in the Lushan sequence are located at depths of 0-6 km, with a distribution suggesting that the three NE-trending faults with surface traces running through or passing close to the aftershock area are

  2. The Devil is in the Details: Using X-Ray Computed Tomography to Develop Accurate 3D Grain Characteristics and Bed Structure Metrics for Gravel Bed Rivers

    NASA Astrophysics Data System (ADS)

    Voepel, H.; Hodge, R. A.; Leyland, J.; Sear, D. A.; Ahmed, S. I.

    2014-12-01

    Uncertainty for bedload estimates in gravel bed rivers is largely driven by our inability to characterize the arrangement and orientation of the sediment grains within the bed. The characteristics of the surface structure are produced by the water working of grains, which leads to structural differences in bedforms through differential patterns of grain sorting, packing, imbrication, mortaring and degree of bed armoring. Until recently the technical and logistical difficulties of characterizing the arrangement of sediment in 3D have prohibited a full understanding of how grains interact with stream flow and the feedback mechanisms that exist. Micro-focus X-ray CT has been used for non-destructive 3D imaging of grains within a series of intact sections of river bed taken from key morphological units (see Figure 1). Volume, center of mass, points of contact, protrusion and spatial orientation of individual surface grains are derived from these 3D images, which in turn, facilitates estimates of 3D static force properties at the grain-scale such as pivoting angles, buoyancy and gravity forces, and grain exposure. By aggregating representative samples of grain-scale properties of localized interacting sediment into overall metrics, we can compare and contrast bed stability at a macro-scale with respect to stream bed morphology. Understanding differences in bed stability through representative metrics derived at the grain-scale will ultimately lead to improved bedload estimates with reduced uncertainty and increased understanding of interactions between grain-scale properties on channel morphology. Figure 1. CT-Scans of a water worked gravel-filled pot. a. 3D rendered scan showing the outer mesh, and b. the same pot with the mesh removed. c. vertical change in porosity of the gravels sampled in 5mm volumes. Values are typical of those measured in the field and lab. d. 2-D slices through the gravels at 20% depth from surface (porosity = 0.35), and e. 75% depth from

  3. Band-structure calculations of noble-gas and alkali halide solids using accurate Kohn-Sham potentials with self-interaction correction

    SciTech Connect

    Li, Y.; Krieger, J.B. ); Norman, M.R. ); Iafrate, G.J. )

    1991-11-15

    The optimized-effective-potential (OEP) method and a method developed recently by Krieger, Li, and Iafrate (KLI) are applied to the band-structure calculations of noble-gas and alkali halide solids employing the self-interaction-corrected (SIC) local-spin-density (LSD) approximation for the exchange-correlation energy functional. The resulting band gaps from both calculations are found to be in fair agreement with the experimental values. The discrepancies are typically within a few percent with results that are nearly the same as those of previously published orbital-dependent multipotential SIC calculations, whereas the LSD results underestimate the band gaps by as much as 40%. As in the LSD---and it is believed to be the case even for the exact Kohn-Sham potential---both the OEP and KLI predict valence-band widths which are narrower than those of experiment. In all cases, the KLI method yields essentially the same results as the OEP.

  4. A Progression of Static Equilibrium Laboratory Exercises

    ERIC Educational Resources Information Center

    Kutzner, Mickey; Kutzner, Andrew

    2013-01-01

    Although simple architectural structures like bridges, catwalks, cantilevers, and Stonehenge have been integral in human societies for millennia, as have levers and other simple tools, modern students of introductory physics continue to grapple with Newton's conditions for static equilibrium. As formulated in typical introductory physics…

  5. Abrupt PN junctions: Analytical solutions under equilibrium and non-equilibrium

    NASA Astrophysics Data System (ADS)

    Khorasani, Sina

    2016-08-01

    We present an explicit solution of carrier and field distributions in abrupt PN junctions under equilibrium. An accurate logarithmic numerical method is implemented and results are compared to the analytical solutions. Analysis of results shows reasonable agreement with numerical solution as well as the depletion layer approximation. We discuss extensions to the asymmetric junctions. Approximate relations for differential capacitance C-V and current-voltage I-V characteristics are also found under non-zero external bias.

  6. Non-equilibrium DMFT - Polaritonics

    NASA Astrophysics Data System (ADS)

    Lubatsch, Andreas; Frank, Regine

    Non-equilibrium physics recently really becomes important with the progress of ultrafast laser sciences. However in our understanding there is still a gap between equilibrium physics and the non-equilibrium, even though numerical methods have been advanced in recent years. We compare in this talk novel results at hand with equilibrium physics. The comparison will show that especially theoretical efforts are needed to explain many - so far - unresolved problems and to predict novel research on the basis of ab initio computing. We specifically discuss several non-equilibrium extensions of DMFT, numerical methods as well as semi-analytical solvers.

  7. Thermal equilibrium of goats.

    PubMed

    Maia, Alex S C; Nascimento, Sheila T; Nascimento, Carolina C N; Gebremedhin, Kifle G

    2016-05-01

    The effects of air temperature and relative humidity on thermal equilibrium of goats in a tropical region was evaluated. Nine non-pregnant Anglo Nubian nanny goats were used in the study. An indirect calorimeter was designed and developed to measure oxygen consumption, carbon dioxide production, methane production and water vapour pressure of the air exhaled from goats. Physiological parameters: rectal temperature, skin temperature, hair-coat temperature, expired air temperature and respiratory rate and volume as well as environmental parameters: air temperature, relative humidity and mean radiant temperature were measured. The results show that respiratory and volume rates and latent heat loss did not change significantly for air temperature between 22 and 26°C. In this temperature range, metabolic heat was lost mainly by convection and long-wave radiation. For temperature greater than 30°C, the goats maintained thermal equilibrium mainly by evaporative heat loss. At the higher air temperature, the respiratory and ventilation rates as well as body temperatures were significantly elevated. It can be concluded that for Anglo Nubian goats, the upper limit of air temperature for comfort is around 26°C when the goats are protected from direct solar radiation. PMID:27157333

  8. The Effect of the N-Terminus on Heme Cavity Structure, Ligand Equilibrium and Rate Constants and Reduction Potentials of Nitrophorin 2 from Rhodnius prolixus†

    PubMed Central

    Berry, Robert E.; Shokhireva, Tatiana Kh.; Filippov, Igor; Shokhirev, Maxim N.; Zhang, Hongjun; Walker, F. Ann

    2008-01-01

    The D1A mutant of recombinant NP2 has been prepared and shown to have the expression-initiation methionine-0 cleaved during expression in E. coli, as is the case for recombinant NP4, where Ala is the first amino acid for the recombinant protein, as well as for the mature native protein. The heme substituent 1H NMR chemical shifts of NP2-D1A and those of its imidazole, N-methylimidazole and cyanide complexes are rather different from those of NP2-M0D1. This difference is likely due to the much smaller size of the N-terminal amino acid (A) of NP2-D1A, which allows formation of the closed loop form of this protein, as it does for NP4 (Weichsel, A.; Andersen, J. F.; Roberts, S. A.; Montfort, W. R Nature Struct. Biol. 2000, 7, 551-554). The ratio of the two hemin rotational isomers A and B is different for the two proteins, and the rate at which the A:B ratio reaches equilibrium is strikingly different (NP2-M0D1 t1/2 for heme rotation ∼2 h, NP2-D1A t1/2 ∼43 h). This difference is consistent with a high stability of the closed loop form of the NP2-D1A protein, and infrequent opening of the loops that could allow heme to at least partially exit the binding pocket in order to rotate about its α,γ-meso axis. Consistent with this, the rates of histamine binding and release to/from NP2-D1A are significantly slower than for NP2-M0D1 at pH 7.5. This work suggests that care must be taken in interpreting data obtained from proteins that carry the expression-initiation M0. PMID:17506528

  9. Planetary cratering 2: Studies of saturation equilibrium

    NASA Astrophysics Data System (ADS)

    Hartmann, William K.; Gaskell, Robert W.

    1997-01-01

    A realistic computer model has been developed to display images of imaginary cratered surfaces, taking into account empirically measured input size distributions of primary and secondary craters, ejecta blanket morphology including feathering with distance, obliteration due to ejecta from outside the imaged area, lighting effects, etc. The model allows us to track surface evolution of morphology as new craters are added. Using the model as well as lunar photos, we have studied the approach to saturation equilibrium (defined as a condition when no further proportionate increase in crater density occurs as input cratering increases). We find that an identifiable saturation equilibrium occurs close to a level previously identified for this state (Hartmann 1984), typically fluctuating around a crater density from about 0.4 to 2 times that level. This result is fairly robust vis-a-vis the range of model parameters we have chosen. Flooding, basin ejecta blankets, and other obliterative effects can introduce structure and oscillations within this range, even after saturation equilibrium is achieved. These findings may constrain or revise certain earlier interpretations of satellite and planet surface evolution and impactor populations which were predicated on the assumed absence of saturation equilibrium. In our fourth experimental run, we found that suppression of "sandblasting" by sub-resolution impacts allows the smallest secondaries to rise above the saturation equilibrium line, a result that might be relevant to a similar situation on Gaspra and perhaps some other asteroids.

  10. Adaptive Implicit Non-Equilibrium Radiation Diffusion

    SciTech Connect

    Philip, Bobby; Wang, Zhen; Berrill, Mark A; Rodriguez Rodriguez, Manuel; Pernice, Michael

    2013-01-01

    We describe methods for accurate and efficient long term time integra- tion of non-equilibrium radiation diffusion systems: implicit time integration for effi- cient long term time integration of stiff multiphysics systems, local control theory based step size control to minimize the required global number of time steps while control- ling accuracy, dynamic 3D adaptive mesh refinement (AMR) to minimize memory and computational costs, Jacobian Free Newton-Krylov methods on AMR grids for efficient nonlinear solution, and optimal multilevel preconditioner components that provide level independent solver convergence.

  11. Internal Dynamics of Equilibrium Colloidal Clusters

    NASA Astrophysics Data System (ADS)

    Perry, Rebecca Wood

    interactions. We find that the interactions allow for control over the intracluster placement of each species, while the masses have no influence. To provide a theoretical framework for understanding these observations, we derive the classical partition function of colloidal clusters in terms of translational, rotational, and vibrational degrees of freedom. We show that the masses of the particles enter the partition function through the kinetic energy but have no effect on the probabilities of states that differ only in where the masses are placed. This result is consistent with our experiments. Overall, this work shows that the equilibrium distribution of self-assembled colloidal clusters is well-modeled by classical statistical physics, and that the rearrangement dynamics of colloidal clusters can be understood by incorporating diffusion and the effect of the interaction potential. Because both the structures and dynamics can be accurately predicted, these clusters are a promising system for self-assembling novel materials and for studying the emergence of phase transitions.

  12. Complexation of Ln(3+) Ions with Cyclam Dipicolinates: A Small Bridge that Makes Huge Differences in Structure, Equilibrium, and Kinetic Properties.

    PubMed

    Rodríguez-Rodríguez, Aurora; Regueiro-Figueroa, Martín; Esteban-Gómez, David; Tripier, Raphaël; Tircsó, Gyula; Kálmán, Ferenc Krisztián; Bényei, Attila Csaba; Tóth, Imre; de Blas, Andrés; Rodríguez-Blas, Teresa; Platas-Iglesias, Carlos

    2016-03-01

    The coordination properties toward the lanthanide ions of two macrocyclic ligands based on a cyclam platform containing picolinate pendant arms have been investigated. The synthesis of the ligands was achieved by using the well-known bis-aminal chemistry. One of the cyclam derivatives (cb-tedpa(2-)) is reinforced with a cross-bridge unit, which results in exceptionally inert [Ln(cb-tedpa)](+) complexes. The X-ray structures of the [La(cb-tedpa)Cl], [Gd(cb-tedpa)](+), and [Lu(Me2tedpa)](+) complexes indicate octadentate binding of the ligands to the metal ions. The analysis of the Yb(3+)-induced shifts in [Yb(Me2tedpa)](+) indicates that this complex presents a solution structure very similar to that observed in the solid state for the Lu(3+) analogue. The X-ray structures of [La(H2Me2tedpa)2](3+) and [Yb(H2Me2tedpa)2](3+) complexes confirm the exocyclic coordination of the metal ions, which gives rise to coordination polymers with the metal coordination environment being fulfilled by oxygen atoms of the picolinate groups and water molecules. The X-ray structure of [Gd(Hcb-tedpa)2](+) also indicates exocyclic coordination that in this case results in a discrete structure with an eight-coordinated metal ion. The nonreinforced complexes [Ln(Me2tedpa)](+) were prepared and isolated as chloride salts in nonaqueous media. However, these complexes were found to undergo dissociation in aqueous solution, except in the case of the complexes with the smallest Ln(3+) ions (Ln(3+) = Yb(3+) and Lu(3+)). A DFT investigation shows that the increased stability of the [Ln(Me2tedpa)](+) complexes in solution across the lanthanide series is the result of an increased binding energy of the ligand due to the increased charge density of the Ln(3+) ion. PMID:26878271

  13. The Nash equilibrium: a perspective.

    PubMed

    Holt, Charles A; Roth, Alvin E

    2004-03-23

    In 1950, John Nash contributed a remarkable one-page PNAS article that defined and characterized a notion of equilibrium for n- person games. This notion, now called the "Nash equilibrium," has been widely applied and adapted in economics and other behavioral sciences. Indeed, game theory, with the Nash equilibrium as its centerpiece, is becoming the most prominent unifying theory of social science. In this perspective, we summarize the historical context and subsequent impact of Nash's contribution. PMID:15024100

  14. Grinding kinetics and equilibrium states

    NASA Technical Reports Server (NTRS)

    Opoczky, L.; Farnady, F.

    1984-01-01

    The temporary and permanent equilibrium occurring during the initial stage of cement grinding does not indicate the end of comminution, but rather an increased energy consumption during grinding. The constant dynamic equilibrium occurs after a long grinding period indicating the end of comminution for a given particle size. Grinding equilibrium curves can be constructed to show the stages of comminution and agglomeration for certain particle sizes.

  15. Understanding water content data in cottons equilibrated to moisture equilibrium

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The accurate measurement of moisture in cottons conditioned to moisture equilibrium and understanding the data are prerequisites to the development of applications of the data. In this study, moisture is measured by Karl Fischer Titration, which is highly selective for water in cotton; the results ...

  16. Napoleon Is in Equilibrium

    PubMed Central

    Phillips, Rob

    2016-01-01

    It has been said that the cell is the test tube of the twenty-first century. If so, the theoretical tools needed to quantitatively and predictively describe what goes on in such test tubes lag sorely behind the stunning experimental advances in biology seen in the decades since the molecular biology revolution began. Perhaps surprisingly, one of the theoretical tools that has been used with great success on problems ranging from how cells communicate with their environment and each other to the nature of the organization of proteins and lipids within the cell membrane is statistical mechanics. A knee-jerk reaction to the use of statistical mechanics in the description of cellular processes is that living organisms are so far from equilibrium that one has no business even thinking about it. But such reactions are probably too hasty given that there are many regimes in which, because of a separation of timescales, for example, such an approach can be a useful first step. In this article, we explore the power of statistical mechanical thinking in the biological setting, with special emphasis on cell signaling and regulation. We show how such models are used to make predictions and describe some recent experiments designed to test them. We also consider the limits of such models based on the relative timescales of the processes of interest. PMID:27429713

  17. Napoleon Is in Equilibrium

    NASA Astrophysics Data System (ADS)

    Phillips, Rob

    2015-03-01

    It has been said that the cell is the test tube of the twenty-first century. If so, the theoretical tools needed to quantitatively and predictively describe what goes on in such test tubes lag sorely behind the stunning experimental advances in biology seen in the decades since the molecular biology revolution began. Perhaps surprisingly, one of the theoretical tools that has been used with great success on problems ranging from how cells communicate with their environment and each other to the nature of the organization of proteins and lipids within the cell membrane is statistical mechanics. A knee-jerk reaction to the use of statistical mechanics in the description of cellular processes is that living organisms are so far from equilibrium that one has no business even thinking about it. But such reactions are probably too hasty given that there are many regimes in which, because of a separation of timescales, for example, such an approach can be a useful first step. In this article, we explore the power of statistical mechanical thinking in the biological setting, with special emphasis on cell signaling and regulation. We show how such models are used to make predictions and describe some recent experiments designed to test them. We also consider the limits of such models based on the relative timescales of the processes of interest.

  18. Accurate ab Initio Spin Densities

    PubMed Central

    2012-01-01

    We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as a basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys.2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CASCI-type wave function provides insight into chemically interesting features of the molecule under study such as the distribution of α and β electrons in terms of Slater determinants, CI coefficients, and natural orbitals. The methodology is applied to an iron nitrosyl complex which we have identified as a challenging system for standard approaches [J. Chem. Theory Comput.2011, 7, 2740]. PMID:22707921

  19. Rapid-Equilibrium Enzyme Kinetics

    ERIC Educational Resources Information Center

    Alberty, Robert A.

    2008-01-01

    Rapid-equilibrium rate equations for enzyme-catalyzed reactions are especially useful because if experimental data can be fit by these simpler rate equations, the Michaelis constants can be interpreted as equilibrium constants. However, for some reactions it is necessary to use the more complicated steady-state rate equations. Thermodynamics is…

  20. Trunk biomechanical models based on equilibrium at a single-level violate equilibrium at other levels.

    PubMed

    Arjmand, N; Shirazi-Adl, A; Parnianpour, M

    2007-05-01

    Accurate estimation of muscle forces in various occupational tasks is critical for a reliable evaluation of spinal loads and subsequent assessment of risk of injury and management of back disorders. The majority of biomechanical models of multi-segmental spine estimate muscle forces and spinal loads based on the balance of net moments at a single level with no consideration for the equilibrium at remaining levels. This work aimed to quantify the extent of equilibrium violation and alterations in estimations when such models are performed at different levels. Results are compared with those of kinematics-driven model that satisfies equilibrium at all levels and EMG data. Regardless of the method used (optimization or EMG-assisted), single-level free body diagram models yielded estimations that substantially altered depending on the level considered (i.e., level dependency). Equilibrium of net moment was also grossly violated at remaining levels with the error increasing in more demanding tasks. These models may, however, be used to estimate spinal compression forces. PMID:17136359

  1. Glyphosate complexation to aluminium(III). An equilibrium and structural study in solution using potentiometry, multinuclear NMR, ATR-FTIR, ESI-MS and DFT calculations.

    PubMed

    Purgel, Mihály; Takács, Zoltán; Jonsson, Caroline M; Nagy, Lajos; Andersson, Ingegärd; Bányai, István; Pápai, Imre; Persson, Per; Sjöberg, Staffan; Tóth, Imre

    2009-11-01

    The stoichiometries and stability constants of a series of Al(3+)-N-phosponomethyl glycine (PMG/H(3)L) complexes have been determined in acidic aqueous solution using a combination of precise potentiometric titration data, quantitative (27)Al and (31)P NMR spectra, ATR-FTIR spectrum and ESI-MS measurements (0.6M NaCl, 25 degrees C). Besides the mononuclear AlH(2)L(2+), Al(H(2)L)(HL), Al(HL)(2)(-) and Al(HL)L(2-), dimeric Al(2)(HL)L(+) and trinuclear Al(3)H(5)L(4)(2+) complexes have been postulated. (1)H and (31)P NMR data show that different isomers co-exist in solution and the isomerization reactions are slow on the (31)P NMR time scale. The geometries of monomeric and dimeric complexes likely double hydroxo bridged and double phosphonate bridged isomers have been optimized using DFT ab initio calculations starting from rational structural proposals. Energy calculations using the PCM solvation method also support the co-existence of isomers in solutions. PMID:19766319

  2. Automated method for determination of dissolved organic carbon-water distribution constants of structurally diverse pollutants using pre-equilibrium solid-phase microextraction.

    PubMed

    Ripszam, Matyas; Haglund, Peter

    2015-02-01

    Dissolved organic carbon (DOC) plays a key role in determining the environmental fate of semivolatile organic environmental contaminants. The goal of the present study was to develop a method using commercially available hardware to rapidly characterize the sorption properties of DOC in water samples. The resulting method uses negligible-depletion direct immersion solid-phase microextraction (SPME) and gas chromatography-mass spectrometry. Its performance was evaluated using Nordic reference fulvic acid and 40 priority environmental contaminants that cover a wide range of physicochemical properties. Two SPME fibers had to be used to cope with the span of properties, 1 coated with polydimethylsiloxane and 1 coated with polystyrene divinylbenzene polydimethylsiloxane, for nonpolar and semipolar contaminants, respectively. The measured DOC-water distribution constants showed reasonably good reproducibility (standard deviation ≤ 0.32) and good correlation (R(2)  = 0.80) with log octanol-water partition coefficients for nonpolar persistent organic pollutants. The sample pretreatment is limited to filtration, and the method is easy to adjust to different DOC concentrations. These experiments also utilized the latest SPME automation that largely decreases total cycle time (to 20 min or shorter) and increases sample throughput, which is advantageous in cases when many samples of DOC must be characterized or when the determinations must be performed quickly, for example, to avoid precipitation, aggregation, and other changes of DOC structure and properties. The data generated by this method are valuable as a basis for transport and fate modeling studies. PMID:25393710

  3. Is Soret equilibrium a non-equilibrium effect?

    NASA Astrophysics Data System (ADS)

    Würger, Alois

    2013-04-01

    Recent thermophoretic experiments on colloidal suspensions revived an old debate, namely whether the Soret effect is properly described by thermostatics, or necessarily requires non-equilibrium thermodynamics. Based on colloidal transport theory and the entropy production of the related viscous flow, our analysis leads to the conclusion that the equilibrium approach may work for small ions, yet fails for colloidal particles and polymers. Regarding binary molecular mixtures, our results shed some doubt on the validity of thermostatic approaches that derive the Soret coefficient from equilibrium potentials.

  4. Structural (EXAFS) and solution equilibrium studies on the oxotechnetium(V) complexes TcOX/sub 4//sup -/ and TcOX/sub 5//sup 2 -/ (X = Cl, Br)

    SciTech Connect

    Thomas, R.W.; Heeg, M.J.; Elder, R.C.; Deutsch, E.

    1985-05-08

    The equilibrium between the technetium(V) complexes TcOCl/sub 4//sup -/ and TcOCl/sub 5//sup 2 -/ has been investigated in 12 M HCl and in CH/sub 2/Cl/sub 2/ solutions by Raman spectroscopy. In both media the five-coordinate complex is the predominant species, but in the aqueous medium water competes for the sixth coordination site and causes formation of the six-coordinate TcOCl/sub 5//sup 2 -/ anion to be even less favorable. Rate constants for the reaction are given. Procedures are described for generating good yields of either TcOX/sub 4//sup -/ or TcOX/sub 5//sup 2 -/ (X = Cl, Br) salts from the same reaction mixture. The complexes TcOCl/sub 4//sup -/, TcOCl/sub 5//sup 2 -/, TcOBr/sub 4//sup -/, TcOBr/sub 5//sup 2 -/, and TcI/sub 6//sup 2 -/ have been structurally characterized by EXAFS techniques. Observed Tc=O and Tc-X bond lengths are consistent with the known dependence of bond length on coordination number, the established structural trans effect induced by the Tc=O linkage, and existing crystallographic data on TcOCl/sub 4//sup -/ and related molybdenum(V) complexes.

  5. A Quasi-Equilibrium Tropical Circulation Model--Formulation*.

    NASA Astrophysics Data System (ADS)

    Neelin, J. David; Zeng, Ning

    2000-06-01

    A class of model for simulation and theory of the tropical atmospheric component of climate variations is introduced. These models are referred to as quasi-equilibrium tropical circulation models, or QTCMs, because they make use of approximations associated with quasi-equilibrium (QE) convective parameterizations. Quasi-equilibrium convective closures tend to constrain the vertical temperature profile in convecting regions. This can be used to generate analytical solutions for the large-scale flow under certain approximations. A tropical atmospheric model of intermediate complexity is constructed by using the analytical solutions as the first basis function in a Galerkin representation of vertical structure. This retains much of the simplicity of the analytical solutions, while retaining full nonlinearity, vertical momentum transport, departures from QE, and a transition between convective and nonconvective zones based on convective available potential energy. The atmospheric model is coupled to a one-layer land surface model with interactive soil moisture and simulates its own tropical climatology. In the QTCM version presented here, the vertical structure of temperature variations is truncated to a single profile associated with deep convection. Though designed to be accurate in and near regions dominated by deep convection, the model simulates the tropical and subtropical climatology reasonably well, and even has a qualitative representation of midlatitude storm tracks.The model is computationally economical, since part of the solution has been carried out analytically, but the main advantage is relative simplicity of analysis under certain conditions. The formulation suggests a slightly different way of looking at the tropical atmosphere than has been traditional in tropical meteorology. While convective scales are unstable, the large-scale motions evolve with a positive effective stratification that takes into account the partial cancellation of adiabatic

  6. NNLOPS accurate associated HW production

    NASA Astrophysics Data System (ADS)

    Astill, William; Bizon, Wojciech; Re, Emanuele; Zanderighi, Giulia

    2016-06-01

    We present a next-to-next-to-leading order accurate description of associated HW production consistently matched to a parton shower. The method is based on reweighting events obtained with the HW plus one jet NLO accurate calculation implemented in POWHEG, extended with the MiNLO procedure, to reproduce NNLO accurate Born distributions. Since the Born kinematics is more complex than the cases treated before, we use a parametrization of the Collins-Soper angles to reduce the number of variables required for the reweighting. We present phenomenological results at 13 TeV, with cuts suggested by the Higgs Cross section Working Group.

  7. Helical axis stellarator equilibrium model

    SciTech Connect

    Koniges, A.E.; Johnson, J.L.

    1985-02-01

    An asymptotic model is developed to study MHD equilibria in toroidal systems with a helical magnetic axis. Using a characteristic coordinate system based on the vacuum field lines, the equilibrium problem is reduced to a two-dimensional generalized partial differential equation of the Grad-Shafranov type. A stellarator-expansion free-boundary equilibrium code is modified to solve the helical-axis equations. The expansion model is used to predict the equilibrium properties of Asperators NP-3 and NP-4. Numerically determined flux surfaces, magnetic well, transform, and shear are presented. The equilibria show a toroidal Shafranov shift.

  8. Understanding thermal equilibrium through activities

    NASA Astrophysics Data System (ADS)

    Pathare, Shirish; Huli, Saurabhee; Nachane, Madhura; Ladage, Savita; Pradhan, Hemachandra

    2015-03-01

    Thermal equilibrium is a basic concept in thermodynamics. In India, this concept is generally introduced at the first year of undergraduate education in physics and chemistry. In our earlier studies (Pathare and Pradhan 2011 Proc. episteme-4 Int. Conf. to Review Research on Science Technology and Mathematics Education pp 169-72) we found that students in India have a rather unsatisfactory understanding of thermal equilibrium. We have designed and developed a module of five activities, which are presented in succession to the students. These activities address the students’ alternative conceptions that underlie their lack of understanding of thermal equilibrium and aim at enhancing their understanding of the concept.

  9. Averaged equilibrium and stability in low-aspect-ratio stellarators

    SciTech Connect

    Garcia, L.; Carreras, B.A.; Dominguez, N.

    1989-01-01

    The MHD equilibrium and stability calculations or stellarators are complex because of the intrinsic three-dimensional (3-D) character of these configurations. The stellarators expansion simplifies the equilibrium calculation by reducing it to a two-dimensional (2-D) problem. The classical stellarator expansion includes terms up to order epsilon/sup 2/, and the vacuum magnetic field is also included up to this order. For large-aspect-ratio configurations, the results of the stellarator expansion agree well with 3-D numerical equilibrium results. But for low-aspect-ratio configurations, these are significant discrepancies with 3-D equilibrium calculations. The main reason for these discrepancies is the approximation in the vacuum field contributions. This problem can be avoided by applying the average method in a vacuum flux coordinate system. In this way, the exact vacuum magnetic field contribution is included and the results agree well with 3-D equilibrium calculations even for low-aspect-ratio configurations. Using the average method in a vacuum flux coordinate system also permit the accurate calculation of local stability properties with the Mercier criterion. The main improvement is in the accurate calculation of the geodesic curvature term. In this paper, we discuss the application of the average method in flux coordinates to the calculation of the Mercier criterion for low-aspect-ratio stellarator configurations. 12 refs., 3 figs.

  10. Philicities, Fugalities, and Equilibrium Constants.

    PubMed

    Mayr, Herbert; Ofial, Armin R

    2016-05-17

    . Benzhydrylium ions (diarylcarbenium ions) with para- and meta-substituents are used as reference compounds for these investigations, because their Lewis acidities and electrophilicities can be varied by many orders of magnitude, while the steric surroundings of the reaction centers are kept constant. The rate constants for their reactions with nucleophiles correlate linearly over a wide range with the Lewis acidities of the benzhydrylium ions: from slow reactions with late transition states to very fast reactions with early, reactant-like transition states (including reactions which proceed without an enthalpic barrier, ΔH(⧧) = 0). Thus, unequivocal evidence is obtained that even within a series of closely related reactions, the Leffler-Hammond α cannot be a measure for the position of the transition state. Differences in intrinsic barriers lead to deviations from the linear rate-equilibrium correlations and give rise to counterintuitive phenomena. Thus, 1,4-diazabicyclo[2.2.2]octane (DABCO) reacts with lower intrinsic barriers than 4-(dimethylamino)pyridine (DMAP) and, therefore, is a stronger nucleophile as well as a better nucleofuge than DMAP. Common synthetically used SN2 reactions are presented, in which weak nucleophiles replace stronger ones. Whereas solvolysis rates of alkoxy- and alkyl-substituted benzhydryl derivatives correlate linearly with the Lewis acidities of the resulting carbenium ions, this is not the case for amino-substituted benzhydrylium ions, where differences in intrinsic barriers play a major role. The common rule that a structural variation, which increases the electrophilicity of a carbocation at the same time reduces its electrofugality, does not hold any longer. The need to systematically analyze the role of intrinsic barriers is emphasized. PMID:27108991

  11. Stochastic linearization of turbulent dynamics of dispersive waves in equilibrium and non-equilibrium state

    NASA Astrophysics Data System (ADS)

    Jiang, Shixiao W.; Lu, Haihao; Zhou, Douglas; Cai, David

    2016-08-01

    Characterizing dispersive wave turbulence in the long time dynamics is central to understanding of many natural phenomena, e.g., in atmosphere ocean dynamics, nonlinear optics, and plasma physics. Using the β-Fermi–Pasta–Ulam nonlinear system as a prototypical example, we show that in thermal equilibrium and non-equilibrium steady state the turbulent state even in the strongly nonlinear regime possesses an effective linear stochastic structure in renormalized normal variables. In this framework, we can well characterize the spatiotemporal dynamics, which are dominated by long-wavelength renormalized waves. We further demonstrate that the energy flux is nearly saturated by the long-wavelength renormalized waves in non-equilibrium steady state. The scenario of such effective linear stochastic dynamics can be extended to study turbulent states in other nonlinear wave systems.

  12. A versatile phenomenological model for the S-shaped temperature dependence of photoluminescence energy for an accurate determination of the exciton localization energy in bulk and quantum well structures

    NASA Astrophysics Data System (ADS)

    Dixit, V. K.; Porwal, S.; Singh, S. D.; Sharma, T. K.; Ghosh, Sandip; Oak, S. M.

    2014-02-01

    Temperature dependence of the photoluminescence (PL) peak energy of bulk and quantum well (QW) structures is studied by using a new phenomenological model for including the effect of localized states. In general an anomalous S-shaped temperature dependence of the PL peak energy is observed for many materials which is usually associated with the localization of excitons in band-tail states that are formed due to potential fluctuations. Under such conditions, the conventional models of Varshni, Viña and Passler fail to replicate the S-shaped temperature dependence of the PL peak energy and provide inconsistent and unrealistic values of the fitting parameters. The proposed formalism persuasively reproduces the S-shaped temperature dependence of the PL peak energy and provides an accurate determination of the exciton localization energy in bulk and QW structures along with the appropriate values of material parameters. An example of a strained InAs0.38P0.62/InP QW is presented by performing detailed temperature and excitation intensity dependent PL measurements and subsequent in-depth analysis using the proposed model. Versatility of the new formalism is tested on a few other semiconductor materials, e.g. GaN, nanotextured GaN, AlGaN and InGaN, which are known to have a significant contribution from the localized states. A quantitative evaluation of the fractional contribution of the localized states is essential for understanding the temperature dependence of the PL peak energy of bulk and QW well structures having a large contribution of the band-tail states.

  13. Accurate Evaluation of Quantum Integrals

    NASA Technical Reports Server (NTRS)

    Galant, David C.; Goorvitch, D.

    1994-01-01

    Combining an appropriate finite difference method with Richardson's extrapolation results in a simple, highly accurate numerical method for solving a Schr\\"{o}dinger's equation. Important results are that error estimates are provided, and that one can extrapolate expectation values rather than the wavefunctions to obtain highly accurate expectation values. We discuss the eigenvalues, the error growth in repeated Richardson's extrapolation, and show that the expectation values calculated on a crude mesh can be extrapolated to obtain expectation values of high accuracy.

  14. Equilibrium and stability properties of detonation waves in the hydrodynamic limit of a kinetic model

    NASA Astrophysics Data System (ADS)

    Marques, Wilson, Jr.; Jacinta Soares, Ana; Pandolfi Bianchi, Miriam; Kremer, Gilberto M.

    2015-06-01

    A shock wave structure problem, like the one which can be formulated for the planar detonation wave, is analyzed here for a binary mixture of ideal gases undergoing the symmetric reaction {{A}1}+{{A}1}\\rightleftharpoons {{A}2}+{{A}2}. The problem is studied at the hydrodynamic Euler limit of a kinetic model of the reactive Boltzmann equation. The chemical rate law is deduced in this frame with a second-order reaction rate, in a chemical regime such that the gas flow is not far away from the chemical equilibrium. The caloric and the thermal equations of state for the specific internal energy and temperature are employed to close the system of balance laws. With respect to other approaches known in the kinetic literature for detonation problems with a reversible reaction, this paper aims to improve some aspects of the wave solution. Within the mathematical analysis of the detonation model, the equation of the equilibrium Hugoniot curve of the final states is explicitly derived for the first time and used to define the correct location of the equilibrium Chapman-Jouguet point in the Hugoniot diagram. The parametric space is widened to investigate the response of the detonation solution to the activation energy of the chemical reaction. Finally, the mathematical formulation of the linear stability problem is given for the wave detonation structure via a normal-mode approach, when bidimensional disturbances perturb the steady solution. The stability equations with their boundary conditions and the radiation condition of the considered model are explicitly derived for small transversal deviations of the shock wave location. The paper shows how a second-order chemical kinetics description, derived at the microscopic level, and an analytic deduction of the equilibrium Hugoniot curve, lead to an accurate picture of the steady detonation with reversible reaction, as well as to a proper bidimensional linear stability analysis.

  15. Equilibrium Constants You Can Smell.

    ERIC Educational Resources Information Center

    Anderson, Michael; Buckley, Amy

    1996-01-01

    Presents a simple experiment involving the sense of smell that students can accomplish during a lecture. Illustrates the important concepts of equilibrium along with the acid/base properties of various ions. (JRH)

  16. Equilibrium ignition for ICF capsules

    SciTech Connect

    Lackner, K.S.; Colgate, S.A.; Johnson, N.L.; Kirkpatrick, R.C.; Menikoff, R.; Petschek, A.G.

    1993-12-31

    There are two fundamentally different approaches to igniting DT fuel in an ICF capsule which can be described as equilibrium and hot spot ignition. In both cases, a capsule which can be thought of as a pusher containing the DT fuel is imploded until the fuel reaches ignition conditions. In comparing high-gain ICF targets using cryogenic DT for a pusher with equilibrium ignition targets using high-Z pushers which contain the radiation. The authors point to the intrinsic advantages of the latter. Equilibrium or volume ignition sacrifices high gain for lower losses, lower ignition temperature, lower implosion velocity and lower sensitivity of the more robust capsule to small fluctuations and asymmetries in the drive system. The reduction in gain is about a factor of 2.5, which is small enough to make the more robust equilibrium ignition an attractive alternative.

  17. DSMC predictions of non-equilibrium reaction rates.

    SciTech Connect

    Gallis, Michail A.; Bond, Ryan Bomar; Torczynski, John Robert

    2010-04-01

    A set of Direct Simulation Monte Carlo (DSMC) chemical-reaction models recently proposed by Bird and based solely on the collision energy and the vibrational energy levels of the species involved is applied to calculate nonequilibrium chemical-reaction rates for atmospheric reactions in hypersonic flows. The DSMC non-equilibrium model predictions are in good agreement with theoretical models and experimental measurements. The observed agreement provides strong evidence that modeling chemical reactions using only the collision energy and the vibrational energy levels provides an accurate method for predicting non-equilibrium chemical-reaction rates.

  18. Edge equilibrium code for tokamaks

    SciTech Connect

    Li, Xujing; Drozdov, Vladimir V.

    2014-01-15

    The edge equilibrium code (EEC) described in this paper is developed for simulations of the near edge plasma using the finite element method. It solves the Grad-Shafranov equation in toroidal coordinate and uses adaptive grids aligned with magnetic field lines. Hermite finite elements are chosen for the numerical scheme. A fast Newton scheme which is the same as implemented in the equilibrium and stability code (ESC) is applied here to adjust the grids.

  19. A search for equilibrium states

    NASA Technical Reports Server (NTRS)

    Zeleznik, F. J.

    1982-01-01

    An efficient search algorithm is described for the location of equilibrium states in a search set of states which differ from one another only by the choice of pure phases. The algorithm has three important characteristics: (1) it ignores states which have little prospect for being an improved approximation to the true equilibrium state; (2) it avoids states which lead to singular iteration equations; (3) it furnishes a search history which can provide clues to alternative search paths.

  20. Bifurcated helical core equilibrium states in tokamaks

    NASA Astrophysics Data System (ADS)

    Cooper, W. A.; Chapman, I. T.; Schmitz, O.; Turnbull, A. D.; Tobias, B. J.; Lazarus, E. A.; Turco, F.; Lanctot, M. J.; Evans, T. E.; Graves, J. P.; Brunetti, D.; Pfefferlé, D.; Reimerdes, H.; Sauter, O.; Halpern, F. D.; Tran, T. M.; Coda, S.; Duval, B. P.; Labit, B.; Pochelon, A.; Turnyanskiy, M. R.; Lao, L.; Luce, T. C.; Buttery, R.; Ferron, J. R.; Hollmann, E. M.; Petty, C. C.; van Zeeland, M.; Fenstermacher, M. E.; Hanson, J. M.; Lütjens, H.

    2013-07-01

    Tokamaks with weak to moderate reversed central shear in which the minimum inverse rotational transform (safety factor) qmin is in the neighbourhood of unity can trigger bifurcated magnetohydrodynamic equilibrium states, one of which is similar to a saturated ideal internal kink mode. Peaked prescribed pressure profiles reproduce the ‘snake’ structures observed in many tokamaks which has led to a novel explanation of the snake as a bifurcated equilibrium state. Snake equilibrium structures are computed in simulations of the tokamak à configuration variable (TCV), DIII-D and mega amp spherical torus (MAST) tokamaks. The internal helical deformations only weakly modulate the plasma-vacuum interface which is more sensitive to ripple and resonant magnetic perturbations. On the other hand, the external perturbations do not alter the helical core deformation in a significant manner. The confinement of fast particles in MAST simulations deteriorate with the amplitude of the helical core distortion. These three-dimensional bifurcated solutions constitute a paradigm shift that motivates the applications of tools developed for stellarator research in tokamak physics investigations.

  1. Accurate Crystal Structure Refinement of La{sub 3}Ta{sub 0.25}Zr{sub 0.50}Ga{sub 5.25}O{sub 14}

    SciTech Connect

    Dudka, A. P.; Chitra, R.; Choudhury, R. R.; Pisarevsky, Yu. V.; Simonov, V. I.

    2010-11-15

    An accurate X-ray diffraction study of a La{sub 3}Ta{sub 0.25}Zr{sub 0.50}Ga{sub 5.25}O{sub 14} single crystal (a = 8.2574(4) A, c = 5.1465(4) A, sp. gr. P321, Z = 1, R/R{sub w} = 0.62/0.57% for 4144 unique reflections and 91 parameters) has been performed with a simultaneous neutron diffraction analysis. Tantalum, zirconium, and gallium atoms are found to occupy the mixed octahedral position (symmetry 32). Gallium atoms and a few zirconium atoms are in the position on axis 2 in the tetrahedron. The tetrahedral position on axis 3 is completely occupied by gallium atoms, while the large polyhedron on axis 2 is occupied by lanthanum atoms. The high resolution and averaging of the results obtained in two independent X-ray experiments with the same sample provided accu- rate structural data, in particular, on the anharmonicity of thermal atomic vibrations (atomic displacements). The X-ray and neutron diffraction data on the atomic displacements are compared.

  2. Equilibrium and non-equilibrium properties of finite-volume crystallites

    NASA Astrophysics Data System (ADS)

    Degawa, Masashi

    Finite volume effects on equilibrium and non-equilibrium properties of nano-crystallites are studied theoretically and compared to both experiment and simulation. When a system is isolated or its size is small compared to the correlation length, all equilibrium and close-to-equilibrium properties will depend on the system boundary condition. Specifically for solid nano-crystallites, their finite size introduces global curvature to the system, which alters its equilibrium properties compared to the thermodynamic limit. Also such global curvature leads to capillary-induced morphology changes of the surface. Interesting dynamics can arise when the crystallite is supported on a substrate, with crossovers of the dominant driving force from the capillary force and crystallite-substrate interactions. To address these questions, we introduce thermodynamic functions for the boundary conditions, which can be derived from microscopic models. For nano-crystallites, the boundary is the surface (including interfaces), the thermodynamic description is based on the steps that define the shape of the surface, and the underlying microscopic model includes kinks. The global curvature of the surface introduces metastable states with different shapes governed by a constant of integration of the extra boundary condition, which we call the shape parameter c. The discrete height of the steps introduces transition states in between the metastable states, and the lowest energy accessible structure (energy barrier less 10k BT) as a function of the volume has been determined. The dynamics of nano-crystallites as they relax from a non-equilibrium structure is described quantitatively in terms of the motion of steps in both capillary-induced and interface-boundary-induced regimes. The step-edge fluctuations of the top facet are also influenced by global curvature and volume conservation and the effect yields different dynamic scaling exponents from a pure 1D system. Theoretical results are

  3. Solution of mathematical programming formulations of subgame perfect equilibrium problems

    SciTech Connect

    Macal, C.M.; Hurter, A.P.

    1992-02-12

    Mathematical programming models have been developed to represent imperfectly competitive (oligopolistic) market structures and the interdependencies of decision-making units in establishing prices and production levels. The solution of these models represents an economic equilibrium. A subgame perfect equilibrium formulation explicitly considers that each agent`s strategies depend on the current state of the system; the state depends solely on previous decisions made by the economic agents. The structure of an industry-wide model that is formulated as a subgame perfect equilibrium problem is a matrix of simultaneous mathematical programming problems, where the rows represent time periods and the columns represent agents. This paper formally defines the subgame perfect equilibrium problem that includes mathematical programs for agent decision problems, and it characterizes the feasible space in a way that is conducive to the solution of the problem. The existence of equilibrium solutions on convex subspaces of the feasible region is proved, and this set is shown to contain the subgame perfect equilibrium solutions. A procedure for computing equilibrium solutions and systematically searching the subspaces is illustrated by a numerical example.

  4. ASHEE-1.0: a compressible, equilibrium-Eulerian model for volcanic ash plumes

    NASA Astrophysics Data System (ADS)

    Cerminara, M.; Esposti Ongaro, T.; Berselli, L. C.

    2016-02-01

    A new fluid-dynamic model is developed to numerically simulate the non-equilibrium dynamics of polydisperse gas-particle mixtures forming volcanic plumes. Starting from the three-dimensional N-phase Eulerian transport equations for a mixture of gases and solid dispersed particles, we adopt an asymptotic expansion strategy to derive a compressible version of the first-order non-equilibrium model, valid for low-concentration regimes (particle volume fraction less than 10-3) and particle Stokes number (St - i.e., the ratio between relaxation time and flow characteristic time) not exceeding about 0.2. The new model, which is called ASHEE (ASH Equilibrium Eulerian), is significantly faster than the N-phase Eulerian model while retaining the capability to describe gas-particle non-equilibrium effects. Direct Numerical Simulation accurately reproduces the dynamics of isotropic, compressible turbulence in subsonic regimes. For gas-particle mixtures, it describes the main features of density fluctuations and the preferential concentration and clustering of particles by turbulence, thus verifying the model reliability and suitability for the numerical simulation of high-Reynolds number and high-temperature regimes in the presence of a dispersed phase. On the other hand, Large-Eddy Numerical Simulations of forced plumes are able to reproduce the averaged and instantaneous flow properties. In particular, the self-similar Gaussian radial profile and the development of large-scale coherent structures are reproduced, including the rate of turbulent mixing and entrainment of atmospheric air. Application to the Large-Eddy Simulation of the injection of the eruptive mixture in a stratified atmosphere describes some of the important features of turbulent volcanic plumes, including air entrainment, buoyancy reversal and maximum plume height. For very fine particles (St → 0, when non-equilibrium effects are negligible) the model reduces to the so-called dusty-gas model. However

  5. Determinants of cation transport selectivity: Equilibrium binding and transport kinetics

    PubMed Central

    2015-01-01

    The crystal structures of channels and transporters reveal the chemical nature of ion-binding sites and, thereby, constrain mechanistic models for their transport processes. However, these structures, in and of themselves, do not reveal equilibrium selectivity or transport preferences, which can be discerned only from various functional assays. In this Review, I explore the relationship between cation transport protein structures, equilibrium binding measurements, and ion transport selectivity. The primary focus is on K+-selective channels and nonselective cation channels because they have been extensively studied both functionally and structurally, but the principles discussed are relevant to other transport proteins and molecules. PMID:26078056

  6. Spectral Quasi-Equilibrium Manifold for Chemical Kinetics.

    PubMed

    Kooshkbaghi, Mahdi; Frouzakis, Christos E; Boulouchos, Konstantinos; Karlin, Iliya V

    2016-05-26

    The Spectral Quasi-Equilibrium Manifold (SQEM) method is a model reduction technique for chemical kinetics based on entropy maximization under constraints built by the slowest eigenvectors at equilibrium. The method is revisited here and discussed and validated through the Michaelis-Menten kinetic scheme, and the quality of the reduction is related to the temporal evolution and the gap between eigenvalues. SQEM is then applied to detailed reaction mechanisms for the homogeneous combustion of hydrogen, syngas, and methane mixtures with air in adiabatic constant pressure reactors. The system states computed using SQEM are compared with those obtained by direct integration of the detailed mechanism, and good agreement between the reduced and the detailed descriptions is demonstrated. The SQEM reduced model of hydrogen/air combustion is also compared with another similar technique, the Rate-Controlled Constrained-Equilibrium (RCCE). For the same number of representative variables, SQEM is found to provide a more accurate description. PMID:27116566

  7. Equilibrium crystal phases of triblock Janus colloids.

    PubMed

    Reinhart, Wesley F; Panagiotopoulos, Athanassios Z

    2016-09-01

    Triblock Janus colloids, which are colloidal spheres decorated with attractive patches at each pole, have recently generated significant interest as potential building blocks for functional materials. Their inherent anisotropy is known to induce self-assembly into open structures at moderate temperatures and pressures, where they are stabilized over close-packed crystals by entropic effects. We present a numerical investigation of the equilibrium phases of triblock Janus particles with many different patch geometries in three dimensions, using Monte Carlo simulations combined with free energy calculations. In all cases, we find that the free energy difference between crystal polymorphs is less than 0.2 kBT per particle. By varying the patch fraction and interaction range, we show that large patches stabilize the formation of structures with four bonds per patch over those with three. This transition occurs abruptly above a patch fraction of 0.30 and has a strong dependence on the interaction range. Furthermore, we find that a short interaction range favors four bonds per patch, with longer range increasingly stabilizing structures with only three bonds per patch. By quantifying the effect of patch geometry on the stability of the equilibrium crystal structures, we provide insights into the fundamental design rules for constructing complex colloidal crystals. PMID:27609002

  8. Tuning universality far from equilibrium

    PubMed Central

    Karl, Markus; Nowak, Boris; Gasenzer, Thomas

    2013-01-01

    Possible universal dynamics of a many-body system far from thermal equilibrium are explored. A focus is set on meta-stable non-thermal states exhibiting critical properties such as self-similarity and independence of the details of how the respective state has been reached. It is proposed that universal dynamics far from equilibrium can be tuned to exhibit a dynamical transition where these critical properties change qualitatively. This is demonstrated for the case of a superfluid two-component Bose gas exhibiting different types of long-lived but non-thermal critical order. Scaling exponents controlled by the ratio of experimentally tuneable coupling parameters offer themselves as natural smoking guns. The results shed light on the wealth of universal phenomena expected to exist in the far-from-equilibrium realm. PMID:23928853

  9. General equilibrium of an ecosystem.

    PubMed

    Tschirhart, J

    2000-03-01

    Ecosystems and economies are inextricably linked: ecosystem models and economic models are not linked. Consequently, using either type of model to design policies for preserving ecosystems or improving economic performance omits important information. Improved policies would follow from a model that links the systems and accounts for the mutual feedbacks by recognizing how key ecosystem variables influence key economic variables, and vice versa. Because general equilibrium economic models already are widely used for policy making, the approach used here is to develop a general equilibrium ecosystem model which captures salient biological functions and which can be integrated with extant economic models. In the ecosystem model, each organism is assumed to be a net energy maximizer that must exert energy to capture biomass from other organisms. The exerted energies are the "prices" that are paid to biomass, and each organism takes the prices as signals over which it has no control. The maximization problem yields the organism's demand for and supply of biomass to other organisms as functions of the prices. The demands and supplies for each biomass are aggregated over all organisms in each species which establishes biomass markets wherein biomass prices are determined. A short-run equilibrium is established when all organisms are maximizing and demand equals supply in every biomass market. If a species exhibits positive (negative) net energy in equilibrium, its population increases (decreases) and a new equilibrium follows. The demand and supply forces in the biomass markets drive each species toward zero stored energy and a long-run equilibrium. Population adjustments are not based on typical Lotka-Volterra differential equations in which one entire population adjusts to another entire population thereby masking organism behavior; instead, individual organism behavior is central to population adjustments. Numerical simulations use a marine food web in Alaska to

  10. Phase coexistence far from equilibrium

    NASA Astrophysics Data System (ADS)

    Dickman, Ronald

    2016-04-01

    Investigation of simple far-from-equilibrium systems exhibiting phase separation leads to the conclusion that phase coexistence is not well defined in this context. This is because the properties of the coexisting nonequilibrium systems depend on how they are placed in contact, as verified in the driven lattice gas with attractive interactions, and in the two-temperature lattice gas, under (a) weak global exchange between uniform systems, and (b) phase-separated (nonuniform) systems. Thus, far from equilibrium, the notions of universality of phase coexistence (i.e., independence of how systems exchange particles and/or energy), and of phases with intrinsic properties (independent of their environment) are lost.

  11. Chemical equilibrium. [maximizing entropy of gas system to derive relations between thermodynamic variables

    NASA Technical Reports Server (NTRS)

    1976-01-01

    The entropy of a gas system with the number of particles subject to external control is maximized to derive relations between the thermodynamic variables that obtain at equilibrium. These relations are described in terms of the chemical potential, defined as equivalent partial derivatives of entropy, energy, enthalpy, free energy, or free enthalpy. At equilibrium, the change in total chemical potential must vanish. This fact is used to derive the equilibrium constants for chemical reactions in terms of the partition functions of the species involved in the reaction. Thus the equilibrium constants can be determined accurately, just as other thermodynamic properties, from a knowledge of the energy levels and degeneracies for the gas species involved. These equilibrium constants permit one to calculate the equilibrium concentrations or partial pressures of chemically reacting species that occur in gas mixtures at any given condition of pressure and temperature or volume and temperature.

  12. Chemical Principles Revisited: Using the Equilibrium Concept.

    ERIC Educational Resources Information Center

    Mickey, Charles D., Ed.

    1981-01-01

    Discusses the concept of equilibrium in chemical systems, particularly in relation to predicting the position of equilibrium, predicting spontaneity of a reaction, quantitative applications of the equilibrium constant, heterogeneous equilibrium, determination of the solubility product constant, common-ion effect, and dissolution of precipitates.…

  13. Equilibrium 2H/1H fractionation in organic molecules: III. Cyclic ketones and hydrocarbons

    NASA Astrophysics Data System (ADS)

    Wang, Ying; Sessions, Alex L.; Nielsen, Robert J.; Goddard, William A.

    2013-04-01

    Quantitative interpretation of stable hydrogen isotope ratios (2H/1H) in organic compounds is greatly aided by knowledge of the relevant equilibrium fractionation factors (ɛeq). Previous efforts have combined experimental measurements and hybrid Density Functional Theory (DFT) calculations to accurately predict equilibrium fractionations in linear (acyclic) organic molecules (Wang et al., 2009a,b), but the calibration produced by that study is not applicable to cyclic compounds. Here we report experimental measurements of equilibrium 2H/1H fractionation in six cyclic ketones, and use those data to evaluate DFT calculations of fractionation in diverse monocyclic and polycyclic compounds commonly found in sedimentary organic matter and petroleum. At 25, 50, and 75 °C, the experimentally measured ɛeq values for secondary and tertiary Hα in isotopic equilibrium with water are in the ranges of -130‰ to -150‰ and +10‰ to -40‰ respectively. Measured data are similar to DFT calculations of ɛeq for axial Hα but not equatorial Hα. In tertiary Cα positions with methyl substituents, this can be understood as a result of the methyl group forcing Hα atoms into a dominantly axial position. For secondary Cα positions containing both axial and equatorial Hα atoms, we propose that axial Hα exchanges with water significantly faster than the equatorial Hα does, due to the hyperconjugation-stabilized transition state. Interconversion of axial and equatorial positions via ring flipping is much faster than isotopic exchange at either position, and as a result the steady-state isotopic composition of both H's is strongly weighted toward that of axial Hα. Based on comparison with measured ɛeq values, a total uncertainty of 10-30‰ remains for theoretical ɛeq values. Using DFT, we systematically estimated the ɛeq values for individual H positions in various cyclic structures. By summing over all individual H positions, the molecular equilibrium fractionation was

  14. Explicit Integration of Extremely Stiff Reaction Networks: Partial Equilibrium Methods

    SciTech Connect

    Guidry, Mike W; Billings, J. J.; Hix, William Raphael

    2013-01-01

    In two preceding papers [1,2] we have shown that, when reaction networks are well removed from equilibrium, explicit asymptotic and quasi-steady-state approximations can give algebraically stabilized integration schemes that rival standard implicit methods in accuracy and speed for extremely stiff systems. However, we also showed that these explicit methods remain accurate but are no longer competitive in speed as the network approaches equilibrium. In this paper we analyze this failure and show that it is associated with the presence of fast equilibration timescales that neither asymptotic nor quasi-steady-state approximations are able to remove efficiently from the numerical integration. Based on this understanding, we develop a partial equilibrium method to deal effectively with the new partial equilibrium methods, give an integration scheme that plausibly can deal with the stiffest networks, even in the approach to equilibrium, with accuracy and speed competitive with that of implicit methods. Thus we demonstrate that algebraically stabilized explicit methods may offer alternatives to implicit integration of even extremely stiff systems, and that these methods may permit integration of much larger networks than have been feasible previously in a variety of fields.

  15. DYNAMIC EQUILIBRIUM IN THERAPEUTIC SITUATIONS.

    ERIC Educational Resources Information Center

    CARROLL, EDWARD J.

    THE CONCEPT OF DYNAMIC EQUILIBRIUM IS USED TO EXAMINE THE OCCURRENCE OF CHANGE IN A THERAPEUTIC INTERVIEW AND TO PROPOSE A THEORY OF THERAPY. BY ANALYZING THE WORKINGS OF THE PSYCHOSOCIAL SYSTEM THROUGH THE GENERAL SYSTEMS THEORY, IT IS POSSIBLE TO SEE HOW CHANGE OCCURS IN AN INDIVIDUAL FAMILY OR COMMUNITY. APPLIED TO A FAMILY INTERVIEW, THE MODEL…

  16. Magnetospheric equilibrium with anisotropic pressure

    SciTech Connect

    Cheng, C.Z.

    1991-07-01

    Self-consistent magnetospheric equilibrium with anisotropic pressure is obtained by employing an iterative metric method for solving the inverse equilibrium equation in an optimal flux coordinate system. A method of determining plasma parallel and perpendicular pressures from either analytic particle distribution or particle distribution measured along the satellite's path is presented. The numerical results of axisymmetric magnetospheric equilibrium including the effects of finite beta, pressure anisotropy, and boundary conditions are presented for a bi-Maxwellian particle distribution. For the isotropic pressure cases, the finite beta effect produces an outward expansion of the constant magnetic flux surfaces in relation to the dipole field lines, and along the magnetic field the toroidal ring current is maximum at the magnetic equator. The effect of pressure anisotropy is found to further expand the flux surfaces outward. Along the magnetic field lines the westward ring current can be peak away from the equator due to an eastward current contribution resulting from pressure anisotropy. As pressure anisotropy increases, the peak westward current can become more singular. The outer boundary flux surface has significant effect on the magnetospheric equilibrium. For the outer flux boundary resembling dayside compressed flux surface due to solar wind pressure, the deformation of the magnetic field can be quite different from that for the outer flux boundary resembling the tail-like surface. 23 refs., 17 figs.

  17. Understanding Thermal Equilibrium through Activities

    ERIC Educational Resources Information Center

    Pathare, Shirish; Huli, Saurabhee; Nachane, Madhura; Ladage, Savita; Pradhan, Hemachandra

    2015-01-01

    Thermal equilibrium is a basic concept in thermodynamics. In India, this concept is generally introduced at the first year of undergraduate education in physics and chemistry. In our earlier studies (Pathare and Pradhan 2011 "Proc. episteme-4 Int. Conf. to Review Research on Science Technology and Mathematics Education" pp 169-72) we…

  18. An investigation of equilibrium concepts

    NASA Technical Reports Server (NTRS)

    Prozan, R. J.

    1982-01-01

    A different approach to modeling of the thermochemistry of rocket engine combustion phenomena is presented. The methodology described is based on the hypothesis of a new variational principle applicable to compressible fluid mechanics. This hypothesis is extended to treat the thermochemical behavior of a reacting (equilibrium) gas in an open system.

  19. Towards Non-Equilibrium Dynamics with Trapped Ions

    NASA Astrophysics Data System (ADS)

    Silbert, Ariel; Jubin, Sierra; Doret, Charlie

    2016-05-01

    Atomic systems are superbly suited to the study of non-equilibrium dynamics. These systems' exquisite isolation from environmental perturbations leads to long relaxation times that enable exploration of far-from-equilibrium phenomena. One example of particular relevance to experiments in trapped ion quantum information processing, metrology, and precision spectroscopy is the approach to thermal equilibrium of sympathetically cooled linear ion chains. Suitable manipulation of experimental parameters permits exploration of the quantum-to-classical crossover between ballistic transport and diffusive, Fourier's Law conduction, a topic of interest not only to the trapped ion community but also for the development of microelectronic devices and other nanoscale structures. We present progress towards trapping chains of multiple co-trapped calcium isotopes geared towards measuring thermal equilibration and discuss plans for future experiments in non-equilibrium statistical mechanics. This work is supported by Cottrell College Science Award from the Research Corporation for Science Advancement and by Williams College.

  20. The Nash Equilibrium Revisited: Chaos and Complexity Hidden in Simplicity

    NASA Astrophysics Data System (ADS)

    Fellman, Philip V.

    The Nash Equilibrium is a much discussed, deceptively complex, method for the analysis of non-cooperative games (McLennan and Berg, 2005). If one reads many of the commonly available definitions the description of the Nash Equilibrium is deceptively simple in appearance. Modern research has discovered a number of new and important complex properties of the Nash Equilibrium, some of which remain as contemporary conundrums of extraordinary difficulty and complexity (Quint and Shubik, 1997). Among the recently discovered features which the Nash Equilibrium exhibits under various conditions are heteroclinic Hamiltonian dynamics, a very complex asymptotic structure in the context of two-player bi-matrix games and a number of computationally complex or computationally intractable features in other settings (Sato, Akiyama and Farmer, 2002). This paper reviews those findings and then suggests how they may inform various market prediction strategies.

  1. Equilibrium and Stability of Coronal Helmet Streamers

    NASA Astrophysics Data System (ADS)

    Glukhov, Vyacheslav Sergeevich

    1997-05-01

    Equilibrium states and stability of partially open magentic field structures in the solar corona are studied. Soft X-ray observations of the birth and evolution of a giant coronal helmet streamer suggest that the energy source responsible for the X-ray manifestation of the structure is most probably located in the lower corona. The downward heat flux is the indication that a significant part of the source's energy is transported to the top of the structure and converted there to a disposable form. It is shown that by applying the thermodynamic equilibrium model of the corona to the two-dimensional X-ray data it is possible to reconstruct the three-dimensional form of the coronal helmet. The general significance of the projective geometry effects for the observation of the solar corona is discussed. The hypothesis of thermal pressure increase as the cause of the observed helmet expansion is verified numerically. It is shown that in the solar corona a relatively small variations of the pressure distribution in the closed field region can cause huge variations in the geometry of a coronal helmet streamer. Numerical simulations of the morphology and energy accumulation in helmet-like structures subject to photospheric shear motion show that the magnetic field surrounding a partially open structure can inhibit catastrophic expansion of the structure as its energy grows. Stability of a coronal streamer in the framework of the neutral current sheet model is studied theoretically. It is shown that effects of viscosity and the finite Larmor radius dominate effects of inertial fluid motion in the tearing mode instability of a neutral current sheet. Two new regimes of the instability are discovered. It is proven that in the solar corona the rates of growth of the neutral current sheet instability are much smaller than previously believed. Implications of the obtained results are discussed.

  2. Testing Hydrostatic Equilibrium of the Intracluster Medium from the Core to the Virial Radius Ic

    NASA Astrophysics Data System (ADS)

    Okabe, Nobuhiro

    2012-01-01

    We repropose to conduct a diagnostic of the intracluster medium (ICM) states and a stringent test for hydrostatic equilibrium from the core to the virial radius on the basis of accurate weak lensing (WL) mass measurements, incorporating with the Suzaku X-ray satellite. Although our proposals were approved in previous semesters, we could not obtain any data due to winter storm or cooling system incident. It is therefore URGENT and important to measure cluster masses through this proposal. We perform a systematic WL study of a sample of three very nearby galaxy clusters with deep Suprime-Cam imaging for making an accurate determination of the cluster mass profile. Our project unveils the physical interplay between the ICM and the dark matter from the central region to the virial radius. We aims to (1) measure accurately mass profile from the WL measurement, (2) compare the lensing mass with the hydrostatic estimate from X-ray observations, (3) constrain the additional pressure to the thermal pressure by comparing the total pressure to balance fully the gravity of the lensing mass, and (4) investigate correlations between the thermalization process and cosmological large-scale structure environments, and mass dependence.

  3. Equilibrium properties of hcp titanium and zirconium

    SciTech Connect

    Lu, Z.; Singh, D.; Krakauer, H.

    1987-11-15

    The electronic and structural properties of hexagonal-close-packed titanium and zirconium are determined from self-consistent linearized augmented-plane-wave (LAPW) calculations within the framework of the local-density-functional approximation (LDA). The equilibrium lattice parameters, bulk moduli, Poisson's ratios, and cohesive energies are obtained from the total energies calculated as functions of the a and c lattice parameters. As found in other LDA calculations, the cohesive energies are overestimated compared to experiment, but otherwise generally good agreement with experiment is obtained. The uncertainty in the results due to the particular choice of the LDA exchange-correlation potential is also examined by performing parallel calculations using the Kohn-Sham-Gaspar X..cap alpha.. (..cap alpha.. = (2/3) exchange-only potential. We find that these calculations yield equilibrium volumes which differ by 6--8 % (with the X..cap alpha.. results in better agreement with experiment) with proportional differences in other structural properties, which we take to be an indication of the intrinsic reliability of the LDA.

  4. Equilibrium properties of hcp titanium and zirconium

    NASA Astrophysics Data System (ADS)

    Lu, Zhi-Wei; Singh, David; Krakauer, Henry

    1987-11-01

    The electronic and structural properties of hexagonal-close-packed titanium and zirconium are determined from self-consistent linearized augmented-plane-wave (LAPW) calculations within the framework of the local-density-functional approximation (LDA). The equilibrium lattice parameters, bulk moduli, Poisson's ratios, and cohesive energies are obtained from the total energies calculated as functions of the a and c lattice parameters. As found in other LDA calculations, the cohesive energies are overestimated compared to experiment, but otherwise generally good agreement with experiment is obtained. The uncertainty in the results due to the particular choice of the LDA exchange-correlation potential is also examined by performing parallel calculations using the Kohn-Sham-Gaspar Xα (α=(2/3) exchange-only potential. We find that these calculations yield equilibrium volumes which differ by 6-8 % (with the Xα results in better agreement with experiment) with proportional differences in other structural properties, which we take to be an indication of the intrinsic reliability of the LDA.

  5. Diluted equilibrium sterile neutrino dark matter

    NASA Astrophysics Data System (ADS)

    Patwardhan, Amol V.; Fuller, George M.; Kishimoto, Chad T.; Kusenko, Alexander

    2015-11-01

    We present a model where sterile neutrinos with rest masses in the range ˜keV to ˜MeV can be the dark matter and be consistent with all laboratory, cosmological, and large-scale structure, as well as x-ray constraints. These sterile neutrinos are assumed to freeze out of thermal and chemical equilibrium with matter and radiation in the very early Universe, prior to an epoch of prodigious entropy generation ("dilution") from out-of-equilibrium decay of heavy particles. In this work, we consider heavy, entropy-producing particles in the ˜TeV to ˜EeV rest-mass range, possibly associated with new physics at high-energy scales. The process of dilution can give the sterile neutrinos the appropriate relic densities, but it also alters their energy spectra so that they could act like cold dark matter, despite relatively low rest masses as compared to conventional dark matter candidates. Moreover, since the model does not rely on active-sterile mixing for producing the relic density, the mixing angles can be small enough to evade current x-ray or lifetime constraints. Nevertheless, we discuss how future x-ray observations, future lepton number constraints, and future observations and sophisticated simulations of large-scale structure could, in conjunction, provide evidence for this model and/or constrain and probe its parameters.

  6. Equilibrium econophysics: A unified formalism for neoclassical economics and equilibrium thermodynamics

    NASA Astrophysics Data System (ADS)

    Sousa, Tânia; Domingos, Tiago

    2006-11-01

    We develop a unified conceptual and mathematical structure for equilibrium econophysics, i.e., the use of concepts and tools of equilibrium thermodynamics in neoclassical microeconomics and vice versa. Within this conceptual structure the results obtained in microeconomic theory are: (1) the definition of irreversibility in economic behavior; (2) the clarification that the Engel curve and the offer curve are not descriptions of real processes dictated by the maximization of utility at constant endowment; (3) the derivation of a relation between elasticities proving that economic elasticities are not all independent; (4) the proof that Giffen goods do not exist in a stable equilibrium; (5) the derivation that ‘economic integrability’ is equivalent to the generalized Le Chatelier principle and (6) the definition of a first order phase transition, i.e., a transition between separate points in the utility function. In thermodynamics the results obtained are: (1) a relation between the non-dimensional isothermal and adiabatic compressibilities and the increase or decrease in the thermodynamic potentials; (2) the distinction between mathematical integrability and optimization behavior and (3) the generalization of the Clapeyron equation.

  7. Marsh Equilibrium Theory: A Paleo Perspective

    NASA Astrophysics Data System (ADS)

    Morris, J. T.; Kemp, A.; Barber, D. C.; Culver, S. J.; Kegel, J.; Horton, B.

    2014-12-01

    Salt marshes adapt to changes in sea level by means of biogeomorphological feedback. These feedbacks maintain a dynamic equilibrium with sea level, within limits. Reconstructions of sea-level changes derived from salt-marsh sediment provide a paleo perspective for evaluating these feedbacks and for predicting the ecological effects of future sea-level rise. The Marsh Equilibrium Model (MEM) was modified to accommodate long records of sea level and sediment physical and chemical variables derived from high resolution (decadal and decimeter) reconstruction of sea level spanning the late Holocene using foraminifera preserved in North Carolina salt-marsh sediments. Model outputs from a run of nearly 1100-yr show periods of time when the marsh was predicted to be positioned near the top of the tidal frame (inundation time near zero) and times when the marsh was much deeper in the intertidal zone (inundation time of ca. 0.4). An elevation at mean sea level would correspond to an inundation time of 0.5, which is close to the lower limit of the vegetation and is indicative of a marsh that is just forming or, alternatively, a marsh that is on the verge of collapse. The model also indicates that the standing biomass on the marsh surface and sediment organic matter (SOM) content would have varied in harmony with the inundation time. In times past when the inundation time and the opportunity for mineral sedimentation decreased, the sediment organic matter (SOM) content increased. The low SOM concentration near the marsh surface today is consistent with a marsh that is low in the tidal frame. The SOM depth profile is a function of the relative elevation of the marsh, as well as changes in the input of inorganic sediment to the estuary. To effectively manage and preserve valuable salt-marsh ecosystems it is critical to accurately predict their response to projected sea-level changes.

  8. Phonon Mapping in Flowing Equilibrium

    NASA Astrophysics Data System (ADS)

    Ruff, J. P. C.

    2015-03-01

    When a material conducts heat, a modification of the phonon population occurs. The equilibrium Bose-Einstein distribution is perturbed towards flowing-equilibrium, for which the distribution function is not analytically known. Here I argue that the altered phonon population can be efficiently mapped over broad regions of reciprocal space, via diffuse x-ray scattering or time-of-flight neutron scattering, while a thermal gradient is applied across a single crystal sample. When compared to traditional transport measurements, this technique offers a superior, information-rich new perspective on lattice thermal conductivity, wherein the band and momentum dependences of the phonon thermal current are directly resolved. The proposed method is benchmarked using x-ray thermal diffuse scattering measurements of single crystal diamond under transport conditions. CHESS is supported by the NSF & NIH/NIGMS via NSF Award DMR-1332208.

  9. Connective stability of competitive equilibrium

    NASA Technical Reports Server (NTRS)

    Siljak, D. D.

    1975-01-01

    The purpose of this paper is to derive necessary and sufficient conditions for the connective stability of nonlinear matrix systems described by the equation x-dot = A(t, x) x, where the matrix A(t, x) has time-varying nonlinear elements. The results obtained can be used to study the stability of competitive equilibrium in fields as diverse as economics and engineering, model ecosystems, and the arms race.-

  10. Punctuated equilibrium comes of age

    NASA Astrophysics Data System (ADS)

    Gould, Stephan Jay; Eldredge, Niles

    1993-11-01

    The intense controversies that surrounded the youth of punctuated equilibrium have helped it mature to a useful extension of evolutionary theory. As a complement to phyletic gradualism, its most important implications remain the recognition of stasis as a meaningful and predominant pattern within the history of species, and in the recasting of macroevolution as the differential success of certain species (and their descendants) within clades.

  11. Oxygen nonstoichiometry and defect equilibrium in Ca1- x Pr x MnO3-δ manganites

    NASA Astrophysics Data System (ADS)

    Leonidov, I. A.; Konstantinova, E. I.; Markov, A. A.; Merkulov, O. V.; Patrakeev, M. V.; Kozhevnikov, V. L.

    2016-08-01

    The content of oxygen in Ca1- x Pr x MnO3-δ ( x = 0.1) material with perovskite-like structure is determined at 750-950°C and oxygen partial pressures in the gas phase from 3 × 10-6 to 0.55 atm. The regions of existence of orthorhombic, tetragonal, and cubic structural modifications are determined. The equilibrium constants, enthalpies, and entropies of reactions of the formation of defects are determined, allowing us to describe the experimental δ ({p_{{O_2}}}, Т) dependences accurately and calculate the concentrations of manganese ions. It is shown that a change in Ca0.9Pr0.1MnO3-δ structure has a considerable effect on the thermodynamic functions of reactions of the formation of defects.

  12. Radiative equilibrium and escape of Pluto's atmosphere

    NASA Astrophysics Data System (ADS)

    Erwin, Justin; Koskinen, Tommi T.; Yelle, Roger V.

    2015-11-01

    Observations of Pluto’s extend atmosphere by the New Horizons spacecraft motivate an update to our modeling effort on Pluto’s atmosphere. New Horizons observations have already improved our constraints on planet radius and surface pressure, which are key to modeling the atmospheric structure. We model the radiative conductive equilibrium in the lower atmosphere combined with the UV driven escape model of the upper atmosphere. The non-LTE radiative transfer model in the lower atmosphere include heating and cooling by CH4, CO, and HCN. The escape model of the upper atmosphere is updated to include diffusion and escape of each molecular component. These results will be used to aid in the analysis and better understanding of the full atmospheric structure.

  13. Morphodynamic equilibrium of alluvial estuaries

    NASA Astrophysics Data System (ADS)

    Tambroni, Nicoletta; Bolla Pittaluga, Michele; Canestrelli, Alberto; Lanzoni, Stefano; Seminara, Giovanni

    2014-05-01

    The evolution of the longitudinal bed profile of an estuary, with given plan-form configuration, subject to given tidal forcing at the mouth and prescribed values of water and sediment supply from the river is investigated numerically. Our main goal is to ascertain whether, starting from some initial condition, the bed evolution tends to reach a unique equilibrium configuration asymptotically in time. Also, we investigate the morphological response of an alluvial estuary to changes in the tidal range and hydrologic forcing (flow and sediment supply). Finally, the solution helps characterizing the transition between the fluvially dominated region and the tidally dominated region of the estuary. All these issues play an important role also in interpreting how the facies changes along the estuary, thus helping to make correct paleo-environmental and sequence-stratigraphic interpretations of sedimentary successions (Dalrymple and Choi, 2007). Results show that the model is able to describe a wide class of settings ranging from tidally dominated estuaries to fluvially dominated estuaries. In the latter case, the solution is found to compare satisfactory with the analytical asymptotic solution recently derived by Seminara et al. (2012), under the hypothesis of fairly 'small' tidal oscillations. Simulations indicate that the system always moves toward an equilibrium configuration in which the net sediment flux in a tidal cycle is constant throughout the estuary and equal to the constant sediment flux discharged from the river. For constant width, the bed equilibrium profile of the estuarine channel is characterized by two distinct regions: a steeper reach seaward, dominated by the tide, and a less steep upstream reach, dominated by the river and characterized by the undisturbed bed slope. Although the latter reach, at equilibrium, is not directly affected by the tidal wave, however starting from an initial uniform stream with the constant 'fluvial' slope, the final

  14. Predict amine solution properties accurately

    SciTech Connect

    Cheng, S.; Meisen, A.; Chakma, A.

    1996-02-01

    Improved process design begins with using accurate physical property data. Especially in the preliminary design stage, physical property data such as density viscosity, thermal conductivity and specific heat can affect the overall performance of absorbers, heat exchangers, reboilers and pump. These properties can also influence temperature profiles in heat transfer equipment and thus control or affect the rate of amine breakdown. Aqueous-amine solution physical property data are available in graphical form. However, it is not convenient to use with computer-based calculations. Developed equations allow improved correlations of derived physical property estimates with published data. Expressions are given which can be used to estimate physical properties of methyldiethanolamine (MDEA), monoethanolamine (MEA) and diglycolamine (DGA) solutions.

  15. Accurate thickness measurement of graphene

    NASA Astrophysics Data System (ADS)

    Shearer, Cameron J.; Slattery, Ashley D.; Stapleton, Andrew J.; Shapter, Joseph G.; Gibson, Christopher T.

    2016-03-01

    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  16. Statistical equilibrium in cometary C2. II - Swan/Phillips band ratios

    NASA Technical Reports Server (NTRS)

    Swamy, K. S. K.; Odell, C. R.

    1979-01-01

    Statistical equilibrium calculations have been made for both the triplet and ground state singlets for C2 in comets, using the exchange rate as a free parameter. The predictions of the results are consistent with optical observations and may be tested definitively by accurate observations of the Phillips and Swan band ratios. Comparison with the one reported observation indicates compatibility with a low exchange rate and resonance fluorescence statistical equilibrium.

  17. Accurate genetic switch in Escherichia coli: novel mechanism of regulation by co-repressor.

    PubMed

    Tabaka, Marcin; Cybulski, Olgierd; Hołyst, Robert

    2008-04-01

    Understanding a biological module involves recognition of its structure and the dynamics of its principal components. In this report we present an analysis of the dynamics of the repression module within the regulation of the trp operon in Escherichia coli. We combine biochemical data for reaction rate constants for the trp repressor binding to trp operator and in vivo data of a number of tryptophan repressors (TrpRs) that bind to the operator. The model of repression presented in this report greatly differs from previous mathematical models. One, two or three TrpRs can bind to the operator and repress the transcription. Moreover, reaction rates for detachment of TrpRs from the operator strongly depend on tryptophan (Trp) concentration, since Trp can also bind to the repressor-operator complex and stabilize it. From the mathematical modeling and analysis of reaction rates and equilibrium constants emerges a high-quality, accurate and effective module of trp repression. This genetic switch responds accurately to fast consumption of Trp from the interior of a cell. It switches with minimal dispersion when the concentration of Trp drops below a thousand molecules per cell. PMID:18313075

  18. Torque equilibrium attitude control for Skylab reentry

    NASA Technical Reports Server (NTRS)

    Glaese, J. R.; Kennel, H. F.

    1979-01-01

    All the available torque equilibrium attitudes (most were useless from the standpoint of lack of electrical power) and the equilibrium seeking method are presented, as well as the actual successful application during the 3 weeks prior to Skylab reentry.

  19. Characterization of non equilibrium effects on high quality critical flows

    SciTech Connect

    Camelo, E.; Lemonnier, H.; Ochterbeck, J.

    1995-09-01

    The appropriate design of various pieces of safety equipment such as relief systems, relies on the accurate description of critical flow phenomena. Most of the systems of industrial interest are willing to be described by one-dimensional area-averaged models and a large fraction of them involves multi-component high gas quality flows. Within these circumstances, the flow is very likely to be of an annular dispersed nature and its description by two-fluid models requires various closure relations. Among the most sensitive closures, there is the interfacial area and the liquid entrained fraction. The critical flowrate depends tremendously on the accurate description of the non equilibrium which results from the correctness of the closure equations. In this study, two-component flows are emphasized and non equilibrium results mainly form the differences in the phase velocities. It is therefore of the utmost importance to have reliable data to characterize non equilibrium phenomena and to assess the validity of the closure models. A comprehensive description of air-water nozzle flows, with emphasis on the effect of the nozzle geometry, has been undertaken and some of the results are presented here which helps understanding the overall flow dynamics. Besides the critical flowrate, the presented material includes pressure profiles, droplet size and velocity, liquid film flowrate and liquid film thickness.

  20. Equilibrium and volumetric data and model development of coal fluids

    SciTech Connect

    Robinson, R.L. Jr.; Gasem, K.A.M.; Park, J.

    1992-04-28

    The long term goal of our efforts is to develop accurate predictive methods for description of equilibrium phase properties for a variety of types of mixtures and operating conditions. The specific objectives of the work specified herein include: (1) development of an experimental facility having the capability to provide data on equilibrium phase compositions (solubilities) and liquid densities, and doing so with greater accuracy and speed than our previous facility, (2) measurement of equilibrium phase properties for systematically-selected mixtures-specifically those containing important solute gases (such as hydrogen, carbon monoxide, methane, ethane, carbonyl sulfide, ammonia) in a series of heavy paraffinic, naphthenic and aromatic solvents (e.g., n-decane, n-eicosane, n-octacosane, n-hexatriacontane, cyclohexane, Decalin, perhydrophenanthrene, perhydropyrene, benzene, naphthalene, phenanthrene, pyrene), (3) testing/development of correlation frameworks for representing the phase behavior of fluids of the type encountered in coal conversion processes, and (4) generalization of parameters in the correlation frameworks to enable accurate predictions for systems of the type studied, permitting predictions to be made for systems and conditions other than those for which experimental data are available.

  1. Non-equilibrium Dynamics of DNA Nanotubes

    NASA Astrophysics Data System (ADS)

    Hariadi, Rizal Fajar

    Can the fundamental processes that underlie molecular biology be understood and simulated by DNA nanotechnology? The early development of DNA nanotechnology by Ned Seeman was driven by the desire to find a solution to the protein crystallization problem. Much of the later development of the field was also driven by envisioned applications in computing and nanofabrication. While the DNA nanotechnology community has assembled a versatile tool kit with which DNA nanostructures of considerable complexity can be assembled, the application of this tool kit to other areas of science and technology is still in its infancy. This dissertation reports on the construction of non-equilibrium DNA nanotube dynamic to probe molecular processes in the areas of hydrodynamics and cytoskeletal behavior. As the first example, we used DNA nanotubes as a molecular probe for elongational flow measurement in different micro-scale flow settings. The hydrodynamic flow in the vicinity of simple geometrical objects, such as a rigid DNA nanotube, is amenable to rigorous theoretical investigation. We measured the distribution of elongational flows produced in progressively more complex settings, ranging from the vicinity of an orifice in a microfluidic chamber to within a bursting bubble of Pacific ocean water. This information can be used to constrain theories on the origin of life in which replication involves a hydrodynamically driven fission process, such as the coacervate fission proposed by Oparin. A second theme of this dissertation is the bottom-up construction of a de novo artificial cytoskeleton with DNA nanotubes. The work reported here encompasses structural, locomotion, and control aspects of non-equilibrium cytoskeletal behavior. We first measured the kinetic parameters of DNA nanotube assembly and tested the accuracy of the existing polymerization models in the literature. Toward recapitulation of non-equilibrium cytoskeletal dynamics, we coupled the polymerization of DNA

  2. Temperature of systems out of thermodynamic equilibrium

    NASA Astrophysics Data System (ADS)

    Garden, J.-L.; Richard, J.; Guillou, H.

    2008-07-01

    Two phenomenological approaches are currently used in the study of the vitreous state. One is based on the concept of fictive temperature introduced by Tool [J. Res. Natl. Bur. Stand. 34, 199 (1945)] and recently revisited by Nieuwenhuizen [Phys. Rev. Lett. 80, 5580 (1998)]. The other is based on the thermodynamics of irreversible processes initiated by De Donder at the beginning of the last century [L'Affinité (Gauthier-Villars, Paris, 1927)] and recently used by Möller et al. for a thorough study of the glass transition [J. Chem. Phys. 125, 094505 (2006)]. This latter approach leads to the possibility of describing the glass transition by means of the freezing-in of one or more order parameters connected to the internal structural degrees of freedom involved in the vitrification process. In this paper, the equivalence of the two preceding approaches is demonstrated, not only for glasses but in a very general way for any system undergoing an irreversible transformation. This equivalence allows the definition of an effective temperature for all systems departed from equilibrium generating a positive amount of entropy. In fact, the initial fictive temperature concept of Tool leads to the generalization of the notion of temperature for systems out of thermodynamic equilibrium, for which glasses are just particular cases.

  3. Non-equilibrium many body dynamics

    SciTech Connect

    Creutz, M.; Gyulassy, M.

    1997-09-22

    This Riken BNL Research Center Symposium on Non-Equilibrium Many Body Physics was held on September 23-25, 1997 as part of the official opening ceremony of the Center at Brookhaven National Lab. A major objective of theoretical work at the center is to elaborate on the full spectrum of strong interaction physics based on QCD, including the physics of confinement and chiral symmetry breaking, the parton structure of hadrons and nuclei, and the phenomenology of ultra-relativistic nuclear collisions related to the up-coming experiments at RHIC. The opportunities and challenges of nuclear and particle physics in this area naturally involve aspects of the many body problem common to many other fields. The aim of this symposium was to find common theoretical threads in the area of non-equilibrium physics and modern transport theories. The program consisted of invited talks on a variety topics from the fields of atomic, condensed matter, plasma, astrophysics, cosmology, and chemistry, in addition to nuclear and particle physics. Separate abstracts have been indexed into the database for contributions to this workshop.

  4. Open problems in non-equilibrium physics

    SciTech Connect

    Kusnezov, D.

    1997-09-22

    The report contains viewgraphs on the following: approaches to non-equilibrium statistical mechanics; classical and quantum processes in chaotic environments; classical fields in non-equilibrium situations: real time dynamics at finite temperature; and phase transitions in non-equilibrium conditions.

  5. EquilTheTA: Thermodynamic and transport properties of complex equilibrium plasmas

    SciTech Connect

    Colonna, G.; D'Angola, A.

    2012-11-27

    EquilTheTA (EQUILibrium for plasma THErmodynamics and Transport Applications) is a web-based software which calculates chemical equilibrium product concentrations from any set of reactants and determines thermodynamic and transport properties for the product mixture in wide temperature and pressure ranges. The program calculates chemical equilibrium by using a hierarchical approach, thermodynamic properties and transport coefficients starting from recent and accurate databases of atomic and molecular energy levels and collision integrals. In the calculations, Debye length and cut-off are consistently updated and virial corrections (up to third order) can be considered. Transport coefficients are calculated by using high order approximations of the Chapman-Enskog method.

  6. Thermal equilibrium in Einstein's elevator.

    PubMed

    Sánchez-Rey, Bernardo; Chacón-Acosta, Guillermo; Dagdug, Leonardo; Cubero, David

    2013-05-01

    We report fully relativistic molecular-dynamics simulations that verify the appearance of thermal equilibrium of a classical gas inside a uniformly accelerated container. The numerical experiments confirm that the local momentum distribution in this system is very well approximated by the Jüttner function-originally derived for a flat spacetime-via the Tolman-Ehrenfest effect. Moreover, it is shown that when the acceleration or the container size is large enough, the global momentum distribution can be described by the so-called modified Jüttner function, which was initially proposed as an alternative to the Jüttner function. PMID:23767501

  7. Princeton spectral equilibrium code: PSEC

    SciTech Connect

    Ling, K.M.; Jardin, S.C.

    1984-03-01

    A fast computer code has been developed to calculate free-boundary solutions to the plasma equilibrium equation that are consistent with the currents in external coils and conductors. The free-boundary formulation is based on the minimization of a mean-square error epsilon while the fixed-boundary solution is based on a variational principle and spectral representation of the coordinates x(psi,theta) and z(psi,theta). Specific calculations using the Columbia University Torus II, the Poloidal Divertor Experiment (PDX), and the Tokamak Fusion Test Reactor (TFTR) geometries are performed.

  8. Collisional Ionization Equilibrium for Optically Thin Plasmas

    NASA Technical Reports Server (NTRS)

    Bryans, P.; Mitthumsiri, W.; Savin, D. W.; Badnell, N. R.; Gorczyca, T. W.; Laming, J. M.

    2006-01-01

    Reliably interpreting spectra from electron-ionized cosmic plasmas requires accurate ionization balance calculations for the plasma in question. However, much of the atomic data needed for these calculations have not been generated using modern theoretical methods and their reliability are often highly suspect. We have utilized state-of-the-art calculations of dielectronic recombination (DR) rate coefficients for the hydrogenic through Na-like ions of all elements from He to Zn. We have also utilized state-of-the-art radiative recombination (RR) rate coefficient calculations for the bare through Na-like ions of all elements from H to Zn. Using our data and the recommended electron impact ionization data of Mazzotta et al. (1998), we have calculated improved collisional ionization equilibrium calculations. We compare our calculated fractional ionic abundances using these data with those presented by Mazzotta et al. (1998) for all elements from H to Ni, and with the fractional abundances derived from the modern DR and RR calculations of Gu (2003a,b, 2004) for Mg, Si, S, Ar, Ca, Fe, and Ni.

  9. Equilibrium & Nonequilibrium Fluctuation Effects in Biopolymer Networks

    NASA Astrophysics Data System (ADS)

    Kachan, Devin Michael

    Fluctuation-induced interactions are an important organizing principle in a variety of soft matter systems. In this dissertation, I explore the role of both thermal and active fluctuations within cross-linked polymer networks. The systems I study are in large part inspired by the amazing physics found within the cytoskeleton of eukaryotic cells. I first predict and verify the existence of a thermal Casimir force between cross-linkers bound to a semi-flexible polymer. The calculation is complicated by the appearance of second order derivatives in the bending Hamiltonian for such polymers, which requires a careful evaluation of the the path integral formulation of the partition function in order to arrive at the physically correct continuum limit and properly address ultraviolet divergences. I find that cross linkers interact along a filament with an attractive logarithmic potential proportional to thermal energy. The proportionality constant depends on whether and how the cross linkers constrain the relative angle between the two filaments to which they are bound. The interaction has important implications for the synthesis of biopolymer bundles within cells. I model the cross-linkers as existing in two phases: bound to the bundle and free in solution. When the cross-linkers are bound, they behave as a one-dimensional gas of particles interacting with the Casimir force, while the free phase is a simple ideal gas. Demanding equilibrium between the two phases, I find a discontinuous transition between a sparsely and a densely bound bundle. This discontinuous condensation transition induced by the long-ranged nature of the Casimir interaction allows for a similarly abrupt structural transition in semiflexible filament networks between a low cross linker density isotropic phase and a higher cross link density bundle network. This work is supported by the results of finite element Brownian dynamics simulations of semiflexible filaments and transient cross-linkers. I

  10. Concept Maps about Chemical Equilibrium and Students' Achievement Scores.

    ERIC Educational Resources Information Center

    Wilson, Jan

    1996-01-01

    Examines relationships between structural characteristics of students' concept maps about chemical equilibrium and independent measures of their achievement in chemistry. Results indicate significant relationships between multidimensional scaling coordinates and test scores of recall of knowledge and its application and also reveal structural…

  11. Mixed quantum-classical equilibrium in global flux surface hopping

    SciTech Connect

    Sifain, Andrew E.; Wang, Linjun; Prezhdo, Oleg V.

    2015-06-14

    Global flux surface hopping (GFSH) generalizes fewest switches surface hopping (FSSH)—one of the most popular approaches to nonadiabatic molecular dynamics—for processes exhibiting superexchange. We show that GFSH satisfies detailed balance and leads to thermodynamic equilibrium with accuracy similar to FSSH. This feature is particularly important when studying electron-vibrational relaxation and phonon-assisted transport. By studying the dynamics in a three-level quantum system coupled to a classical atom in contact with a classical bath, we demonstrate that both FSSH and GFSH achieve the Boltzmann state populations. Thermal equilibrium is attained significantly faster with GFSH, since it accurately represents the superexchange process. GFSH converges closer to the Boltzmann averages than FSSH and exhibits significantly smaller statistical errors.

  12. Magnetospheric equilibrium with anisotropic pressure

    SciTech Connect

    Cheng, C.Z. )

    1992-02-01

    Self-consistent magnetospheric equilibria with anisotropic pressure are obtained by employing an iterative metric method for solving the inverse equilibrium equation in an optimal flux coordinate system. A method of determining plasma parallel and perpendicular pressures from either analytic particle distributions or particle distributions measured along a satellite's path is presented. The numerical results of axisymmetric magnetospheric equilibria including the effects of finite beta, pressure anisotropy, and boundary conditions are presented for a bi-Maxwellian particle distribution. For the isotropic pressure cases the finite beta effect produces an outward expansion of the constant magnetic flux surfaces in relation to the dipole field lines, and along the magnetic field the toroidal ring current is maximum at the magnetic equator. The effect of pressure anisotropy is found to further expand the flux surfaces outward. Along the magnetic field lines the westward ring current can be peak away from the equator owing to an eastward current contribution resulting from pressure anisotropy. As pressure anisotropy increases, the peak westward current can become more singular. The outer boundary flux surface has a significant effect on the magnetospheric equilibrium. For the outer flux boundary resembling the dayside compressed flux surface due to solar wind pressure, the deformation of the magnetic field can be quite different from that for the outer flux boundary resembling the taillike flux surface.

  13. Equilibrium Studies of Designed Metalloproteins.

    PubMed

    Gibney, B R

    2016-01-01

    Complete thermodynamic descriptions of the interactions of cofactors with proteins via equilibrium studies are challenging, but are essential to the evaluation of designed metalloproteins. While decades of studies on protein-protein interaction thermodynamics provide a strong underpinning to the successful computational design of novel protein folds and de novo proteins with enzymatic activity, the corresponding paucity of data on metal-protein interaction thermodynamics limits the success of computational metalloprotein design efforts. By evaluating the thermodynamics of metal-protein interactions via equilibrium binding studies, protein unfolding free energy determinations, proton competition equilibria, and electrochemistry, a more robust basis for the computational design of metalloproteins may be provided. Our laboratory has shown that such studies provide detailed insight into the assembly and stability of designed metalloproteins, allow for parsing apart the free energy contributions of metal-ligand interactions from those of porphyrin-protein interactions in hemeproteins, and even reveal their mechanisms of proton-coupled electron transfer. Here, we highlight studies that reveal the complex interplay between the various equilibria that underlie metalloprotein assembly and stability and the utility of making these detailed measurements. PMID:27586343

  14. Are the Concepts of Dynamic Equilibrium and the Thermodynamic Criteria for Spontaneity, Nonspontaneity, and Equilibrium Compatible?

    ERIC Educational Resources Information Center

    Silverberg, Lee J.; Raff, Lionel M.

    2015-01-01

    Thermodynamic spontaneity-equilibrium criteria require that in a single-reaction system, reactions in either the forward or reverse direction at equilibrium be nonspontaneous. Conversely, the concept of dynamic equilibrium holds that forward and reverse reactions both occur at equal rates at equilibrium to the extent allowed by kinetic…

  15. Carbon dioxide hydrate phase equilibrium and cage occupancy calculations using ab initio intermolecular potentials.

    PubMed

    Velaga, Srinath C; Anderson, Brian J

    2014-01-16

    Gas hydrate deposits are receiving increased attention as potential locations for CO2 sequestration, with CO2 replacing the methane that is recovered as an energy source. In this scenario, it is very important to correctly characterize the cage occupancies of CO2 to correctly assess the sequestration potential as well as the methane recoverability. In order to predict accurate cage occupancies, the guest–host interaction potential must be represented properly. Earlier, these potential parameters were obtained by fitting to experimental equilibrium data and these fitted parameters do not match with those obtained by second virial coefficient or gas viscosity data. Ab initio quantum mechanical calculations provide an independent means to directly obtain accurate intermolecular potentials. A potential energy surface (PES) between H2O and CO2 was computed at the MP2/aug-cc-pVTZ level and corrected for basis set superposition error (BSSE), an error caused due to the lower basis set, by using the half counterpoise method. Intermolecular potentials were obtained by fitting Exponential-6 and Lennard-Jones 6-12 models to the ab initio PES, correcting for many-body interactions. We denoted this model as the “VAS” model. Reference parameters for structure I carbon dioxide hydrate were calculated using the VAS model (site–site ab initio intermolecular potentials) as Δμ(w)(0) = 1206 ± 2 J/mol and ΔH(w)(0) = 1260 ± 12 J/mol. With these reference parameters and the VAS model, pure CO2 hydrate equilibrium pressure was predicted with an average absolute deviation of less than 3.2% from the experimental data. Predictions of the small cage occupancy ranged from 32 to 51%, and the large cage is more than 98% occupied. The intermolecular potentials were also tested by calculating the pure CO2 density and diffusion of CO2 in water using molecular dynamics simulations. PMID:24328234

  16. The Equilibrium Spreading Tension of Pulmonary Surfactant.

    PubMed

    Dagan, Maayan P; Hall, Stephen B

    2015-12-01

    Monomolecular films at an air/water interface coexist at the equilibrium spreading tension (γ(e)) with the bulk phase from which they form. For individual phospholipids, γ(e) is single-valued, and separates conditions at which hydrated vesicles adsorb from tensions at which overcompressed monolayers collapse. With pulmonary surfactant, isotherms show that monolayers compressed on the surface of bubbles coexist with the three-dimensional collapsed phase over a range of surface tensions. γ(e) therefore represents a range rather than a single value of surface tension. Between the upper and lower ends of this range, rates of collapse for spread and adsorbed films decrease substantially. Changes during adsorption across this narrow region of coexistence between the two- and three-dimensional structures at least partially explain how alveolar films of pulmonary surfactant become resistant to collapse. PMID:26583569

  17. Accurate basis set truncation for wavefunction embedding

    NASA Astrophysics Data System (ADS)

    Barnes, Taylor A.; Goodpaster, Jason D.; Manby, Frederick R.; Miller, Thomas F.

    2013-07-01

    Density functional theory (DFT) provides a formally exact framework for performing embedded subsystem electronic structure calculations, including DFT-in-DFT and wavefunction theory-in-DFT descriptions. In the interest of efficiency, it is desirable to truncate the atomic orbital basis set in which the subsystem calculation is performed, thus avoiding high-order scaling with respect to the size of the MO virtual space. In this study, we extend a recently introduced projection-based embedding method [F. R. Manby, M. Stella, J. D. Goodpaster, and T. F. Miller III, J. Chem. Theory Comput. 8, 2564 (2012)], 10.1021/ct300544e to allow for the systematic and accurate truncation of the embedded subsystem basis set. The approach is applied to both covalently and non-covalently bound test cases, including water clusters and polypeptide chains, and it is demonstrated that errors associated with basis set truncation are controllable to well within chemical accuracy. Furthermore, we show that this approach allows for switching between accurate projection-based embedding and DFT embedding with approximate kinetic energy (KE) functionals; in this sense, the approach provides a means of systematically improving upon the use of approximate KE functionals in DFT embedding.

  18. Non-Equilibrium Effects on Hypersonic Turbulent Boundary Layers

    NASA Astrophysics Data System (ADS)

    Kim, Pilbum

    Understanding non-equilibrium effects of hypersonic turbulent boundary layers is essential in order to build cost efficient and reliable hypersonic vehicles. It is well known that non-equilibrium effects on the boundary layers are notable, but our understanding of the effects are limited. The overall goal of this study is to improve the understanding of non-equilibrium effects on hypersonic turbulent boundary layers. A new code has been developed for direct numerical simulations of spatially developing hypersonic turbulent boundary layers over a flat plate with finite-rate reactions. A fifth-order hybrid weighted essentially non-oscillatory scheme with a low dissipation finite-difference scheme is utilized in order to capture stiff gradients while resolving small motions in turbulent boundary layers. The code has been validated by qualitative and quantitative comparisons of two different simulations of a non-equilibrium flow and a spatially developing turbulent boundary layer. With the validated code, direct numerical simulations of four different hypersonic turbulent boundary layers, perfect gas and non-equilibrium flows of pure oxygen and nitrogen, have been performed. In order to rule out uncertainties in comparisons, the same inlet conditions are imposed for each species, and then mean and turbulence statistics as well as near-wall turbulence structures are compared at a downstream location. Based on those comparisons, it is shown that there is no direct energy exchanges between internal and turbulent kinetic energies due to thermal and chemical non-equilibrium processes in the flow field. Instead, these non-equilibria affect turbulent boundary layers by changing the temperature without changing the main characteristics of near-wall turbulence structures. This change in the temperature induces the changes in the density and viscosity and the mean flow fields are then adjusted to satisfy the conservation laws. The perturbation fields are modified according to

  19. Accurate ab initio Quartic Force Fields of Cyclic and Bent HC2N Isomers

    NASA Technical Reports Server (NTRS)

    Inostroza, Natalia; Huang, Xinchuan; Lee, Timothy J.

    2012-01-01

    Highly correlated ab initio quartic force field (QFFs) are used to calculate the equilibrium structures and predict the spectroscopic parameters of three HC2N isomers. Specifically, the ground state quasilinear triplet and the lowest cyclic and bent singlet isomers are included in the present study. Extensive treatment of correlation effects were included using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, denoted CCSD(T). Dunning s correlation-consistent basis sets cc-pVXZ, X=3,4,5, were used, and a three-point formula for extrapolation to the one-particle basis set limit was used. Core-correlation and scalar relativistic corrections were also included to yield highly accurate QFFs. The QFFs were used together with second-order perturbation theory (with proper treatment of Fermi resonances) and variational methods to solve the nuclear Schr dinger equation. The quasilinear nature of the triplet isomer is problematic, and it is concluded that a QFF is not adequate to describe properly all of the fundamental vibrational frequencies and spectroscopic constants (though some constants not dependent on the bending motion are well reproduced by perturbation theory). On the other hand, this procedure (a QFF together with either perturbation theory or variational methods) leads to highly accurate fundamental vibrational frequencies and spectroscopic constants for the cyclic and bent singlet isomers of HC2N. All three isomers possess significant dipole moments, 3.05D, 3.06D, and 1.71D, for the quasilinear triplet, the cyclic singlet, and the bent singlet isomers, respectively. It is concluded that the spectroscopic constants determined for the cyclic and bent singlet isomers are the most accurate available, and it is hoped that these will be useful in the interpretation of high-resolution astronomical observations or laboratory experiments.

  20. Directed percolation identified as equilibrium pre-transition towards non-equilibrium arrested gel states

    NASA Astrophysics Data System (ADS)

    Laurati, Marco; Capellmann, Ronja; Kohl, Matthias; Egelhaaf, Stefan; Schmiedeberg, Michael

    The macroscopic properties of gels arise from their slow dynamics and load bearing network structure, which are exploited by nature and in numerous industrial products. However, a link between these structural and dynamical properties has remained elusive. Here we present confocal microscopy exper- iments and simulations of gel-forming colloid-polymer mixtures with competing interactions. They reveal that gel formation is preceded by continuous and directed percolation. Both transitions lead to system spanning networks, but only directed percolation results in extremely slow dynamics, ageing and a shrinking of the gel that resembles syneresis. Therefore, dynamical arrest in gels is found to be linked to a structural transition, namely directed percolation, which is quantitatively associated with the mean number of bonded neighbours. Directed percolation is a universality class of transitions out of equilibrium, our study hence connects gel formation to a well-developed theoretical framework which now can be exploited to achieve a detailed understanding of arrested gels.

  1. Accurate wavelength calibration method for flat-field grating spectrometers.

    PubMed

    Du, Xuewei; Li, Chaoyang; Xu, Zhe; Wang, Qiuping

    2011-09-01

    A portable spectrometer prototype is built to study wavelength calibration for flat-field grating spectrometers. An accurate calibration method called parameter fitting is presented. Both optical and structural parameters of the spectrometer are included in the wavelength calibration model, which accurately describes the relationship between wavelength and pixel position. Along with higher calibration accuracy, the proposed calibration method can provide information about errors in the installation of the optical components, which will be helpful for spectrometer alignment. PMID:21929865

  2. Accurate Thermal Stresses for Beams: Normal Stress

    NASA Technical Reports Server (NTRS)

    Johnson, Theodore F.; Pilkey, Walter D.

    2003-01-01

    Formulations for a general theory of thermoelasticity to generate accurate thermal stresses for structural members of aeronautical vehicles were developed in 1954 by Boley. The formulation also provides three normal stresses and a shear stress along the entire length of the beam. The Poisson effect of the lateral and transverse normal stresses on a thermally loaded beam is taken into account in this theory by employing an Airy stress function. The Airy stress function enables the reduction of the three-dimensional thermal stress problem to a two-dimensional one. Numerical results from the general theory of thermoelasticity are compared to those obtained from strength of materials. It is concluded that the theory of thermoelasticity for prismatic beams proposed in this paper can be used instead of strength of materials when precise stress results are desired.

  3. Accurate Thermal Stresses for Beams: Normal Stress

    NASA Technical Reports Server (NTRS)

    Johnson, Theodore F.; Pilkey, Walter D.

    2002-01-01

    Formulations for a general theory of thermoelasticity to generate accurate thermal stresses for structural members of aeronautical vehicles were developed in 1954 by Boley. The formulation also provides three normal stresses and a shear stress along the entire length of the beam. The Poisson effect of the lateral and transverse normal stresses on a thermally loaded beam is taken into account in this theory by employing an Airy stress function. The Airy stress function enables the reduction of the three-dimensional thermal stress problem to a two-dimensional one. Numerical results from the general theory of thermoelasticity are compared to those obtained from strength of materials. It is concluded that the theory of thermoelasticity for prismatic beams proposed in this paper can be used instead of strength of materials when precise stress results are desired.

  4. Thermodynamic equilibrium at heterogeneous pressure

    NASA Astrophysics Data System (ADS)

    Vrijmoed, Johannes C.; Podladchikov, Yuri Y.

    2014-05-01

    Recent advances in metamorphic petrology point out the importance of grain-scale pressure variations in high-temperature metamorphic rocks. Pressures derived from chemical zonation using unconventional geobarometry based on equal chemical potentials fit mechanically feasible pressure variations. Here a thermodynamic equilibrium method is presented that predicts chemical zoning as a result of pressure variations by Gibbs energy minimization. Equilibrium thermodynamic prediction of the chemical zoning in the case of pressure heterogeneity is done by constraint Gibbs minimization using linear programming techniques. Compositions of phases considered in the calculation are discretized into 'pseudo-compounds' spanning the entire compositional space. Gibbs energies of these discrete compounds are generated for a given range and resolution of pressures for example derived by barometry or from mechanical model predictions. Gibbs energy minimization is subsequently performed considering all compounds of different composition and pressure. In addition to constraining the system composition a certain proportion of the system is constraint at a specified pressure. Input pressure variations need to be discretized and each discrete pressure defines an additional constraint for the minimization. The proportion of the system at each different pressure is equally distributed over the number of input pressures. For example if two input pressures P1 and P2 are specified, two constraints are added: 50 percent of the system is constraint at P1 while the remaining 50 percent is constraint at P2. The method has been tested for a set of 10 input pressures obtained by Tajčmanová et al. (2014) using their unconventional geobarometry method in a plagioclase rim around kyanite. Each input pressure is added as constraint to the minimization (1/10 percent of the system for each discrete pressure). Constraining the system composition to the average composition of the plagioclase rim

  5. Modeling equilibrium Fe isotope fractionation

    NASA Astrophysics Data System (ADS)

    Anbar, A.; Jarzecki, A.; Spiro, T.

    2003-04-01

    Research into the stable isotope biogeochemistry of Fe and other transition metals has been driven primarily by analytical innovations which have revealed significant isotope effects in nature and the laboratory. Further development of these new isotope systems requires complementary theoretical research to guide analytical efforts. The results of the first such studies show some discrepancies with experiments. For example, Johnson et al. (2002) report an experimentally-determined 56Fe/54Fe equilibrium fractionation factor between Fe(II) and Fe(III) aquo complexes of ˜1.0025. This effect is ˜50% smaller than predicted theoretically by Schauble et al. (2001). It is important to resolve such discrepancies. Equilibrium isotope fractionation factors can be predicted from vibrational spectroscopic data of isotopically-substituted complexes, or from theoretical predictions of some or all of these frequencies obtained using force field models. The pioneering work of Schauble et al. (2001) utilized a modified Urey-Bradley force field (MUBFF) model. This approach is limiting in at least three ways: First, it is not ab initio, requiring as input some measured vibrational frequencies. Such data are not always available, or may have significant uncertainties. Second, the MUBFF does not include potentially important effects of solvent interaction. Third, because it makes certain assumptions about molecular symmetry, the MUBFF-based approach is not able to model the spectra of mixed-ligand complexes. To address these limitations, we are evaluating the use of density functional theory (DFT) as an ab initio method to predict vibrational frequencies of isotopically-substituted complexes and, hence, equilibrium fractionation factors. In a preliminary examination of the frequency shift upon isotope substitution of the bending and asymmetric stretching modes of the tetrahedral FeCl_42- complex, we find substantial differences between MUBFF and DFT predictions. Results for other Fe

  6. 3D Equilibrium Reconstructions in DIII-D

    NASA Astrophysics Data System (ADS)

    Lao, L. L.; Ferraro, N. W.; Strait, E. J.; Turnbull, A. D.; King, J. D.; Hirshman, H. P.; Lazarus, E. A.; Sontag, A. C.; Hanson, J.; Trevisan, G.

    2013-10-01

    Accurate and efficient 3D equilibrium reconstruction is needed in tokamaks for study of 3D magnetic field effects on experimentally reconstructed equilibrium and for analysis of MHD stability experiments with externally imposed magnetic perturbations. A large number of new magnetic probes have been recently installed in DIII-D to improve 3D equilibrium measurements and to facilitate 3D reconstructions. The V3FIT code has been in use in DIII-D to support 3D reconstruction and the new magnetic diagnostic design. V3FIT is based on the 3D equilibrium code VMEC that assumes nested magnetic surfaces. V3FIT uses a pseudo-Newton least-square algorithm to search for the solution vector. In parallel, the EFIT equilibrium reconstruction code is being extended to allow for 3D effects using a perturbation approach based on an expansion of the MHD equations. EFIT uses the cylindrical coordinate system and can include the magnetic island and stochastic effects. Algorithms are being developed to allow EFIT to reconstruct 3D perturbed equilibria directly making use of plasma response to 3D perturbations from the GATO, MARS-F, or M3D-C1 MHD codes. DIII-D 3D reconstruction examples using EFIT and V3FIT and the new 3D magnetic data will be presented. Work supported in part by US DOE under DE-FC02-04ER54698, DE-FG02-95ER54309 and DE-AC05-06OR23100.

  7. Anatomically accurate individual face modeling.

    PubMed

    Zhang, Yu; Prakash, Edmond C; Sung, Eric

    2003-01-01

    This paper presents a new 3D face model of a specific person constructed from the anatomical perspective. By exploiting the laser range data, a 3D facial mesh precisely representing the skin geometry is reconstructed. Based on the geometric facial mesh, we develop a deformable multi-layer skin model. It takes into account the nonlinear stress-strain relationship and dynamically simulates the non-homogenous behavior of the real skin. The face model also incorporates a set of anatomically-motivated facial muscle actuators and underlying skull structure. Lagrangian mechanics governs the facial motion dynamics, dictating the dynamic deformation of facial skin in response to the muscle contraction. PMID:15455936

  8. Novel mapping in non-equilibrium stochastic processes

    NASA Astrophysics Data System (ADS)

    Heseltine, James; Kim, Eun-jin

    2016-04-01

    We investigate the time-evolution of a non-equilibrium system in view of the change in information and provide a novel mapping relation which quantifies the change in information far from equilibrium and the proximity of a non-equilibrium state to the attractor. Specifically, we utilize a nonlinear stochastic model where the stochastic noise plays the role of incoherent regulation of the dynamical variable x and analytically compute the rate of change in information (information velocity) from the time-dependent probability distribution function. From this, we quantify the total change in information in terms of information length { L } and the associated action { J }, where { L } represents the distance that the system travels in the fluctuation-based, statistical metric space parameterized by time. As the initial probability density function’s mean position (μ) is decreased from the final equilibrium value {μ }* (the carrying capacity), { L } and { J } increase monotonically with interesting power-law mapping relations. In comparison, as μ is increased from {μ }*,{ L } and { J } increase slowly until they level off to a constant value. This manifests the proximity of the state to the attractor caused by a strong correlation for large μ through large fluctuations. Our proposed mapping relation provides a new way of understanding the progression of the complexity in non-equilibrium system in view of information change and the structure of underlying attractor.

  9. Equilibrium Potentials of Membrane Electrodes

    PubMed Central

    Wang, Jui H.; Copeland, Eva

    1973-01-01

    A simple thermodynamic theory of the equilibrium potentials of membrane electrodes is formulated and applied to the glass electrode for measurement of pH. The new formulation assumes the selective adsorption or binding of specific ions on the surface of the membrane which may or may not be permeable to the ion, and includes the conventional derivation based on reversible ion transport across membranes as a special case. To test the theory, a platinum wire was coated with a mixture of stearic acid and methyl-tri-n-octyl-ammonium stearate. When this coated electrode was immersed in aqueous phosphate solution, its potential was found to be a linear function of pH from pH 2 to 12 with a slope equal to the theoretical value of 59.0 mV per pH unit at 24°. PMID:4516194

  10. Neoclassical equilibrium in gyrokinetic simulations

    SciTech Connect

    Garbet, X.; Dif-Pradalier, G.; Nguyen, C.; Sarazin, Y.; Grandgirard, V.; Ghendrih, Ph.

    2009-06-15

    This paper presents a set of model collision operators, which reproduce the neoclassical equilibrium and comply with the constraints of a full-f global gyrokinetic code. The assessment of these operators is based on an entropy variational principle, which allows one to perform a fast calculation of the neoclassical diffusivity and poloidal velocity. It is shown that the force balance equation is recovered at lowest order in the expansion parameter, the normalized gyroradius, hence allowing one to calculate correctly the radial electric field. Also, the conventional neoclassical transport and the poloidal velocity are reproduced in the plateau and banana regimes. The advantages and drawbacks of the various model operators are discussed in view of the requirements for neoclassical and turbulent transport.

  11. String fluid in local equilibrium

    NASA Astrophysics Data System (ADS)

    Schubring, Daniel; Vanchurin, Vitaly

    2014-10-01

    We study the solutions of string fluid equations under the assumption of a local equilibrium which was previously obtained in the context of the kinetic theory. We show that the fluid can be foliated into noninteracting submanifolds whose equations of motion are exactly that of the wiggly strings considered previously by Vilenkin and Carter. In a special case of negligible statistical variance in either the left- or the right-moving directions of microscopic strings, the submanifolds are described by the action of a null-current-carrying chiral string. When both variances vanish the submanifolds are described by the Nambu-Goto action and the string fluid reduces to the string dust introduced by Stachel.

  12. Local non-equilibrium thermodynamics

    PubMed Central

    Jinwoo, Lee; Tanaka, Hajime

    2015-01-01

    Local Shannon entropy lies at the heart of modern thermodynamics, with much discussion of trajectory-dependent entropy production. When taken at both boundaries of a process in phase space, it reproduces the second law of thermodynamics over a finite time interval for small scale systems. However, given that entropy is an ensemble property, it has never been clear how one can assign such a quantity locally. Given such a fundamental omission in our knowledge, we construct a new ensemble composed of trajectories reaching an individual microstate, and show that locally defined entropy, information, and free energy are properties of the ensemble, or trajectory-independent true thermodynamic potentials. We find that the Boltzmann-Gibbs distribution and Landauer's principle can be generalized naturally as properties of the ensemble, and that trajectory-free state functions of the ensemble govern the exact mechanism of non-equilibrium relaxation. PMID:25592077

  13. Equilibrium calculations of firework mixtures

    SciTech Connect

    Hobbs, M.L.; Tanaka, Katsumi; Iida, Mitsuaki; Matsunaga, Takehiro

    1994-12-31

    Thermochemical equilibrium calculations have been used to calculate detonation conditions for typical firework components including three report charges, two display charges, and black powder which is used as a fuse or launch charge. Calculations were performed with a modified version of the TIGER code which allows calculations with 900 gaseous and 600 condensed product species at high pressure. The detonation calculations presented in this paper are thought to be the first report on the theoretical study of firework detonation. Measured velocities for two report charges are available and compare favorably to predicted detonation velocities. However, the measured velocities may not be true detonation velocities. Fast deflagration rather than an ideal detonation occurs when reactants contain significant amounts of slow reacting constituents such as aluminum or titanium. Despite such uncertainties in reacting pyrotechnics, the detonation calculations do show the complex nature of condensed phase formation at elevated pressures and give an upper bound for measured velocities.

  14. Local non-equilibrium thermodynamics.

    PubMed

    Jinwoo, Lee; Tanaka, Hajime

    2015-01-01

    Local Shannon entropy lies at the heart of modern thermodynamics, with much discussion of trajectory-dependent entropy production. When taken at both boundaries of a process in phase space, it reproduces the second law of thermodynamics over a finite time interval for small scale systems. However, given that entropy is an ensemble property, it has never been clear how one can assign such a quantity locally. Given such a fundamental omission in our knowledge, we construct a new ensemble composed of trajectories reaching an individual microstate, and show that locally defined entropy, information, and free energy are properties of the ensemble, or trajectory-independent true thermodynamic potentials. We find that the Boltzmann-Gibbs distribution and Landauer's principle can be generalized naturally as properties of the ensemble, and that trajectory-free state functions of the ensemble govern the exact mechanism of non-equilibrium relaxation. PMID:25592077

  15. Toward Improving Atmospheric Models and Ozone Projections: Laboratory UV Absorption Cross Sections and Equilibrium Constant of ClOOCl

    NASA Astrophysics Data System (ADS)

    Wilmouth, D. M.; Klobas, J. E.; Anderson, J. G.

    2015-12-01

    Thirty years have now passed since the discovery of the Antarctic ozone hole, and despite comprehensive international agreements being in place to phase out CFCs and halons, polar ozone losses generally remain severe. The relevant halogen compounds have very long atmospheric lifetimes, which ensures that seasonal polar ozone depletion will likely continue for decades to come. Changes in the climate system can further impact stratospheric ozone abundance through changes in the temperature and water vapor structure of the atmosphere and through the potential initiation of solar radiation management efforts. In many ways, the rate at which climate is changing must now be considered fast relative to the slow removal of halogens from the atmosphere. Photochemical models of Earth's atmosphere play a critical role in understanding and projecting ozone levels, but in order for these models to be accurate, they must be built on a foundation of accurate laboratory data. ClOOCl is the centerpiece of the catalytic cycle that accounts for more than 50% of the chlorine-catalyzed ozone loss in the Arctic and Antarctic stratosphere every spring, and so uncertainties in the ultraviolet cross sections of ClOOCl are particularly important. Additionally, the equilibrium constant of the dimerization reaction of ClO merits further study, as there are important discrepancies between in situ measurements and lab-based models, and the JPL-11 recommended equilibrium constant includes high error bars at atmospherically relevant temperatures (~75% at 200 K). Here we analyze available data for the ClOOCl ultraviolet cross sections and equilibrium constant and present new laboratory spectroscopic results.

  16. Determination of equilibrium free energy from nonequilibrium work measurements

    PubMed Central

    Chen, L. Y.; Bastien, D. A.; Espejel, H. E.

    2010-01-01

    The fluctuation–dissipation theorem (FDT) of Brownian dynamics (BD) is applied to extract the equilibrium free-energy profile from the nonequilibrium, irreversible work measured in single-molecule pulling experiments. Two sets of in silico experiments are performed to explore the free-energy landscape of deca-alanine peptide as a function of its end-to-end distance and to determine the free-energy profile of water permeation through the channels of aquaglyceroporin GlpF. With a small number of pulling paths sampled, the BD-FDT is shown to produce accurate estimates of the free-energy profiles for both systems. PMID:20463999

  17. Predicting equilibrium uranium isotope fractionation in crystals and solution

    NASA Astrophysics Data System (ADS)

    Schauble, E. A.

    2015-12-01

    Despite the rapidly growing interest in using 238U/235U measurements as a proxy for changes in oxygen abundance in surface and near-surface environments, the present theoretical understanding of uranium isotope fractionation is limited to a few simple gas-phase molecules and analogues of dissolved species (e.g., 1,2,3). Understanding uranium isotope fractionation behavior in more complicated species, such as crystals and adsorption complexes, will help in the design and interpretation of experiments and field studies, and may suggest other uses for 38U/235U measurements. In this study, a recently developed first-principles method for estimating the nuclear volume component of field shift fractionation in crystals and complex molecular species (4) is combined with mass-dependent fractionation theory to predict equilibrium 38U/235U fractionations in aqueous and crystalline uranium compounds, including uraninite (UO2). The nuclear field shift effect, caused by the interaction of electrons with the finite volume of the positive charge distribution in uranium nuclei, is estimated using Density Functional Theory and the Projector Augmented Wave method (DFT-PAW). Tests against relativistic electronic structure calculations and Mössbauer isomer shift data indicate that the DFT-PAW method is reasonably accurate, while being much better suited to models of complex and crystalline species. Initial results confirm previous predictions that the nuclear volume effect overwhelms mass depdendent fractionation in U(VI)-U(IV) exchange reactions, leading to higher 238U/235U in U(IV) species (i.e., for UO2 xtal vs. UO22+aq, ln αNV ≈ +1.8‰ , ln αMD ≈ -0.8‰, ln αTotal ≈ +1.0‰ at 25ºC). UO2 and U(H2O)94+, are within ~0.4‰ of each other, while U(VI) species appear to be more variable. This suggests that speciation is likely to significantly affect natural uranium isotope fractionations, in addition to oxidation state. Tentatively, it appears that uranyl-type (UO22

  18. A procedure for computing accurate ab initio quartic force fields: Application to HO2+ and H2O

    NASA Astrophysics Data System (ADS)

    Huang, Xinchuan; Lee, Timothy J.

    2008-07-01

    A procedure for the calculation of molecular quartic force fields (QFFs) is proposed and investigated. The goal is to generate highly accurate ab initio QFFs that include many of the so-called ``small'' effects that are necessary to achieve high accuracy. The small effects investigated in the present study include correlation of the core electrons (core correlation), extrapolation to the one-particle basis set limit, correction for scalar relativistic contributions, correction for higher-order correlation effects, and inclusion of diffuse functions in the one-particle basis set. The procedure is flexible enough to allow for some effects to be computed directly, while others may be added as corrections. A single grid of points is used and is centered about an initial reference geometry that is designed to be as close as possible to the final ab initio equilibrium structure (with all effects included). It is shown that the least-squares fit of the QFF is not compromised by the added corrections, and the balance between elimination of contamination from higher-order force constants while retaining energy differences large enough to yield meaningful quartic force constants is essentially unchanged from the standard procedures we have used for many years. The initial QFF determined from the least-squares fit is transformed to the exact minimum in order to eliminate gradient terms and allow for the use of second-order perturbation theory for evaluation of spectroscopic constants. It is shown that this step has essentially no effect on the quality of the QFF largely because the initial reference structure is, by design, very close to the final ab initio equilibrium structure. The procedure is used to compute an accurate, purely ab initio QFF for the H2O molecule, which is used as a benchmark test case. The procedure is then applied to the ground and first excited electronic states of the HO2+ molecular cation. Fundamental vibrational frequencies and spectroscopic

  19. On the importance of having accurate data for astrophysical modelling

    NASA Astrophysics Data System (ADS)

    Lique, Francois

    2016-06-01

    The Herschel telescope and the ALMA and NOEMA interferometers have opened new windows of observation for wavelengths ranging from far infrared to sub-millimeter with spatial and spectral resolutions previously unmatched. To make the most of these observations, an accurate knowledge of the physical and chemical processes occurring in the interstellar and circumstellar media is essential.In this presentation, I will discuss what are the current needs of astrophysics in terms of molecular data and I will show that accurate molecular data are crucial for the proper determination of the physical conditions in molecular clouds.First, I will focus on collisional excitation studies that are needed for molecular lines modelling beyond the Local Thermodynamic Equilibrium (LTE) approach. In particular, I will show how new collisional data for the HCN and HNC isomers, two tracers of star forming conditions, have allowed solving the problem of their respective abundance in cold molecular clouds. I will also present the last collisional data that have been computed in order to analyse new highly resolved observations provided by the ALMA interferometer.Then, I will present the calculation of accurate rate constants for the F+H2 → HF+H and Cl+H2 ↔ HCl+H reactions, which have allowed a more accurate determination of the physical conditions in diffuse molecular clouds. I will also present the recent work on the ortho-para-H2 conversion due to hydrogen exchange that allow more accurate determination of the ortho-to-para-H2 ratio in the universe and that imply a significant revision of the cooling mechanism in astrophysical media.

  20. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2013-07-01 2013-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  1. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  2. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2011-07-01 2011-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  3. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2014-07-01 2014-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  4. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2012-07-01 2012-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  5. Non equilibrium statistical mechanics of geophysical flows

    NASA Astrophysics Data System (ADS)

    Bouchet, F.

    2012-04-01

    Onsager first proposed to explain the self organization of turbulent flows using the statistical mechanics framework. Generalization of those ideas to the class of 2D-Euler and Quasi-Gestrophic models led to the Robert-Sommeria-Miller theory. This approach was successful in modeling many geophysical phenomena: the Great Red Spot of Jupiter [2, 1], drift of mesoscale ocean vortices [3, 1], self-organization of Quasi-Geostrophic dynamics in mid-basin jets similar to the Gulf-Stream and the Kuroshio [3, 1], and so on. However, this type of equilibrium theories fail to take into account forces and dissipation. This is a strong limitation for many geophysical phenomena. Interestingly, it is possible to circumvent these difficulties using the most modern theoretical development of non-equilibrium statistical mechanics: large deviation [4] and instanton theories. As an example, we will discuss geophysical turbulent flows which have more than one attractor (bistability or mutistability). For instance, paths of the Kuroshio [5], the Earth's magnetic field reversal, atmospheric flows [6], MHD experiments [7], 2D turbulence experiments [8, 9], 3D flows [10] show this kind of behavior. On Navier-Stokes and Quasi-Geostrophic turbulent flows, we predict the conditions for existence of rare transitions between attractors, and the dynamics of those transitions. We discuss how these results are probably connected to the long debated existence of multi-stability in the atmosphere and oceans, and how non-equilibrium statistical mechanics can allow to settle this issue. Generalization of statistical mechanics to more comprehensive hydrodynamical models, which include gravity wave dynamics and allow for the possibility of energy transfer through wave motion, would be extremely interesting. Namely, both are essential in understanding energy balance of geophysical flows. However, due to difficulties in essential theoretical parts of the statistical mechanics approach, previous methods

  6. Oppositely charged colloids out of equilibrium

    NASA Astrophysics Data System (ADS)

    Vissers, T.

    2010-11-01

    potential and charge are studied by electrophoresis. Here, the velocity of the particles is measured while they are moving in an electric field. Using our real-space CLSM setup, we find that for a single-component system, the charge on the particles decreases with increasing volume fraction. Apart from structures that oppositely charged particles form close to thermodynamic equilibrium, we also study pattern formation when the system is driven out of equilibrium by an electric field. When oppositely charged particles are driven in opposite directions, the collisions between them cause particle of the same kind to form lanes. By combining our CLSM experiments with Brownian dynamics computer simulations, we study the structure and the dynamics of the suspension on the single-particle level. We find that the number of particles in a lane increases continuously with the field strength. By studying the dynamics and fluctuations parallel and perpendicular to the electric field direction, we identify the key mechanism of lane-formation. We show that pattern formation can easily become more complicated when we introduce alternating current (AC) fields. In addition to the formation of lanes parallel to the field-axis, bands of like-charged particles can form perpendicular to it. When the particles are sufficiently mobile, the system can be remixed again by changing the frequency. When AC-fields with higher field strengths are used, we show that complex patterns, including rotating instabilities, can emerge. The results in this thesis yield fundamental insight in electrophoresis, crystallization and pattern formation when systems are driven out of equilibrium. The results on lane- and band-formation can be relevant for the design of electronic ink (e-ink), where electrically driven oppositely charged particles are used to change the image on a piece of electronic paper.

  7. Accurate description of phase diagram of clathrate hydrates at the molecular level

    NASA Astrophysics Data System (ADS)

    Belosludov, Rodion V.; Subbotin, Oleg S.; Mizuseki, Hiroshi; Kawazoe, Yoshiyuki; Belosludov, Vladimir R.

    2009-12-01

    In order to accurately estimate the thermodynamic properties of hydrogen clathrate hydrates, we developed a method based on the solid solution theory of van der Waals and Platteeuw. This model allows one to take into account the influence of guest molecules on the host lattice and guest-guest interactions—especially when more than one guest molecule occupies a cage. The free energies, equations of state, and chemical potentials of hydrogen and mixed propane-hydrogen clathrate hydrates of cubic structure II with different cage fillings have been estimated using this approach. Moreover, the proposed theory has been used for construction p -T phase diagrams of hydrogen hydrate and mixed hydrogen-propane hydrates in a wide range of pressures and temperatures. For the systems with well defined interactions the calculated curves of "guest gas-hydrate-ice Ih" equilibrium agree with the available experimental data. We also believe that the present model allows one not only to calculate the hydrogen storage ability of known hydrogen hydrate but also predict this value for structures that have not yet been realized by experiment.

  8. Evaluating equilibrium and non-equilibrium transport of bromide and isoproturon in disturbed and undisturbed soil columns.

    PubMed

    Dousset, S; Thevenot, M; Pot, V; Simunek, J; Andreux, F

    2007-12-01

    In this study, displacement experiments of isoproturon were conducted in disturbed and undisturbed columns of a silty clay loam soil under similar rainfall intensities. Solute transport occurred under saturated conditions in the undisturbed soil and under unsaturated conditions in the sieved soil because of a greater bulk density of the compacted undisturbed soil compared to the sieved soil. The objective of this work was to determine transport characteristics of isoproturon relative to bromide tracer. Triplicate column experiments were performed with sieved (structure partially destroyed to simulate conventional tillage) and undisturbed (structure preserved) soils. Bromide experimental breakthrough curves were analyzed using convective-dispersive and dual-permeability (DP) models (HYDRUS-1D). Isoproturon breakthrough curves (BTCs) were analyzed using the DP model that considered either chemical equilibrium or non-equilibrium transport. The DP model described the bromide elution curves of the sieved soil columns well, whereas it overestimated the tailing of the bromide BTCs of the undisturbed soil columns. A higher degree of physical non-equilibrium was found in the undisturbed soil, where 56% of total water was contained in the slow-flow matrix, compared to 26% in the sieved soil. Isoproturon BTCs were best described in both sieved and undisturbed soil columns using the DP model combined with the chemical non-equilibrium. Higher degradation rates were obtained in the transport experiments than in batch studies, for both soils. This was likely caused by hysteresis in sorption of isoproturon. However, it cannot be ruled out that higher degradation rates were due, at least in part, to the adopted first-order model. Results showed that for similar rainfall intensity, physical and chemical non-equilibrium were greater in the saturated undisturbed soil than in the unsaturated sieved soil. Results also suggested faster transport of isoproturon in the undisturbed soil due

  9. Experimental studies in non-equilibrium physics

    NASA Astrophysics Data System (ADS)

    Cressman, John Robert, Jr.

    This work is a collection of three experiments aimed at studying different facets of non-equilibrium dynamics. Chapter I concerns strongly compressible turbulence, which turns out to be very different from incompressible turbulence. The focus is on the dispersion of contaminants in such a flow. This type of turbulence can be studied, at very low mach number, by measuring the velocity fields of particles that float on a turbulently stirred body of water. It turns out that in the absence of incompressibility, the turbulence causes particles to cluster rather than to disperse. The implications of the observations are far reaching and include the transport of pollutants on the oceans surface, phytoplankton growth, as well as industrial applications. Chapter II deals with the effects of polymer additives on drag reduction and turbulent suppression, a well-known phenomenon that is not yet understood. In an attempt to simplify the problem, the effects of a polymer additive were investigated in a vortex street formed in a flowing soap film. Measurements suggest that an increase in elongational viscosity is responsible for a substantial reduction in periodic velocity fluctuations. This study also helps to illuminate the mechanism responsible for vortex separation in the wake of a bluff body. Chapter III describes an experiment designed to test a theoretical approach aimed at generalizing the classical fluctuation dissipation theorem (FDT). This theorem applies to systems driven only slightly away from thermal equilibrium, whereas ours, a liquid crystal under-going electroconvection, is so strongly driven, that the FDT does not apply. Both theory and experiment focus on the flux in global power fluctuations. Physical limitations did not permit a direct test of the theory, however it was possible to establish several interesting characteristics of the system: the source of the fluctuations is the transient defect structures that are generated when the system is driven hard

  10. A Progression of Static Equilibrium Laboratory Exercises

    NASA Astrophysics Data System (ADS)

    Kutzner, Mickey; Kutzner, Andrew

    2013-10-01

    Although simple architectural structures like bridges, catwalks, cantilevers, and Stonehenge have been integral in human societies for millennia, as have levers and other simple tools, modern students of introductory physics continue to grapple with Newton's conditions for static equilibrium. As formulated in typical introductory physics textbooks, these two conditions appear as ΣF=0(1) and Στ=0,(2) where each torque τ is defined as the cross product between the lever arm vector r and the corresponding applied force F, τ =r×F,(3) having magnitude, τ =Frsinθ.(4) The angle θ here is between the two vectors F and r. In Eq. (1), upward (downward) forces are considered positive (negative). In Eq. (2), counterclockwise (clockwise) torques are considered positive (negative). Equation (1) holds that the vector sum of the external forces acting on an object must be zero to prevent linear accelerations; Eq. (2) states that the vector sum of torques due to external forces about any axis must be zero to prevent angular accelerations. In our view these conditions can be problematic for students because a) the equations contain the unfamiliar summation notation Σ, b) students are uncertain of the role of torques in causing rotations, and c) it is not clear why the sum of torques is zero regardless of the choice of axis. Gianino5 describes an experiment using MBL and a force sensor to convey the meaning of torque as applied to a rigid-body lever system without exploring quantitative aspects of the conditions for static equilibrium.

  11. Mathematical modeling of non-equilibrium sorption

    NASA Astrophysics Data System (ADS)

    Kaliev, Ibragim A.; Mukhambetzhanov, Saltanbek T.; Sabitova, Gulnara S.; Sakhit, Anghyz E.

    2016-08-01

    We consider the system of equations modeling the process of non-equilibrium sorption. Difference approximation of differential problem by the implicit scheme is formulated. The solution of the difference problem is constructed using the sweep method. Based on the numerical results we can conclude the following: when the relaxation time decreases to 0, then the solution of non-equilibrium problem tends with increasing time to solution of the equilibrium problem.

  12. Computational methods for reactive transport modeling: A Gibbs energy minimization approach for multiphase equilibrium calculations

    NASA Astrophysics Data System (ADS)

    Leal, Allan M. M.; Kulik, Dmitrii A.; Kosakowski, Georg

    2016-02-01

    We present a numerical method for multiphase chemical equilibrium calculations based on a Gibbs energy minimization approach. The method can accurately and efficiently determine the stable phase assemblage at equilibrium independently of the type of phases and species that constitute the chemical system. We have successfully applied our chemical equilibrium algorithm in reactive transport simulations to demonstrate its effective use in computationally intensive applications. We used FEniCS to solve the governing partial differential equations of mass transport in porous media using finite element methods in unstructured meshes. Our equilibrium calculations were benchmarked with GEMS3K, the numerical kernel of the geochemical package GEMS. This allowed us to compare our results with a well-established Gibbs energy minimization algorithm, as well as their performance on every mesh node, at every time step of the transport simulation. The benchmark shows that our novel chemical equilibrium algorithm is accurate, robust, and efficient for reactive transport applications, and it is an improvement over the Gibbs energy minimization algorithm used in GEMS3K. The proposed chemical equilibrium method has been implemented in Reaktoro, a unified framework for modeling chemically reactive systems, which is now used as an alternative numerical kernel of GEMS.

  13. Equilibrium sampling by reweighting nonequilibrium simulation trajectories

    NASA Astrophysics Data System (ADS)

    Yang, Cheng; Wan, Biao; Xu, Shun; Wang, Yanting; Zhou, Xin

    2016-03-01

    Based on equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space of complex systems, which are separated into some metastable regions by high free energy barriers. Nonequilibrium simulations could enhance transitions among these metastable regions and then be applied to sample equilibrium distributions in complex systems, since the associated nonequilibrium effects can be removed by employing the Jarzynski equality (JE). Here we present such a systematical method, named reweighted nonequilibrium ensemble dynamics (RNED), to efficiently sample equilibrium conformations. The RNED is a combination of the JE and our previous reweighted ensemble dynamics (RED) method. The original JE reproduces equilibrium from lots of nonequilibrium trajectories but requires that the initial distribution of these trajectories is equilibrium. The RED reweights many equilibrium trajectories from an arbitrary initial distribution to get the equilibrium distribution, whereas the RNED has both advantages of the two methods, reproducing equilibrium from lots of nonequilibrium simulation trajectories with an arbitrary initial conformational distribution. We illustrated the application of the RNED in a toy model and in a Lennard-Jones fluid to detect its liquid-solid phase coexistence. The results indicate that the RNED sufficiently extends the application of both the original JE and the RED in equilibrium sampling of complex systems.

  14. Equilibrium sampling by reweighting nonequilibrium simulation trajectories.

    PubMed

    Yang, Cheng; Wan, Biao; Xu, Shun; Wang, Yanting; Zhou, Xin

    2016-03-01

    Based on equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space of complex systems, which are separated into some metastable regions by high free energy barriers. Nonequilibrium simulations could enhance transitions among these metastable regions and then be applied to sample equilibrium distributions in complex systems, since the associated nonequilibrium effects can be removed by employing the Jarzynski equality (JE). Here we present such a systematical method, named reweighted nonequilibrium ensemble dynamics (RNED), to efficiently sample equilibrium conformations. The RNED is a combination of the JE and our previous reweighted ensemble dynamics (RED) method. The original JE reproduces equilibrium from lots of nonequilibrium trajectories but requires that the initial distribution of these trajectories is equilibrium. The RED reweights many equilibrium trajectories from an arbitrary initial distribution to get the equilibrium distribution, whereas the RNED has both advantages of the two methods, reproducing equilibrium from lots of nonequilibrium simulation trajectories with an arbitrary initial conformational distribution. We illustrated the application of the RNED in a toy model and in a Lennard-Jones fluid to detect its liquid-solid phase coexistence. The results indicate that the RNED sufficiently extends the application of both the original JE and the RED in equilibrium sampling of complex systems. PMID:27078486

  15. Determining Equilibrium Position For Acoustical Levitation

    NASA Technical Reports Server (NTRS)

    Barmatz, M. B.; Aveni, G.; Putterman, S.; Rudnick, J.

    1989-01-01

    Equilibrium position and orientation of acoustically-levitated weightless object determined by calibration technique on Earth. From calibration data, possible to calculate equilibrium position and orientation in presence of Earth gravitation. Sample not levitated acoustically during calibration. Technique relies on Boltzmann-Ehrenfest adiabatic-invariance principle. One converts resonant-frequency-shift data into data on normalized acoustical potential energy. Minimum of energy occurs at equilibrium point. From gradients of acoustical potential energy, one calculates acoustical restoring force or torque on objects as function of deviation from equilibrium position or orientation.

  16. 1-D EQUILIBRIUM DISCRETE DIFFUSION MONTE CARLO

    SciTech Connect

    T. EVANS; ET AL

    2000-08-01

    We present a new hybrid Monte Carlo method for 1-D equilibrium diffusion problems in which the radiation field coexists with matter in local thermodynamic equilibrium. This method, the Equilibrium Discrete Diffusion Monte Carlo (EqDDMC) method, combines Monte Carlo particles with spatially discrete diffusion solutions. We verify the EqDDMC method with computational results from three slab problems. The EqDDMC method represents an incremental step toward applying this hybrid methodology to non-equilibrium diffusion, where it could be simultaneously coupled to Monte Carlo transport.

  17. Passive equilibrium studies on ZT-P

    SciTech Connect

    Pickrell, M.M.; Reass, W.A.

    1987-12-01

    The poloidal field system of ZT-P was modified by the addition of a transformer, which coupled the magnetizing and equilibrium circuits. ZT-P is a small, air core, Reversed Field Pinch, operated at the Los Alamos National Laboratory. It is used as test bed for the much larger ZT-H, RFP experiment, now under construction at LANL. Planned experiments include size scaling measurements and determining the effect of low time constant measurements and determining the effect of low time constant shell operation. ZT-P has had an entirely passive equilibrium system, which did not provide a well centered equilibrium, although a tolerable equilibrium was realized by removing half of the equilibrium coil set. The transformer was added to the poloidal field system to adjust the equilibrium current for a centered plasma, while using the entire coil set. It also had the effect of reducing the dependence of the equilibrium on the plasma resistance. Stable, well centered discharges were achieved over a broad range of plasma currents. The improved equilibrium also lowered the loop voltage and extended the discharge lifetime. These experiments also investigated the unique problems of equilibrium systems on air core RFP devices. 26 refs., 6 figs.

  18. Equilibrium coexistence of three amphiboles

    USGS Publications Warehouse

    Robinson, P.; Jaffe, H.W.; Klein, C., Jr.; Ross, M.

    1969-01-01

    Electron probe and wet chemical analyses of amphibole pairs from the sillimanite zone of central Massachusetts and adjacent New Hampshire indicated that for a particular metamorphic grade there should be a restricted composition range in which three amphiboles can coexist stably. An unequivocal example of such an equilibrium three amphibole rock has been found in the sillimanite-orthoclase zone. It contains a colorless primitive clinoamphibole, space group P21/m, optically and chemically like cummingtonite with blue-green hornblende exsolution lamellae on (100) and (-101) of the host; blue-green hornblende, space group C2/m, with primitive cummingtonite exsolution lamellae on (100) and (-101) of the host; and pale pinkish tan anthophyllite, space group Pnma, that is free of visible exsolution lamellae but is a submicroscopic intergrowth of two orthorhombic amphiboles. Mutual contacts and coarse, oriented intergrowths of two and three host amphiboles indicate the three grew as an equilibrium assemblage prior to exsolution. Electron probe analyses at mutual three-amphibole contacts showed little variation in the composition of each amphibole. Analyses believed to represent most closely the primary amphibole compositions gave atomic proportions on the basis of 23 oxygens per formula unit as follows: for primitive cummingtonite (Na0.02Ca0.21- Mn0.06Fe2+2.28Mg4.12Al0.28) (Al0.17Si7.83), for hornblende (Na0.35Ca1.56Mn0.02Fe1.71Mg2.85Al0.92) (Al1.37Si6.63), and for anthophyllite (Na0.10Ca0.06Mn0.06Fe2.25Mg4.11Al0.47) (Al0.47Si7.53). The reflections violating C-symmetry, on X-ray single crystal photographs of the primitive cummingtonite, are weak and diffuse, and suggest a partial inversion from a C-centered to a primitive clinoamphibole. Single crystal photographs of the anthophyllite show split reflections indicating it is an intergrowth of about 80% anthophyllite and about 20% gedrite which differ in their b crystallographic dimensions. Split reflections are

  19. Accurate, meshless methods for magnetohydrodynamics

    NASA Astrophysics Data System (ADS)

    Hopkins, Philip F.; Raives, Matthias J.

    2016-01-01

    Recently, we explored new meshless finite-volume Lagrangian methods for hydrodynamics: the `meshless finite mass' (MFM) and `meshless finite volume' (MFV) methods; these capture advantages of both smoothed particle hydrodynamics (SPH) and adaptive mesh refinement (AMR) schemes. We extend these to include ideal magnetohydrodynamics (MHD). The MHD equations are second-order consistent and conservative. We augment these with a divergence-cleaning scheme, which maintains nabla \\cdot B≈ 0. We implement these in the code GIZMO, together with state-of-the-art SPH MHD. We consider a large test suite, and show that on all problems the new methods are competitive with AMR using constrained transport (CT) to ensure nabla \\cdot B=0. They correctly capture the growth/structure of the magnetorotational instability, MHD turbulence, and launching of magnetic jets, in some cases converging more rapidly than state-of-the-art AMR. Compared to SPH, the MFM/MFV methods exhibit convergence at fixed neighbour number, sharp shock-capturing, and dramatically reduced noise, divergence errors, and diffusion. Still, `modern' SPH can handle most test problems, at the cost of larger kernels and `by hand' adjustment of artificial diffusion. Compared to non-moving meshes, the new methods exhibit enhanced `grid noise' but reduced advection errors and diffusion, easily include self-gravity, and feature velocity-independent errors and superior angular momentum conservation. They converge more slowly on some problems (smooth, slow-moving flows), but more rapidly on others (involving advection/rotation). In all cases, we show divergence control beyond the Powell 8-wave approach is necessary, or all methods can converge to unphysical answers even at high resolution.

  20. Equilibrium partitioning of Ficoll in composite hydrogels.

    PubMed

    Kosto, Kimberly B; Panuganti, Swapna; Deen, William M

    2004-09-15

    Equilibrium partition coefficients (phi, the concentration in the gel divided by that in free solution) of fluorescein-labeled Ficolls in pure agarose and agarose-dextran composite gels were measured as a function of gel composition and Ficoll size. The four narrow fractions of Ficoll, a spherical polysaccharide, had Stokes-Einstein radii ranging from 2.7 to 5.9 nm. Gels with agarose volume fractions of 0.040 and 0.080 were studied, with dextran volume fractions (calculated as if the chain were a long fiber) up to 0.011. As expected, phi generally decreased as the Ficoll size increased (for a given gel composition) or as the amount of dextran incorporated into the gel increased (for a given agarose concentration and Ficoll size). The decrease in phi that accompanied dextran addition was predicted well by an excluded volume theory in which agarose and dextran were both treated as rigid, straight, randomly positioned and oriented fibers. Modeling dextran as a spherical coil within a fibrous agarose gel produced much less accurate predictions. The diffusional permeabilities of these gels were assessed by combining the current partitioning data with relative diffusivities (Kd, the diffusivity in the gel divided by that in free solution) reported previously. The values of phi Kd for a synthetic gel with 8.0% agarose and 1.1% dextran (by volume) were found to be very similar to those for the glomerular basement membrane, a physiologically important material which also has a total solids content of approximately 10%. PMID:15341852

  1. Accurate Weather Forecasting for Radio Astronomy

    NASA Astrophysics Data System (ADS)

    Maddalena, Ronald J.

    2010-01-01

    The NRAO Green Bank Telescope routinely observes at wavelengths from 3 mm to 1 m. As with all mm-wave telescopes, observing conditions depend upon the variable atmospheric water content. The site provides over 100 days/yr when opacities are low enough for good observing at 3 mm, but winds on the open-air structure reduce the time suitable for 3-mm observing where pointing is critical. Thus, to maximum productivity the observing wavelength needs to match weather conditions. For 6 years the telescope has used a dynamic scheduling system (recently upgraded; www.gb.nrao.edu/DSS) that requires accurate multi-day forecasts for winds and opacities. Since opacity forecasts are not provided by the National Weather Services (NWS), I have developed an automated system that takes available forecasts, derives forecasted opacities, and deploys the results on the web in user-friendly graphical overviews (www.gb.nrao.edu/ rmaddale/Weather). The system relies on the "North American Mesoscale" models, which are updated by the NWS every 6 hrs, have a 12 km horizontal resolution, 1 hr temporal resolution, run to 84 hrs, and have 60 vertical layers that extend to 20 km. Each forecast consists of a time series of ground conditions, cloud coverage, etc, and, most importantly, temperature, pressure, humidity as a function of height. I use the Liebe's MWP model (Radio Science, 20, 1069, 1985) to determine the absorption in each layer for each hour for 30 observing wavelengths. Radiative transfer provides, for each hour and wavelength, the total opacity and the radio brightness of the atmosphere, which contributes substantially at some wavelengths to Tsys and the observational noise. Comparisons of measured and forecasted Tsys at 22.2 and 44 GHz imply that the forecasted opacities are good to about 0.01 Nepers, which is sufficient for forecasting and accurate calibration. Reliability is high out to 2 days and degrades slowly for longer-range forecasts.

  2. General multi-group macroscopic modeling for thermo-chemical non-equilibrium gas mixtures

    NASA Astrophysics Data System (ADS)

    Liu, Yen; Panesi, Marco; Sahai, Amal; Vinokur, Marcel

    2015-04-01

    This paper opens a new door to macroscopic modeling for thermal and chemical non-equilibrium. In a game-changing approach, we discard conventional theories and practices stemming from the separation of internal energy modes and the Landau-Teller relaxation equation. Instead, we solve the fundamental microscopic equations in their moment forms but seek only optimum representations for the microscopic state distribution function that provides converged and time accurate solutions for certain macroscopic quantities at all times. The modeling makes no ad hoc assumptions or simplifications at the microscopic level and includes all possible collisional and radiative processes; it therefore retains all non-equilibrium fluid physics. We formulate the thermal and chemical non-equilibrium macroscopic equations and rate coefficients in a coupled and unified fashion for gases undergoing completely general transitions. All collisional partners can have internal structures and can change their internal energy states after transitions. The model is based on the reconstruction of the state distribution function. The internal energy space is subdivided into multiple groups in order to better describe non-equilibrium state distributions. The logarithm of the distribution function in each group is expressed as a power series in internal energy based on the maximum entropy principle. The method of weighted residuals is applied to the microscopic equations to obtain macroscopic moment equations and rate coefficients succinctly to any order. The model's accuracy depends only on the assumed expression of the state distribution function and the number of groups used and can be self-checked for accuracy and convergence. We show that the macroscopic internal energy transfer, similar to mass and momentum transfers, occurs through nonlinear collisional processes and is not a simple relaxation process described by, e.g., the Landau-Teller equation. Unlike the classical vibrational energy

  3. General multi-group macroscopic modeling for thermo-chemical non-equilibrium gas mixtures

    SciTech Connect

    Liu, Yen Vinokur, Marcel; Panesi, Marco; Sahai, Amal

    2015-04-07

    This paper opens a new door to macroscopic modeling for thermal and chemical non-equilibrium. In a game-changing approach, we discard conventional theories and practices stemming from the separation of internal energy modes and the Landau-Teller relaxation equation. Instead, we solve the fundamental microscopic equations in their moment forms but seek only optimum representations for the microscopic state distribution function that provides converged and time accurate solutions for certain macroscopic quantities at all times. The modeling makes no ad hoc assumptions or simplifications at the microscopic level and includes all possible collisional and radiative processes; it therefore retains all non-equilibrium fluid physics. We formulate the thermal and chemical non-equilibrium macroscopic equations and rate coefficients in a coupled and unified fashion for gases undergoing completely general transitions. All collisional partners can have internal structures and can change their internal energy states after transitions. The model is based on the reconstruction of the state distribution function. The internal energy space is subdivided into multiple groups in order to better describe non-equilibrium state distributions. The logarithm of the distribution function in each group is expressed as a power series in internal energy based on the maximum entropy principle. The method of weighted residuals is applied to the microscopic equations to obtain macroscopic moment equations and rate coefficients succinctly to any order. The model’s accuracy depends only on the assumed expression of the state distribution function and the number of groups used and can be self-checked for accuracy and convergence. We show that the macroscopic internal energy transfer, similar to mass and momentum transfers, occurs through nonlinear collisional processes and is not a simple relaxation process described by, e.g., the Landau-Teller equation. Unlike the classical vibrational energy

  4. General multi-group macroscopic modeling for thermo-chemical non-equilibrium gas mixtures.

    PubMed

    Liu, Yen; Panesi, Marco; Sahai, Amal; Vinokur, Marcel

    2015-04-01

    This paper opens a new door to macroscopic modeling for thermal and chemical non-equilibrium. In a game-changing approach, we discard conventional theories and practices stemming from the separation of internal energy modes and the Landau-Teller relaxation equation. Instead, we solve the fundamental microscopic equations in their moment forms but seek only optimum representations for the microscopic state distribution function that provides converged and time accurate solutions for certain macroscopic quantities at all times. The modeling makes no ad hoc assumptions or simplifications at the microscopic level and includes all possible collisional and radiative processes; it therefore retains all non-equilibrium fluid physics. We formulate the thermal and chemical non-equilibrium macroscopic equations and rate coefficients in a coupled and unified fashion for gases undergoing completely general transitions. All collisional partners can have internal structures and can change their internal energy states after transitions. The model is based on the reconstruction of the state distribution function. The internal energy space is subdivided into multiple groups in order to better describe non-equilibrium state distributions. The logarithm of the distribution function in each group is expressed as a power series in internal energy based on the maximum entropy principle. The method of weighted residuals is applied to the microscopic equations to obtain macroscopic moment equations and rate coefficients succinctly to any order. The model's accuracy depends only on the assumed expression of the state distribution function and the number of groups used and can be self-checked for accuracy and convergence. We show that the macroscopic internal energy transfer, similar to mass and momentum transfers, occurs through nonlinear collisional processes and is not a simple relaxation process described by, e.g., the Landau-Teller equation. Unlike the classical vibrational energy

  5. Non-equilibrium dynamics contribute to ion selectivity in the KcsA channel.

    PubMed

    Ngo, Van; Stefanovski, Darko; Haas, Stephan; Farley, Robert A

    2014-01-01

    The ability of biological ion channels to conduct selected ions across cell membranes is critical for the survival of both animal and bacterial cells. Numerous investigations of ion selectivity have been conducted over more than 50 years, yet the mechanisms whereby the channels select certain ions and reject others are not well understood. Here we report a new application of Jarzynski's Equality to investigate the mechanism of ion selectivity using non-equilibrium molecular dynamics simulations of Na(+) and K(+) ions moving through the KcsA channel. The simulations show that the selectivity filter of KcsA adapts and responds to the presence of the ions with structural rearrangements that are different for Na(+) and K(+). These structural rearrangements facilitate entry of K(+) ions into the selectivity filter and permeation through the channel, and rejection of Na(+) ions. A mechanistic model of ion selectivity by this channel based on the results of the simulations relates the structural rearrangement of the selectivity filter to the differential dehydration of ions and multiple-ion occupancy and describes a mechanism to efficiently select and conduct K(+). Estimates of the K(+)/Na(+) selectivity ratio and steady state ion conductance for KcsA from the simulations are in good quantitative agreement with experimental measurements. This model also accurately describes experimental observations of channel block by cytoplasmic Na(+) ions, the "punch through" relief of channel block by cytoplasmic positive voltages, and is consistent with the knock-on mechanism of ion permeation. PMID:24465882

  6. Ringed Accretion Disks: Equilibrium Configurations

    NASA Astrophysics Data System (ADS)

    Pugliese, D.; Stuchlík, Z.

    2015-12-01

    We investigate a model of a ringed accretion disk, made up by several rings rotating around a supermassive Kerr black hole attractor. Each toroid of the ringed disk is governed by the general relativity hydrodynamic Boyer condition of equilibrium configurations of rotating perfect fluids. Properties of the tori can then be determined by an appropriately defined effective potential reflecting the background Kerr geometry and the centrifugal effects. The ringed disks could be created in various regimes during the evolution of matter configurations around supermassive black holes. Therefore, both corotating and counterrotating rings have to be considered as being a constituent of the ringed disk. We provide constraints on the model parameters for the existence and stability of various ringed configurations and discuss occurrence of accretion onto the Kerr black hole and possible launching of jets from the ringed disk. We demonstrate that various ringed disks can be characterized by a maximum number of rings. We present also a perturbation analysis based on evolution of the oscillating components of the ringed disk. The dynamics of the unstable phases of the ringed disk evolution seems to be promising in relation to high-energy phenomena demonstrated in active galactic nuclei.

  7. The Equilibrium Thermodynamics of Various Peptide Sequences

    NASA Astrophysics Data System (ADS)

    Yaşar, Fatih

    The equilibrium thermodynamic properties of two peptide sequences of β-casein in the α-helix regions were studied by three-dimensional molecular modeling in vacuum. All the three-dimensional conformations of each peptide sequences were obtained by multicanonical simulations using ECEPP/2 force field and each simulation was started from completely random initial conformation. No a-priori information about ground-state is used in the simulations. In the present study, we calculated the average values of total energy, specific heat, fourth-order cumulant for two peptide sequences of β-casein as a function of temperature. We observed that the specific heat shows two peaks as a function of temperature for both peptides. Because our sequences have highly helical structure and two peaks in the specific heat, we have also studied the helix-coil transitions to determine these peaks. Our data indeed show these peptides have highly helical structure and better agreement with the results of spectroscopic techniques and other prediction methods.

  8. Accurate Mass Measurements in Proteomics

    SciTech Connect

    Liu, Tao; Belov, Mikhail E.; Jaitly, Navdeep; Qian, Weijun; Smith, Richard D.

    2007-08-01

    proteins can also be extensively modified by PTMs26-31 or by their interactions with other biomolecules or small molecules.32,33 Thus, it is highly desirable that proteins, the primary functional macromolecules involved in almost all biological activities, can be studied directly and systematically to determine their diverse properties and interplay. Such proteome-wide analysis is expected to provide a wealth of biological information, such as sequence, quantity, PTMs, interactions, activities, subcellular distribution and structure of proteins, which is critical to the comprehensive understanding of the biological systems. However, the de novo analysis of proteins isolated from cells, tissues or bodily fluids poses significant challenges due to the tremendous complexity and depth of the proteome, which necessitates high-throughput and highly sensitive analytical techniques. It is therefore not surprising that mass spectrometry (MS) has become an indispensable technology for proteome analysis.

  9. New Claus catalyst tests accurately reflect process conditions

    SciTech Connect

    Maglio, A.; Schubert, P.F.

    1988-09-12

    Methods for testing Claus catalysts are developed that more accurately represent the actual operating conditions in commercial sulfur recovery units. For measuring catalyst activity, an aging method has been developed that results in more meaningful activity data after the catalyst has been aged, because all catalysts undergo rapid initial deactivation in commercial units. An activity test method has been developed where catalysts can be compared at less than equilibrium conversion. A test has also been developed to characterize abrasion loss of Claus catalysts, in contrast to the traditional method of determining physical properties by measuring crush strengths. Test results from a wide range of materials correlated well with actual pneumatic conveyance attrition. Substantial differences in Claus catalyst properties were observed as a result of using these tests.

  10. Accurate bond dissociation energies (D 0) for FHF- isotopologues

    NASA Astrophysics Data System (ADS)

    Stein, Christopher; Oswald, Rainer; Sebald, Peter; Botschwina, Peter; Stoll, Hermann; Peterson, Kirk A.

    2013-09-01

    Accurate bond dissociation energies (D 0) are determined for three isotopologues of the bifluoride ion (FHF-). While the zero-point vibrational contributions are taken from our previous work (P. Sebald, A. Bargholz, R. Oswald, C. Stein, P. Botschwina, J. Phys. Chem. A, DOI: 10.1021/jp3123677), the equilibrium dissociation energy (D e ) of the reaction ? was obtained by a composite method including frozen-core (fc) CCSD(T) calculations with basis sets up to cardinal number n = 7 followed by extrapolation to the complete basis set limit. Smaller terms beyond fc-CCSD(T) cancel each other almost completely. The D 0 values of FHF-, FDF-, and FTF- are predicted to be 15,176, 15,191, and 15,198 cm-1, respectively, with an uncertainty of ca. 15 cm-1.

  11. How Accurate Are Transition States from Simulations of Enzymatic Reactions?

    PubMed Central

    2015-01-01

    The rate expression of traditional transition state theory (TST) assumes no recrossing of the transition state (TS) and thermal quasi-equilibrium between the ground state and the TS. Currently, it is not well understood to what extent these assumptions influence the nature of the activated complex obtained in traditional TST-based simulations of processes in the condensed phase in general and in enzymes in particular. Here we scrutinize these assumptions by characterizing the TSs for hydride transfer catalyzed by the enzyme Escherichia coli dihydrofolate reductase obtained using various simulation approaches. Specifically, we compare the TSs obtained with common TST-based methods and a dynamics-based method. Using a recently developed accurate hybrid quantum mechanics/molecular mechanics potential, we find that the TST-based and dynamics-based methods give considerably different TS ensembles. This discrepancy, which could be due equilibrium solvation effects and the nature of the reaction coordinate employed and its motion, raises major questions about how to interpret the TSs determined by common simulation methods. We conclude that further investigation is needed to characterize the impact of various TST assumptions on the TS phase-space ensemble and on the reaction kinetics. PMID:24860275

  12. Efficient chemical equilibrium calculations for geochemical speciation and reactive transport modelling

    NASA Astrophysics Data System (ADS)

    Leal, Allan M. M.; Blunt, Martin J.; LaForce, Tara C.

    2014-04-01

    Chemical equilibrium calculations are essential for many environmental problems. It is also a fundamental tool for chemical kinetics and reactive transport modelling, since these applications may require hundreds to billions equilibrium calculations in a single simulation. Therefore, an equilibrium method for such critical applications must be very efficient, robust and accurate. In this work we demonstrate the potential effectiveness of a novel Gibbs energy minimisation algorithm for reactive transport simulations. The algorithm includes strategies to converge from poor initial guesses; capabilities to specify non-linear equilibrium constraints such as pH of an aqueous solution and activity or fugacity of a species; a rigorous phase stability test to determine the unstable phases; and a strategy to boost the convergence speed of the calculations to quadratic rates, requiring only few iterations to converge. We use this equilibrium method to solve geochemical problems relevant to carbon storage in saline aquifers, where aqueous, gaseous and minerals phases are present. The problems are formulated to mimic the ones found in kinetics and transport simulations, where a sequence of equilibrium calculations are performed, each one using the previous solution as the initial guess. The efficiency and convergence rates of the calculations are presented, which require an average of 1-2 iterations. These results indicate that critical applications such as chemical kinetics and reactive transport modelling can potentially benefit by using this multiphase equilibrium algorithm.

  13. Equilibrium Tail Distribution Due to Touschek Scattering

    SciTech Connect

    Nash,B.; Krinsky, S.

    2009-05-04

    Single large angle Coulomb scattering is referred to as Touschek scattering. In addition to causing particle loss when the scattered particles are outside the momentum aperture, the process also results in a non-Gaussian tail, which is an equilibrium between the Touschek scattering and radiation damping. Here we present an analytical calculation for this equilibrium distribution.

  14. A Holistic Equilibrium Theory of Organization Development

    ERIC Educational Resources Information Center

    Yang, Baiyin; Zheng, Wei

    2005-01-01

    This paper proposes a holistic equilibrium theory of organizational development (OD). The theory states that there are three driving forces in organizational change and development--rationality, reality, and liberty. OD can be viewed as a planned process of change in an organization so as to establish equilibrium among these three interacting…

  15. Zeroth Law, Entropy, Equilibrium, and All That

    ERIC Educational Resources Information Center

    Canagaratna, Sebastian G.

    2008-01-01

    The place of the zeroth law in the teaching of thermodynamics is examined in the context of the recent discussion by Gislason and Craig of some problems involving the establishment of thermal equilibrium. The concept of thermal equilibrium is introduced through the zeroth law. The relation between the zeroth law and the second law in the…

  16. Equilibrium figures in geodesy and geophysics.

    NASA Astrophysics Data System (ADS)

    Moritz, H.

    There is an enormous literature on geodetic equilibrium figures, but the various works have not always been interrelated, also for linguistic reasons (English, French, German, Italian, Russian). The author attempts to systematize the various approaches and to use the standard second-order theory for a study of the deviation of the actual earth and of the equipotential reference ellipsoid from an equilibrium figure.

  17. Implementing an Equilibrium Law Teaching Sequence for Secondary School Students to Learn Chemical Equilibrium

    ERIC Educational Resources Information Center

    Ghirardi, Marco; Marchetti, Fabio; Pettinari, Claudio; Regis, Alberto; Roletto, Ezio

    2015-01-01

    A didactic sequence is proposed for the teaching of chemical equilibrium law. In this approach, we have avoided the kinetic derivation and the thermodynamic justification of the equilibrium constant. The equilibrium constant expression is established empirically by a trial-and-error approach. Additionally, students learn to use the criterion of…

  18. Investigation of Non-Equilibrium Radiation for Earth Entry

    NASA Technical Reports Server (NTRS)

    Brandis, Aaron; Johnston, Chris; Cruden, Brett

    2016-01-01

    This paper presents measurements and simulations of non-equilibrium shock layer radiation relevant to high-speed Earth entry data obtained in the NASA Ames Research Center's Electric Arc Shock Tube (EAST) facility. The experiments were aimed at measuring the spatially and spectrally resolved radiance at relevant entry conditions for both an approximate Earth atmosphere (79 N2 : 21 O2) as well as a more accurate composition featuring the trace species Ar and CO2 (78.08 N2 : 20.95 O2 : 0.04 CO2 : 0.93 Ar). The experiments were configured to target a wide range of conditions, of which shots from 8 to 11.5 km/s at 0.2 Torr (26.7 Pa) are examined in this paper. The non-equilibrium component was chosen to be the focus of this study as it can account for a significant percentage of the emitted radiation for Earth entry, and more importantly, non-equilibrium has traditionally been assigned a large uncertainty for vehicle design. The main goals of this study are to present the shock tube data in the form of a non-equilibrium metric, evaluate the level of agreement between the experiment and simulations, identify key discrepancies and to promote discussion about various aspects of modeling non-equilibrium radiating flows. Radiance profiles integrated over discreet wavelength regions, ranging from the VUV through to the NIR, were compared in order to maximize both the spectral coverage and the number of experiments that could be used in the analysis. A previously defined non-equilibrium metric has been used to allow comparisons with several shots and reveal trends in the data. Overall, LAURAHARA is shown to under-predict EAST by as much as 50 and over-predict by as much as 20 depending on the shock speed. DPLRNEQAIR is shown to under-predict EAST by as much as 40 and over-predict by as much as 12 depending on the shock speed. In terms of an upper bound estimate for the absolute error in wall-directed heat flux, at the lower speeds investigated in this paper, 8 to 9 km/s, even

  19. Disturbances in equilibrium function after major earthquake

    NASA Astrophysics Data System (ADS)

    Honma, Motoyasu; Endo, Nobutaka; Osada, Yoshihisa; Kim, Yoshiharu; Kuriyama, Kenichi

    2012-10-01

    Major earthquakes were followed by a large number of aftershocks and significant outbreaks of dizziness occurred over a large area. However it is unclear why major earthquake causes dizziness. We conducted an intergroup trial on equilibrium dysfunction and psychological states associated with equilibrium dysfunction in individuals exposed to repetitive aftershocks versus those who were rarely exposed. Greater equilibrium dysfunction was observed in the aftershock-exposed group under conditions without visual compensation. Equilibrium dysfunction in the aftershock-exposed group appears to have arisen from disturbance of the inner ear, as well as individual vulnerability to state anxiety enhanced by repetitive exposure to aftershocks. We indicate potential effects of autonomic stress on equilibrium function after major earthquake. Our findings may contribute to risk management of psychological and physical health after major earthquakes with aftershocks, and allow development of a new empirical approach to disaster care after such events.

  20. Probing local equilibrium in nonequilibrium fluids.

    PubMed

    del Pozo, J J; Garrido, P L; Hurtado, P I

    2015-08-01

    We use extensive computer simulations to probe local thermodynamic equilibrium (LTE) in a quintessential model fluid, the two-dimensional hard-disks system. We show that macroscopic LTE is a property much stronger than previously anticipated, even in the presence of important finite-size effects, revealing a remarkable bulk-boundary decoupling phenomenon in fluids out of equilibrium. This allows us to measure the fluid's equation of state in simulations far from equilibrium, with an excellent accuracy comparable to the best equilibrium simulations. Subtle corrections to LTE are found in the fluctuations of the total energy which strongly point to the nonlocality of the nonequilibrium potential governing the fluid's macroscopic behavior out of equilibrium. PMID:26382354

  1. How Far from Equilibrium Is Active Matter?

    NASA Astrophysics Data System (ADS)

    Fodor, Étienne; Nardini, Cesare; Cates, Michael E.; Tailleur, Julien; Visco, Paolo; van Wijland, Frédéric

    2016-07-01

    Active matter systems are driven out of thermal equilibrium by a lack of generalized Stokes-Einstein relation between injection and dissipation of energy at the microscopic scale. We consider such a system of interacting particles, propelled by persistent noises, and show that, at small but finite persistence time, their dynamics still satisfy a time-reversal symmetry. To do so, we compute perturbatively their steady-state measure and show that, for short persistent times, the entropy production rate vanishes. This endows such systems with an effective fluctuation-dissipation theorem akin to that of thermal equilibrium systems. Last, we show how interacting particle systems with viscous drags and correlated noises can be seen as in equilibrium with a viscoelastic bath but driven out of equilibrium by nonconservative forces, hence providing energetic insight into the departure of active systems from equilibrium.

  2. Loop Electrostatics Asymmetry Modulates the Preexisting Conformational Equilibrium in Thrombin.

    PubMed

    Pozzi, Nicola; Zerbetto, Mirco; Acquasaliente, Laura; Tescari, Simone; Frezzato, Diego; Polimeno, Antonino; Gohara, David W; Di Cera, Enrico; De Filippis, Vincenzo

    2016-07-19

    Thrombin exists as an ensemble of active (E) and inactive (E*) conformations that differ in their accessibility to the active site. Here we show that redistribution of the E*-E equilibrium can be achieved by perturbing the electrostatic properties of the enzyme. Removal of the negative charge of the catalytic Asp102 or Asp189 in the primary specificity site destabilizes the E form and causes a shift in the 215-217 segment that compromises substrate entrance. Solution studies and existing structures of D102N document stabilization of the E* form. A new high-resolution structure of D189A also reveals the mutant in the collapsed E* form. These findings establish a new paradigm for the control of the E*-E equilibrium in the trypsin fold. PMID:27347732

  3. Radiative-convective equilibrium models of Jupiter and Saturn

    NASA Astrophysics Data System (ADS)

    Appleby, J. F.; Hogan, J. S.

    1984-09-01

    Radiative-convective equilibrium models for Jupiter and Saturn have been produced in a study concentrating on the stratospheric energy balance and the possible role of aerosol heating. These models are compared directly with the thermal structure profiles obtained from Voyager radio occultation measurements. The method is based on a straightforward flux divergence formulation derived from earlier work. The balance between absorbed and emitted energies is computed iteratively at each level in the atmosphere, assuming local thermodynamic equilibrium and employing a standard treatment of opacities. Results for Jupiter indicate that a dust-free model furnishes a good mean thermal profile for the stratosphere when compared with the Voyager 1 radio occultation measurements. Observations of the equatorial region exhibit periodic vertical structure. The Saturn models are relatively simple and in good agreement with the Voyager 2 radio occultation temperature profiles at all levels. Aerosol heating played a minor role in Saturn's midlatitude stratospheric energy balance at the time of the Voyager 2 encounter.

  4. Imaging the equilibrium state and magnetization dynamics of partially built hard disk write heads

    SciTech Connect

    Valkass, R. A. J. Yu, W.; Shelford, L. R.; Keatley, P. S.; Loughran, T. H. J.; Hicken, R. J.; Cavill, S. A.; Laan, G. van der; Dhesi, S. S.; Bashir, M. A.; Gubbins, M. A.; Czoschke, P. J.; Lopusnik, R.

    2015-06-08

    Four different designs of partially built hard disk write heads with a yoke comprising four repeats of NiFe (1 nm)/CoFe (50 nm) were studied by both x-ray photoemission electron microscopy (XPEEM) and time-resolved scanning Kerr microscopy (TRSKM). These techniques were used to investigate the static equilibrium domain configuration and the magnetodynamic response across the entire structure, respectively. Simulations and previous TRSKM studies have made proposals for the equilibrium domain configuration of similar structures, but no direct observation of the equilibrium state of the writers has yet been made. In this study, static XPEEM images of the equilibrium state of writer structures were acquired using x-ray magnetic circular dichroism as the contrast mechanism. These images suggest that the crystalline anisotropy dominates the equilibrium state domain configuration, but competition with shape anisotropy ultimately determines the stability of the equilibrium state. Dynamic TRSKM images were acquired from nominally identical devices. These images suggest that a longer confluence region may hinder flux conduction from the yoke into the pole tip: the shorter confluence region exhibits clear flux beaming along the symmetry axis, whereas the longer confluence region causes flux to conduct along one edge of the writer. The observed variations in dynamic response agree well with the differences in the equilibrium magnetization configuration visible in the XPEEM images, confirming that minor variations in the geometric design of the writer structure can have significant effects on the process of flux beaming.

  5. Corrigendum to "The importance of suppressing spin diffusion effects in the accurate determination of the spatial structure of a flexible molecule by nuclear Overhauser effect spectroscopy" [J. Mol. Struct. 1106 (2016) 373-381

    NASA Astrophysics Data System (ADS)

    Khodov, I. A.; Efimov, S. V.; Kiselev, M. G.; Batista de Carvalho, L. A. E.; Klochkov, V. V.

    2016-06-01

    The original article to which this erratum refers was published in Journal of Molecular Structure, vol. 1106 (2016) [1]. In the original version of this article, Table 1 contained an error in column 10 (interatom distance averaging following the (r6)-algorithm, proton pairs H9-H5 and H7-H9). Analogous mistype was also present in Table 2 in Ref. [2] for distances H7-H9. Values present in Refs. [1,2] were far too small, but they were presented only for the sake of comparison of different averaging methods and did not influence the final conformer distribution. The Table 1 is reproduced below with the error corrected.

  6. Conformational stability of dimeric proteins: quantitative studies by equilibrium denaturation.

    PubMed Central

    Neet, K. E.; Timm, D. E.

    1994-01-01

    The conformational stability of dimeric globular proteins can be measured by equilibrium denaturation studies in solvents such as guanidine hydrochloride or urea. Many dimeric proteins denature with a 2-state equilibrium transition, whereas others have stable intermediates in the process. For those proteins showing a single transition of native dimer to denatured monomer, the conformational stabilities, delta Gu (H2O), range from 10 to 27 kcal/mol, which is significantly greater than the conformational stability found for monomeric proteins. The relative contribution of quaternary interactions to the overall stability of the dimer can be estimated by comparing delta Gu (H2O) from equilibrium denaturation studies to the free energy associated with simple dissociation in the absence of denaturant. In many cases the large stabilization energy of dimers is primarily due to the intersubunit interactions and thus gives a rationale for the formation of oligomers. The magnitude of the conformational stability is related to the size of the polypeptide in the subunit and depends upon the type of structure in the subunit interface. The practical use, interpretation, and utility of estimation of conformational stability of dimers by equilibrium denaturation methods are discussed. PMID:7756976

  7. Equilibrium configurations of flexible fibers in a flow

    NASA Astrophysics Data System (ADS)

    Allaire, Ryan; Nita, Bogdan; Vaidya, Ashwin

    2015-11-01

    In this presentation, we discuss the equilibrium configurations of flexible fibers attached to a sphere and immersed in a laminar flow. Comsol Multiphysics is used to solve this coupled problem and the resulting drag and lift forces, bending angles and Vogel exponents are computed. Specifically, the three-dimensional aspects of the flow structure interaction are numerically analyzed and compared with experiments and also to its two-dimensional counterpart.

  8. Fast and accurate determination of sites along the FUT2 in vitro transcript that are accessible to antisense oligonucleotides by application of secondary structure predictions and RNase H in combination with MALDI-TOF mass spectrometry

    PubMed Central

    Gabler, Angelika; Krebs, Stefan; Seichter, Doris; Förster, Martin

    2003-01-01

    Alteration of gene expression by use of antisense oligonucleotides has considerable potential for therapeutic purposes and scientific studies. Although applied for almost 25 years, this technique is still associated with difficulties in finding antisense-effective regions along the target mRNA. This is mainly due to strong secondary structures preventing binding of antisense oligonucleotides and RNase H, playing a major role in antisense-mediated degradation of the mRNA. These difficulties make empirical testing of a large number of sequences complementary to various sites in the target mRNA a very lengthy and troublesome procedure. To overcome this problem, more recent strategies to find efficient antisense sites are based on secondary structure prediction and RNase H-dependent mechanisms. We were the first who directly combined these two strategies; antisense oligonucleotides complementary to predicted unpaired target mRNA regions were designed and hybridized to the corresponding RNAs. Incubation with RNase H led to cleavage of the RNA at the respective hybridization sites. Analysis of the RNA fragments by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, which has not been used in this context before, allowed exact determination of the cleavage site. Thus the technique described here is very promising when searching for effective antisense sites. PMID:12888531

  9. Communication: An accurate global potential energy surface for the ground electronic state of ozone

    SciTech Connect

    Dawes, Richard E-mail: hguo@unm.edu; Lolur, Phalgun; Li, Anyang; Jiang, Bin; Guo, Hua E-mail: hguo@unm.edu

    2013-11-28

    We report a new full-dimensional and global potential energy surface (PES) for the O + O{sub 2} → O{sub 3} ozone forming reaction based on explicitly correlated multireference configuration interaction (MRCI-F12) data. It extends our previous [R. Dawes, P. Lolur, J. Ma, and H. Guo, J. Chem. Phys. 135, 081102 (2011)] dynamically weighted multistate MRCI calculations of the asymptotic region which showed the widely found submerged reef along the minimum energy path to be the spurious result of an avoided crossing with an excited state. A spin-orbit correction was added and the PES tends asymptotically to the recently developed long-range electrostatic model of Lepers et al. [J. Chem. Phys. 137, 234305 (2012)]. This PES features: (1) excellent equilibrium structural parameters, (2) good agreement with experimental vibrational levels, (3) accurate dissociation energy, and (4) most-notably, a transition region without a spurious reef. The new PES is expected to allow insight into the still unresolved issues surrounding the kinetics, dynamics, and isotope signature of ozone.

  10. [Biological experiments in microgravity: equilibrium function].

    PubMed

    Gorgiladze, G I; Shipov, A A; Horn, E

    2012-01-01

    The review deals with the investigations of structural and functional modifications in the equilibrium organ (EO) in invertebrates (coelenterates, shells, crustaceans and insects) and vertebrates (fishes, amphibians, rats, primates) on different ontogenetic stages in the condition of microgravity and during readaptation to the Earth's gravity. Results of the investigations detail the adaptive strategy of terrestrial organism in the environment lacking the gravitational components that leads to the discrepancy of an inner model of the body-environment schema constructed by the central nervous system at 1 g and the novel reality. It is manifested by ataxic behavior and increased graviceptors' afferentation against efferent system inactivation. The new condition is defined as a sensibilization phase ensued by the eluding phase: behavior obeys the innate motion strategy, whereas graviceptors' afferentation decreases due to activation of the efferent system. Readaptation to 1 G takes several to 50 days and proceeds as a sequence of slow in motion behavior, ataxia and vestibular sensitization. Reactivity of the gravitosensory system to microgravity was found to be age-dependent. Gain in the EO inertial mass in microgravity and reduction with return to 1 g indicates gravity relevance to EO genesis. PMID:23402139

  11. Non-equilibrium Transport of Light

    NASA Astrophysics Data System (ADS)

    Wang, Chiao-Hsuan; Taylor, Jacob

    Non-equilibrium Transport of Light The thermalization of light under conditions of parametric coupling to a bath provides a robust chemical potential for light. We study non-equilibrium transport of light using non-equilibrium Green's function approach under the parametric coupling scheme, and explore a potential photonic analogue to the Landauer transport equation. Our results provide understandings of many-body states of photonic matter with chemical potential imbalances. The transport theory of light paves the way for quantum simulation and even practical applications of diode-like circuits using quantum photonic sources in the microwave and optical domain.

  12. Modeling rocky coastline evolution and equilibrium

    NASA Astrophysics Data System (ADS)

    Limber, P. W.; Murray, A. B.

    2010-12-01

    Many of the world’s rocky coastlines exhibit planform roughness in the form of alternating headlands and embayments. Along cliffed coasts, it is often assumed that headlands consist of rock that is more resistant to wave attack than in neighboring bays, because of either structural or lithologic variations. Bays would then retreat landward faster than headlands, creating the undulating planform profiles characteristic of a rocky coastal landscape. While the interplay between alongshore rock strength and nearshore wave energy is, in some circumstances, a fundamental control on coastline shape, beach sediment is also important. Laboratory experiments and field observations have shown that beach sediment, in small volumes, can act as an abrasive tool to encourage sea cliff retreat. In large volumes, though, sediment discourages wave attack on the cliff face, acting as a protective barrier. This nonlinearity suggests a means for headland persistence, even without alongshore variations in rock strength: bare-rock headlands could retreat more slowly than, or at the same rate as, neighboring sediment-filled embayments because of alongshore variations in the availability of beach sediment. Accordingly, nearshore sediment dynamics (i.e. sediment production from sea cliff retreat and alongshore sediment transport) could promote the development of autogenic planform geometry. To explore these ideas, we present numerical and analytical modeling of large-scale (> one kilometer) and long-term (millennial-scale) planform rocky coastline evolution, in which sediment is supplied by both sea cliff erosion and coastal rivers and is distributed by alongshore sediment transport. We also compare model predictions with real landscapes. Previously, our modeling exercises focused on a basic rocky coastline configuration where lithologically-homogeneous sea cliffs supplied all beach sediment and maintained a constant alongshore height. Results showed that 1) an equilibrium alongshore

  13. Equilibrium state of a cylindrical particle with flat ends in nematic liquid crystals

    NASA Astrophysics Data System (ADS)

    Hashemi, S. Masoomeh; Ejtehadi, Mohammad Reza

    2015-01-01

    A continuum theory is employed to numerically study the equilibrium orientation and defect structures of a circular cylindrical particle with flat ends under a homeotropic anchoring condition in a uniform nematic medium. Different aspect ratios of this colloidal geometry from thin discotic to long rodlike shapes and several colloidal length scales ranging from mesoscale to nanoscale are investigated. We show that the equilibrium state of this colloidal geometry is sensitive to the two geometrical parameters: aspect ratio and length scale of the particle. For a large enough mesoscopic particle, there is a specific asymptotic equilibrium angle associated to each aspect ratio. Upon reducing the particle size to nanoscale, the equilibrium angle follows a descending or ascending trend in such a way that the equilibrium angle of a particle with the aspect ratio bigger than 1:1 (a discotic particle) goes to a parallel alignment with respect to the far-field nematic, whereas the equilibrium angle for a particle with the aspect ratio 1:1 and smaller (a rodlike particle) tends toward a perpendicular alignment to the uniform nematic direction. The discrepancy between the equilibrium angles of the mesoscopic and nanoscopic particles originates from the significant differences between their defect structures. The possible defect structures related to mesoscopic and nanoscopic colloidal particles of this geometry are also introduced.

  14. Equilibrium state of a cylindrical particle with flat ends in nematic liquid crystals.

    PubMed

    Hashemi, S Masoomeh; Ejtehadi, Mohammad Reza

    2015-01-01

    A continuum theory is employed to numerically study the equilibrium orientation and defect structures of a circular cylindrical particle with flat ends under a homeotropic anchoring condition in a uniform nematic medium. Different aspect ratios of this colloidal geometry from thin discotic to long rodlike shapes and several colloidal length scales ranging from mesoscale to nanoscale are investigated. We show that the equilibrium state of this colloidal geometry is sensitive to the two geometrical parameters: aspect ratio and length scale of the particle. For a large enough mesoscopic particle, there is a specific asymptotic equilibrium angle associated to each aspect ratio. Upon reducing the particle size to nanoscale, the equilibrium angle follows a descending or ascending trend in such a way that the equilibrium angle of a particle with the aspect ratio bigger than 1:1 (a discotic particle) goes to a parallel alignment with respect to the far-field nematic, whereas the equilibrium angle for a particle with the aspect ratio 1:1 and smaller (a rodlike particle) tends toward a perpendicular alignment to the uniform nematic direction. The discrepancy between the equilibrium angles of the mesoscopic and nanoscopic particles originates from the significant differences between their defect structures. The possible defect structures related to mesoscopic and nanoscopic colloidal particles of this geometry are also introduced. PMID:25679634

  15. New Simulator for Non-Equilibrium Modeling of Hydrate Reservoirs

    NASA Astrophysics Data System (ADS)

    Kvamme, B.; Qorbani Nashaqi, K.; Jemai, K.; Vafaei, M.

    2014-12-01

    Due to Gibbs phase rule and combination of first and second law of thermodynamics, hydrate in nature cannot be in equilibrium since they come from different parent phases. In this system hydrate formation and dissociation is affected by local variables such as pressure, temperature and composition with mass and energy transport restrictions. Available simulators have attempted to model hydrate phase transition as an equilibrium reaction. Although those which treated the processes of formation and dissociation as kinetics used model of Kim and Bishnoi based on laboratory PVT experiment, and consequently hard to accept up scaling to real reservoirs condition. Additionally, they merely check equilibrium in terms of pressure and temperature projections and disregard thermodynamic requirements for equilibrium especially along axes of concentrations in phases. Non-equilibrium analysis of hydrate involves putting aside all the phase transitions which are not possible and use kinetic evaluation to measure phase transitions progress in each grid block for each time step. This procedure is Similar to geochemical reservoir simulators logic. As a result RetrasoCodeBright has been chosen as hydrate reservoir simulator and our work involves extension of this code. RetrasoCodeBright (RCB) is able to handle competing processes of formation and dissociation of hydrates as pseudo reactions at each node and each time step according to the temperature, pressure and concentration. Hydrates can therefore be implemented into the structure as pseudo minerals, with appropriate kinetic models. In order to implement competing nature of phase transition kinetics of hydrate formation, we use classical nucleation theory based on Kvamme et al. as a simplified model inside RCB and use advanced theories to fit parameters for the model (PFT). Hydrate formation and dissociation can directly be observed through porosity changes in the specific areas of the porous media. In this work which is in

  16. The Conceptual Change Approach to Teaching Chemical Equilibrium

    ERIC Educational Resources Information Center

    Canpolat, Nurtac; Pinarbasi, Tacettin; Bayrakceken, Samih; Geban, Omer

    2006-01-01

    This study investigates the effect of a conceptual change approach over traditional instruction on students' understanding of chemical equilibrium concepts (e.g. dynamic nature of equilibrium, definition of equilibrium constant, heterogeneous equilibrium, qualitative interpreting of equilibrium constant, changing the reaction conditions). This…

  17. Accurate adjoint design sensitivities for nano metal optics.

    PubMed

    Hansen, Paul; Hesselink, Lambertus

    2015-09-01

    We present a method for obtaining accurate numerical design sensitivities for metal-optical nanostructures. Adjoint design sensitivity analysis, long used in fluid mechanics and mechanical engineering for both optimization and structural analysis, is beginning to be used for nano-optics design, but it fails for sharp-cornered metal structures because the numerical error in electromagnetic simulations of metal structures is highest at sharp corners. These locations feature strong field enhancement and contribute strongly to design sensitivities. By using high-accuracy FEM calculations and rounding sharp features to a finite radius of curvature we obtain highly-accurate design sensitivities for 3D metal devices. To provide a bridge to the existing literature on adjoint methods in other fields, we derive the sensitivity equations for Maxwell's equations in the PDE framework widely used in fluid mechanics. PMID:26368483

  18. Direct Determination of the Equilibrium Unbinding Potential Profile for a Short DNA Duplex from Force Spectroscopy Data

    SciTech Connect

    Noy, A

    2004-05-04

    Modern force microscopy techniques allow researchers to use mechanical forces to probe interactions between biomolecules. However, such measurements often happen in non-equilibrium regime, which precludes straightforward extraction of the equilibrium energy information. Here we use the work averaging method based on Jarzynski equality to reconstruct the equilibrium interaction potential from the unbinding of a complementary 14-mer DNA duplex from the results of non-equilibrium single-molecule measurements. The reconstructed potential reproduces most of the features of the DNA stretching transition, previously observed only in equilibrium stretching of long DNA sequences. We also compare the reconstructed potential with the thermodynamic parameters of DNA duplex unbinding and show that the reconstruction accurately predicts duplex melting enthalpy.

  19. An Elementary Discussion of Chemical Equilibrium.

    ERIC Educational Resources Information Center

    David, Carl W.

    1988-01-01

    This discussion uses a more difficult reaction as the prototype to derive the standard equation for chemical equilibrium. It can be used by students who can understand and use partial derivatives. (CW)

  20. Spreadsheet Templates for Chemical Equilibrium Calculations.

    ERIC Educational Resources Information Center

    Joshi, Bhairav D.

    1993-01-01

    Describes two general spreadsheet templates to carry out all types of one-equation chemical equilibrium calculations encountered by students in undergraduate chemistry courses. Algorithms, templates, macros, and representative examples are presented to illustrate the approach. (PR)

  1. Stochastic approach to equilibrium and nonequilibrium thermodynamics

    NASA Astrophysics Data System (ADS)

    Tomé, Tânia; de Oliveira, Mário J.

    2015-04-01

    We develop the stochastic approach to thermodynamics based on stochastic dynamics, which can be discrete (master equation) and continuous (Fokker-Planck equation), and on two assumptions concerning entropy. The first is the definition of entropy itself and the second the definition of entropy production rate, which is non-negative and vanishes in thermodynamic equilibrium. Based on these assumptions, we study interacting systems with many degrees of freedom in equilibrium or out of thermodynamic equilibrium and how the macroscopic laws are derived from the stochastic dynamics. These studies include the quasiequilibrium processes; the convexity of the equilibrium surface; the monotonic time behavior of thermodynamic potentials, including entropy; the bilinear form of the entropy production rate; the Onsager coefficients and reciprocal relations; and the nonequilibrium steady states of chemical reactions.

  2. Equilibrium Reconstruction on the Large Helical Device

    SciTech Connect

    Samuel A. Lazerson, D. Gates, D. Monticello, H. Neilson, N. Pomphrey, A. Reiman S. Sakakibara, and Y. Suzuki

    2012-07-27

    Equilibrium reconstruction is commonly applied to axisymmetric toroidal devices. Recent advances in computational power and equilibrium codes have allowed for reconstructions of three-dimensional fields in stellarators and heliotrons. We present the first reconstructions of finite beta discharges in the Large Helical Device (LHD). The plasma boundary and magnetic axis are constrained by the pressure profile from Thomson scattering. This results in a calculation of plasma beta without a-priori assumptions of the equipartition of energy between species. Saddle loop arrays place additional constraints on the equilibrium. These reconstruction utilize STELLOPT, which calls VMEC. The VMEC equilibrium code assumes good nested flux surfaces. Reconstructed magnetic fields are fed into the PIES code which relaxes this constraint allowing for the examination of the effect of islands and stochastic regions on the magnetic measurements.

  3. Points of Equilibrium in Electrostatic Fields.

    ERIC Educational Resources Information Center

    Rogers, Peter J.

    1979-01-01

    Discusses the electric field line pattern for four equal charges of the same sign placed at the corners of a square. The electric field intensity and the point of equilibrium are interpreted, taking into account three dimensions. (HM)

  4. IEHI: Ionization Equilibrium for Heavy Ions

    NASA Astrophysics Data System (ADS)

    Cranmer, Steven R.

    2015-07-01

    IEHI, written in Fortran, outputs a simple "coronal" ionization equilibrium (i.e., collisional ionization and auto-ionization balanced by radiative and dielectronic recombination) for a plasma at a given electron temperature.

  5. Surface roughness effects on equilibrium temperature.

    NASA Technical Reports Server (NTRS)

    Houchens, A. F.; Hering, R. G.

    1972-01-01

    An analysis is presented for evaluation of equilibrium temperature distribution on radiatively adiabatic, adjoint planes which are uniformly irradiated by a collimated solar flux. The analysis employs a semigrey spectral model. Radiation properties for surface emitted radiation are obtained from the expressions of electromagnetic theory for smooth surfaces. Rough surface properties for solar radiation are given by the Beckmann bidirectional reflectance model. Numerical solutions to the governing equations yield equilibrium temperature distributions for a range of the influencing parameters. Surface roughness has little influence on equilibrium temperature for materials with high values for solar absorptance. However, for low or intermediate values of solar absorptance, roughness effects on the spatial distribution of reflected solar radiation can significantly alter equilibrium temperature particularly at surface elements where radiant interaction is small.

  6. Stochastic approach to equilibrium and nonequilibrium thermodynamics.

    PubMed

    Tomé, Tânia; de Oliveira, Mário J

    2015-04-01

    We develop the stochastic approach to thermodynamics based on stochastic dynamics, which can be discrete (master equation) and continuous (Fokker-Planck equation), and on two assumptions concerning entropy. The first is the definition of entropy itself and the second the definition of entropy production rate, which is non-negative and vanishes in thermodynamic equilibrium. Based on these assumptions, we study interacting systems with many degrees of freedom in equilibrium or out of thermodynamic equilibrium and how the macroscopic laws are derived from the stochastic dynamics. These studies include the quasiequilibrium processes; the convexity of the equilibrium surface; the monotonic time behavior of thermodynamic potentials, including entropy; the bilinear form of the entropy production rate; the Onsager coefficients and reciprocal relations; and the nonequilibrium steady states of chemical reactions. PMID:25974471

  7. Optimization of Electrospray Ionization by Statistical Design of Experiments and Response Surface Methodology: Protein-Ligand Equilibrium Dissociation Constant Determinations

    NASA Astrophysics Data System (ADS)

    Pedro, Liliana; Van Voorhis, Wesley C.; Quinn, Ronald J.

    2016-09-01

    Electrospray ionization mass spectrometry (ESI-MS) binding studies between proteins and ligands under native conditions require that instrumental ESI source conditions are optimized if relative solution-phase equilibrium concentrations between the protein-ligand complex and free protein are to be retained. Instrumental ESI source conditions that simultaneously maximize the relative ionization efficiency of the protein-ligand complex over free protein and minimize the protein-ligand complex dissociation during the ESI process and the transfer from atmospheric pressure to vacuum are generally specific for each protein-ligand system and should be established when an accurate equilibrium dissociation constant (KD) is to be determined via titration. In this paper, a straightforward and systematic approach for ESI source optimization is presented. The method uses statistical design of experiments (DOE) in conjunction with response surface methodology (RSM) and is demonstrated for the complexes between Plasmodium vivax guanylate kinase ( PvGK) and two ligands: 5'-guanosine monophosphate (GMP) and 5'-guanosine diphosphate (GDP). It was verified that even though the ligands are structurally similar, the most appropriate ESI conditions for KD determination by titration are different for each.

  8. Optimization of Electrospray Ionization by Statistical Design of Experiments and Response Surface Methodology: Protein-Ligand Equilibrium Dissociation Constant Determinations.

    PubMed

    Pedro, Liliana; Van Voorhis, Wesley C; Quinn, Ronald J

    2016-09-01

    Electrospray ionization mass spectrometry (ESI-MS) binding studies between proteins and ligands under native conditions require that instrumental ESI source conditions are optimized if relative solution-phase equilibrium concentrations between the protein-ligand complex and free protein are to be retained. Instrumental ESI source conditions that simultaneously maximize the relative ionization efficiency of the protein-ligand complex over free protein and minimize the protein-ligand complex dissociation during the ESI process and the transfer from atmospheric pressure to vacuum are generally specific for each protein-ligand system and should be established when an accurate equilibrium dissociation constant (KD) is to be determined via titration. In this paper, a straightforward and systematic approach for ESI source optimization is presented. The method uses statistical design of experiments (DOE) in conjunction with response surface methodology (RSM) and is demonstrated for the complexes between Plasmodium vivax guanylate kinase (PvGK) and two ligands: 5'-guanosine monophosphate (GMP) and 5'-guanosine diphosphate (GDP). It was verified that even though the ligands are structurally similar, the most appropriate ESI conditions for KD determination by titration are different for each. Graphical Abstract ᅟ. PMID:27225419

  9. Optimization of Electrospray Ionization by Statistical Design of Experiments and Response Surface Methodology: Protein-Ligand Equilibrium Dissociation Constant Determinations

    NASA Astrophysics Data System (ADS)

    Pedro, Liliana; Van Voorhis, Wesley C.; Quinn, Ronald J.

    2016-05-01

    Electrospray ionization mass spectrometry (ESI-MS) binding studies between proteins and ligands under native conditions require that instrumental ESI source conditions are optimized if relative solution-phase equilibrium concentrations between the protein-ligand complex and free protein are to be retained. Instrumental ESI source conditions that simultaneously maximize the relative ionization efficiency of the protein-ligand complex over free protein and minimize the protein-ligand complex dissociation during the ESI process and the transfer from atmospheric pressure to vacuum are generally specific for each protein-ligand system and should be established when an accurate equilibrium dissociation constant (KD) is to be determined via titration. In this paper, a straightforward and systematic approach for ESI source optimization is presented. The method uses statistical design of experiments (DOE) in conjunction with response surface methodology (RSM) and is demonstrated for the complexes between Plasmodium vivax guanylate kinase (PvGK) and two ligands: 5'-guanosine monophosphate (GMP) and 5'-guanosine diphosphate (GDP). It was verified that even though the ligands are structurally similar, the most appropriate ESI conditions for KD determination by titration are different for each.

  10. Investigation of Non-Equilibrium Radiation for Earth Entry

    NASA Technical Reports Server (NTRS)

    Brandis, A. M.; Johnston, C. O.; Cruden, B. A.

    2016-01-01

    For Earth re-entry at velocities between 8 and 11.5 km/s, the accuracy of NASA's computational uid dynamic and radiative simulations of non-equilibrium shock layer radiation is assessed through comparisons with measurements. These measurements were obtained in the NASA Ames Research Center's Electric Arc Shock Tube (EAST) facility. The experiments were aimed at measuring the spatially and spectrally resolved radiance at relevant entry conditions for both an approximate Earth atmosphere (79% N2 : 21% O2 by mole) as well as a more accurate composition featuring the trace species Ar and CO2 (78.08% N2 : 20.95% O2 : 0.04% CO2 : 0.93% Ar by mole). The experiments were configured to target a wide range of conditions, of which shots from 8 to 11.5 km/s at 0.2 Torr (26.7 Pa) are examined in this paper. The non-equilibrium component was chosen to be the focus of this study as it can account for a significant percentage of the emitted radiation for Earth re-entry, and more importantly, non-equilibrium has traditionally been assigned a large uncertainty for vehicle design. The main goals of this study are to present the shock tube data in the form of a non-equilibrium metric, evaluate the level of agreement between the experiment and simulations, identify key discrepancies and to examine critical aspects of modeling non-equilibrium radiating flows. Radiance pro les integrated over discreet wavelength regions, ranging from the Vacuum Ultra Violet (VUV) through to the Near Infra-Red (NIR), were compared in order to maximize both the spectral coverage and the number of experiments that could be used in the analysis. A previously defined non-equilibrium metric has been used to allow comparisons with several shots and reveal trends in the data. Overall, LAURA/HARA is shown to under-predict EAST by as much as 40% and over-predict by as much as 12% depending on the shock speed. DPLR/NEQAIR is shown to under-predict EAST by as much as 50% and over-predict by as much as 20% depending

  11. Differential equation based method for accurate approximations in optimization

    NASA Technical Reports Server (NTRS)

    Pritchard, Jocelyn I.; Adelman, Howard M.

    1990-01-01

    A method to efficiently and accurately approximate the effect of design changes on structural response is described. The key to this method is to interpret sensitivity equations as differential equations that may be solved explicitly for closed form approximations, hence, the method is denoted the Differential Equation Based (DEB) method. Approximations were developed for vibration frequencies, mode shapes and static displacements. The DEB approximation method was applied to a cantilever beam and results compared with the commonly-used linear Taylor series approximations and exact solutions. The test calculations involved perturbing the height, width, cross-sectional area, tip mass, and bending inertia of the beam. The DEB method proved to be very accurate, and in most cases, was more accurate than the linear Taylor series approximation. The method is applicable to simultaneous perturbation of several design variables. Also, the approximations may be used to calculate other system response quantities. For example, the approximations for displacements are used to approximate bending stresses.

  12. Equilibrium fluctuation energy of gyrokinetic plasma

    SciTech Connect

    Krommes, J.A.; Lee, W.W.; Oberman, C.

    1985-11-01

    The thermal equilibrium electric field fluctuation energy of the gyrokinetic model of magnetized plasma is computed, and found to be smaller than the well-known result (k)/8..pi.. = 1/2T/(1 + (klambda/sub D/)/sup 2/) valid for arbitrarily magnetized plasmas. It is shown that, in a certain sense, the equilibrium electric field energy is minimum in the gyrokinetic regime. 13 refs., 2 figs.

  13. Edge Equilibrium Code (EEC) For Tokamaks

    SciTech Connect

    Li, Xujling

    2014-02-24

    The edge equilibrium code (EEC) described in this paper is developed for simulations of the near edge plasma using the finite element method. It solves the Grad-Shafranov equation in toroidal coordinate and uses adaptive grids aligned with magnetic field lines. Hermite finite elements are chosen for the numerical scheme. A fast Newton scheme which is the same as implemented in the equilibrium and stability code (ESC) is applied here to adjust the grids

  14. Statistical equilibrium predictions of jets and spots on Jupiter.

    PubMed

    Turkington, B; Majda, A; Haven, K; DiBattista, M

    2001-10-23

    An equilibrium statistical theory of coherent structures is applied to midlatitude bands in the northern and southern hemispheres of Jupiter. The theory imposes energy and circulation constraints on the large-scale motion and uses a prior distribution on potential vorticity fluctuations to parameterize the small-scale turbulent eddies. Nonlinearly stable coherent structures are computed by solving the constrained maximum entropy principle governing the equilibrium states of the statistical theory. The theoretical predictions are consistent with the observed large-scale features of the weather layer if and only if the prior distribution has anticyclonic skewness, meaning that intense anticyclones predominate at small scales. Then the computations show that anticyclonic vortices emerge at the latitudes of the Great Red Spot and the White Ovals in the southern band, whereas in the northern band no vortices form within the zonal jets. Recent observational data from the Galileo mission support the occurrence of intense small-scale anticyclonic forcing. The results suggest the possibility of using equilibrium statistical theory for inverse modeling of the small-scale characteristics of the Jovian atmosphere from observed features. PMID:11592986

  15. Statistical equilibrium predictions of jets and spots on Jupiter

    PubMed Central

    Turkington, Bruce; Majda, Andrew; Haven, Kyle; DiBattista, Mark

    2001-01-01

    An equilibrium statistical theory of coherent structures is applied to midlatitude bands in the northern and southern hemispheres of Jupiter. The theory imposes energy and circulation constraints on the large-scale motion and uses a prior distribution on potential vorticity fluctuations to parameterize the small-scale turbulent eddies. Nonlinearly stable coherent structures are computed by solving the constrained maximum entropy principle governing the equilibrium states of the statistical theory. The theoretical predictions are consistent with the observed large-scale features of the weather layer if and only if the prior distribution has anticyclonic skewness, meaning that intense anticyclones predominate at small scales. Then the computations show that anticyclonic vortices emerge at the latitudes of the Great Red Spot and the White Ovals in the southern band, whereas in the northern band no vortices form within the zonal jets. Recent observational data from the Galileo mission support the occurrence of intense small-scale anticyclonic forcing. The results suggest the possibility of using equilibrium statistical theory for inverse modeling of the small-scale characteristics of the Jovian atmosphere from observed features. PMID:11592986

  16. Theory for non-equilibrium statistical mechanics.

    PubMed

    Attard, Phil

    2006-08-21

    This paper reviews a new theory for non-equilibrium statistical mechanics. This gives the non-equilibrium analogue of the Boltzmann probability distribution, and the generalization of entropy to dynamic states. It is shown that this so-called second entropy is maximized in the steady state, in contrast to the rate of production of the conventional entropy, which is not an extremum. The relationships of the new theory to Onsager's regression hypothesis, Prigogine's minimal entropy production theorem, the Langevin equation, the formula of Green and Kubo, the Kawasaki distribution, and the non-equilibrium fluctuation and work theorems, are discussed. The theory is worked through in full detail for the case of steady heat flow down an imposed temperature gradient. A Monte Carlo algorithm based upon the steady state probability density is summarized, and results for the thermal conductivity of a Lennard-Jones fluid are shown to be in agreement with known values. Also discussed is the generalization to non-equilibrium mechanical work, and to non-equilibrium quantum statistical mechanics. As examples of the new theory two general applications are briefly explored: a non-equilibrium version of the second law of thermodynamics, and the origin and evolution of life. PMID:16883388

  17. Non-equilibrium Helium Ionization in an MHD Simulation of the Solar Atmosphere

    NASA Astrophysics Data System (ADS)

    Golding, Thomas Peter; Leenaarts, Jorrit; Carlsson, Mats

    2016-02-01

    The ionization state of the gas in the dynamic solar chromosphere can depart strongly from the instantaneous statistical equilibrium commonly assumed in numerical modeling. We improve on earlier simulations of the solar atmosphere that only included non-equilibrium hydrogen ionization by performing a 2D radiation-magnetohydrodynamics simulation featuring non-equilibrium ionization of both hydrogen and helium. The simulation includes the effect of hydrogen Lyα and the EUV radiation from the corona on the ionization and heating of the atmosphere. Details on code implementation are given. We obtain helium ion fractions that are far from their equilibrium values. Comparison with models with local thermodynamic equilibrium (LTE) ionization shows that non-equilibrium helium ionization leads to higher temperatures in wavefronts and lower temperatures in the gas between shocks. Assuming LTE ionization results in a thermostat-like behavior with matter accumulating around the temperatures where the LTE ionization fractions change rapidly. Comparison of DEM curves computed from our models shows that non-equilibrium ionization leads to more radiating material in the temperature range 11-18 kK, compared to models with LTE helium ionization. We conclude that non-equilibrium helium ionization is important for the dynamics and thermal structure of the upper chromosphere and transition region. It might also help resolve the problem that intensities of chromospheric lines computed from current models are smaller than those observed.

  18. BOOK REVIEW: Relativistic Figures of Equilibrium

    NASA Astrophysics Data System (ADS)

    Mars, M.

    2009-08-01

    Compact fluid bodies in equilibrium under its own gravitational field are abundant in the Universe and a proper treatment of them can only be carried out using the full theory of General Relativity. The problem is of enormous complexity as it involves two very different regimes, namely the interior and the exterior of the fluid, coupled through the surface of the body. This problem is very challenging both from a purely theoretical point of view, as well as regarding the obtaining of realistic models and the description of their physical properties. It is therefore an excellent piece of news that the book 'Relativistic Figures of Equilibrium' by R Meinel, M Ansorg, A Kleinwächter, G Neugebauer and D Petroff has been recently published. This book approaches the topic in depth and its contents will be of interest to a wide range of scientists working on gravitation, including theoreticians in general relativity, mathematical physicists, astrophysicists and numerical relativists. This is an advanced book that intends to present some of the present-day results on this topic. The most basic results are presented rather succinctly, and without going into the details, of their derivations. Although primarily not intended to serve as a textbook, the presentation is nevertheless self-contained and can therefore be of interest both for experts on the field as well as for anybody wishing to learn more about rotating self-gravitating compact bodies in equilibrium. It should be remarked, however, that this book makes a rather strong selection of topics and concentrates fundamentally on presenting the main results obtained by the authors during their research in this field. The book starts with a chapter where the fundamental aspects of rotating fluids in equilibrium, including its thermodynamic properties, are summarized. Of particular interest are the so-called mass-shedding limit, which is the limit where the body is rotating so fast that it is on the verge of starting

  19. Mill profiler machines soft materials accurately

    NASA Technical Reports Server (NTRS)

    Rauschl, J. A.

    1966-01-01

    Mill profiler machines bevels, slots, and grooves in soft materials, such as styrofoam phenolic-filled cores, to any desired thickness. A single operator can accurately control cutting depths in contour or straight line work.

  20. Remote balance weighs accurately amid high radiation

    NASA Technical Reports Server (NTRS)

    Eggenberger, D. N.; Shuck, A. B.

    1969-01-01

    Commercial beam-type balance, modified and outfitted with electronic controls and digital readout, can be remotely controlled for use in high radiation environments. This allows accurate weighing of breeder-reactor fuel pieces when they are radioactively hot.