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.
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.
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.
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.
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.
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.
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.
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.
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.
Accurate Prediction of Docked Protein Structure Similarity.
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
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.
Isomerism of Cyanomethanimine: Accurate Structural, Energetic, and Spectroscopic Characterization.
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
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.
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.
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)°.
Accurate and efficient reconstruction of deep phylogenies from structured RNAs
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
Accurate and efficient reconstruction of deep phylogenies from structured RNAs.
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
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.
EFFECT OF SOLAR CHROMOSPHERIC NEUTRALS ON EQUILIBRIUM FIELD STRUCTURES
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.
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.
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.
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
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.
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.
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.
Financial Structure and Economic Welfare: Applied General Equilibrium Development Economics
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
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.
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
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.
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.
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)
Accurate protein structure modeling using sparse NMR data and homologous structure information
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
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.
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.
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.
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.
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.
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.
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.
Equilibrium structures of anisometric, quadrupolar particles confined to a monolayer.
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
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.
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.
DNA viewed as an out-of-equilibrium structure.
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
On calculating the equilibrium structure of molecular crystals.
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.
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.
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.
Assembly of nothing: equilibrium fluids with designed structured porosity.
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
Tubular precipitation structures: materials synthesis under non-equilibrium conditions.
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
On the time needed to reach an equilibrium structure of the radiation belts
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
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.
Equilibrium structure of the GeI/sub 4/ molecule
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.
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
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.
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.
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.
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.
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.
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.
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.
Accurate Electron Affinity of Iron and Fine Structures of Negative Iron ions
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
Accurate Electron Affinity of Iron and Fine Structures of Negative Iron ions.
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
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.
Electronic structure and bonding of HBeLi, HmgLi, and HCaLi in their bent equilibrium geometries.
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
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
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.
CoMOGrad and PHOG: From Computer Vision to Fast and Accurate Protein Tertiary Structure Retrieval
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
CoMOGrad and PHOG: From Computer Vision to Fast and Accurate Protein Tertiary Structure Retrieval.
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
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
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
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
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
Equilibrium and structural studies on metal complexes of carbohyrates and their derivatives.
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
An equilibrium double-twist model for the radial structure of collagen fibrils.
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
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
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
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
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.
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
Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers
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
Polarity, cell division, and out-of-equilibrium dynamics control the growth of epithelial structures
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
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.
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.
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
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.
DR-TAMAS: Diffeomorphic Registration for Tensor Accurate Alignment of Anatomical Structures.
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
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.
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
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.
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.
conSSert: Consensus SVM Model for Accurate Prediction of Ordered Secondary Structure.
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
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.
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
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.
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.
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
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
Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.
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
Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations
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
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
Processing and crystallographic structure of non-equilibrium Si-doped HfO{sub 2}
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.
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.
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.
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.
Discrete state model and accurate estimation of loop entropy of RNA secondary structures.
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
Can structured data fields accurately measure quality of care? The example of falls.
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
Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials.
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
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.
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.
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.
Supramolecular Magnetic Brushes: The Impact of Dipolar Interactions on the Equilibrium Structure
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
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.
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
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
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.
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
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
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.
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
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
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
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.
Thermodynamics and equilibrium structure of Ne38 cluster: quantum mechanics versus classical.
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
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.
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).
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
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
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.
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
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
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
Local atomic structure in equilibrium and supercooled liquid Zr[subscript 75.5]Pd[subscript 24.5
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.
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.
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
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.
Equilibrium Sorption of Structurally Diverse Organic Ions to Bovine Serum Albumin.
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
PROMALS3D web server for accurate multiple protein sequence and structure alignments.
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
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
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.
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.
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.}
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.
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
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.
Equilibrium point defects in intermetallics with the [ital B]2 structure: NiAl and FeAl
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.
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
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
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.
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
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.
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.
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.
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
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
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
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
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
Non-equilibrium structures induced by ion irradiation in Ni[sub 4]Mo
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.
Non-equilibrium structures induced by ion irradiation in Ni{sub 4}Mo
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.
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.
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.
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.
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).
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.
Accurate structure prediction of peptide–MHC complexes for identifying highly immunogenic antigens
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.
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.
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
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.
A FIB-nanotomography method for accurate 3D reconstruction of open nanoporous structures.
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
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.
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.
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.
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.
Solution structure of a modified 2′,5′-linked RNA hairpin involved in an equilibrium with duplex
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
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.
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
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
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
Semiclassical shell-structure moment of inertia for equilibrium rotation of a simple Fermi system
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.
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.
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...
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.
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).
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
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
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.
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.
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
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
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.
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
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.
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.
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.
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.
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.
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
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
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
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."
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.
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
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).
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.
Accurate Method for Determining Adhesion of Cantilever Beams
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.
Accurate method for determining adhesion of cantilever beams
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.}
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.
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.
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.
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.
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
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
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
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.
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.
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)
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.
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
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
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.
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.
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
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
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.
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
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.
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
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
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
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
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
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.
How to accurately bypass damage
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
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.
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.
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.
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
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
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.
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
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
Shape characteristics of equilibrium and non-equilibrium fractal clusters.
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
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
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.
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.
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
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
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
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
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
The Theory of Variances in Equilibrium Reconstruction
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.