Validity of virial theorem in all-electron mixed basis density functional, Hartree–Fock, and GW calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuwahara, Riichi; Accelrys K. K., Kasumigaseki Tokyu Building 17F, 3-7-1 Kasumigaseki, Chiyoda-ku, Tokyo 100-0013; Tadokoro, Yoichi

In this paper, we calculate kinetic and potential energy contributions to the electronic ground-state total energy of several isolated atoms (He, Be, Ne, Mg, Ar, and Ca) by using the local density approximation (LDA) in density functional theory, the Hartree–Fock approximation (HFA), and the self-consistent GW approximation (GWA). To this end, we have implemented self-consistent HFA and GWA routines in our all-electron mixed basis code, TOMBO. We confirm that virial theorem is fairly well satisfied in all of these approximations, although the resulting eigenvalue of the highest occupied molecular orbital level, i.e., the negative of the ionization potential, is inmore » excellent agreement only in the case of the GWA. We find that the wave function of the lowest unoccupied molecular orbital level of noble gas atoms is a resonating virtual bound state, and that of the GWA spreads wider than that of the LDA and thinner than that of the HFA.« less

Ferromagnetic insulating state in tensile-strained LaCoO3 thin films from LDA + U calculations

NASA Astrophysics Data System (ADS)

Hsu, Han; Blaha, Peter; Wentzcovitch, Renata M.

2012-04-01

With local density approximation+Hubbard U (LDA+U) calculations, we show that the ferromagnetic (FM) insulating state observed in tensile-strained LaCoO3 epitaxial thin films is most likely a mixture of low-spin (LS) and high-spin (HS) Co, namely, a HS/LS mixture state. Compared with other FM states, including the intermediate-spin (IS) state (metallic within LDA+U), which consists of IS Co only, and the insulating IS/LS mixture state, the HS/LS state is the most favorable one. The FM order in the HS/LS state is stabilized via the superexchange interactions between adjacent LS and HS Co. We also show that the Co spin state can be identified by measuring the electric field gradient at the Co nucleus via nuclear magnetic resonance spectroscopy.

A density-functional study on the electronic and vibrational properties of layered antimony telluride.

PubMed

Stoffel, Ralf P; Deringer, Volker L; Simon, Ronnie E; Hermann, Raphaël P; Dronskowski, Richard

2015-03-04

We present a comprehensive survey of electronic and lattice-dynamical properties of crystalline antimony telluride (Sb2Te3). In a first step, the electronic structure and chemical bonding have been investigated, followed by calculations of the atomic force constants, phonon dispersion relationships and densities of states. Then, (macroscopic) physical properties of Sb2Te3 have been computed, namely, the atomic thermal displacement parameters, the Grüneisen parameter γ, the volume expansion of the lattice, and finally the bulk modulus B. We compare theoretical results from three popular and economic density-functional theory (DFT) approaches: the local density approximation (LDA), the generalized gradient approximation (GGA), and a posteriori dispersion corrections to the latter. Despite its simplicity, the LDA shows excellent performance for all properties investigated-including the Grüneisen parameter, which only the LDA is able to recover with confidence. In the absence of computationally more demanding hybrid DFT methods, the LDA seems to be a good choice for further lattice dynamical studies of Sb2Te3 and related layered telluride materials.

Jahn-Teller transition in TiF3 investigated using density-functional theory

NASA Astrophysics Data System (ADS)

Perebeinos, Vasili; Vogt, Tom

2004-03-01

We use first-principles density-functional theory to calculate the electronic and magnetic properties of TiF3 using the full-potential-linearized augmented-plane-wave method. The local density approximation (LDA) predicts a fully saturated ferromagnetic metal and finds degenerate energy minima for high- and low-symmetry structures. The experimentally observed Jahn-Teller phase transition at Tc=370 K cannot be driven by the electron-phonon interaction alone, which is usually described accurately by the LDA. Electron correlations beyond the LDA are essential to lift the degeneracy of the singly occupied Ti t2g orbital. Although the on-site Coulomb correlations are important, the direction of the t2g-level splitting is determined by dipole-dipole interactions. The LDA+U functional predicts an aniferromagnetic insulator with an orbitally ordered ground state. The input parameters U=8.1 eV and J=0.9 eV for the Ti 3d orbital were found by varying the total charge on the TiF2-6 ion using the molecular NRLMOL code. We estimate the Heisenberg exchange constant for spin 1/2 on a cubic lattice to be approximately 24 K. The symmetry lowering energy in LDA+U is about 900 K per TiF3 formula unit.

Vibrational and thermodynamic properties of β-HMX: a first-principles investigation.

PubMed

Wu, Zhongqing; Kalia, Rajiv K; Nakano, Aiichiro; Vashishta, Priya

2011-05-28

Thermodynamic properties of β-HMX crystal are investigated using the quasi-harmonic approximation and density functional theory within the local density approximation (LDA), generalized gradient approximation (GGA), and GGA + empirical van der Waals (vdW) correction. It is found that GGA well describes the thermal expansion coefficient and heat capacity but fails to produce correct bulk modulus and equilibrium volume. The vdW correction improves the bulk modulus and volume, but worsens the thermal expansion coefficient and heat capacity. In contrast, LDA describes all thermodynamic properties with reasonable accuracy, and overall is a good exchange-correlation functional for β-HMX molecular crystal. The results also demonstrate significant contributions of phonons to the equation of state. The static calculation of equilibrium volume for β-HMX differs from the room-temperature value incorporating lattice vibrations by over 5%. Therefore, for molecular crystals, it is essential to include phonon contributions when calculated equation of state is compared with experimental data at ambient condition. © 2011 American Institute of Physics

Electronic structure and properties of lanthanum

NASA Astrophysics Data System (ADS)

Nixon, Lane; Papaconstantopoulos, Dimitrios

2008-03-01

The total energy and electronic structure of lanthanum have been calculated in the bcc, fcc, hcp and dhcp structures for pressures up to 50 GPa. The full potential linearized-augmented-planewave method was used with both the local-density and general-gradient approximations. The correct phase ordering has been found, with lattice parameters and bulk moduli in good agreement with experimental data. The GGA method shows excellent agreement overall while the LDA results show larger discrepancies. The calculated strain energies for the fcc and bcc structures demonstrate the respective stable and unstable configurations at ambient conditions. The calculated superconductivity properties under pressure for the fcc structure are also found to agree well with measurements. Both LDA and GGA, with minor differences, reproduce well the experimental results for Tc.

Characterization of Thin Film Materials using SCAN meta-GGA, an Accurate Nonempirical Density Functional

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buda, I. G.; Lane, C.; Barbiellini, B.

We discuss self-consistently obtained ground-state electronic properties of monolayers of graphene and a number of ’beyond graphene’ compounds, including films of transition-metal dichalcogenides (TMDs), using the recently proposed strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) to the density functional theory. The SCAN meta-GGA results are compared with those based on the local density approximation (LDA) as well as the generalized gradient approximation (GGA). As expected, the GGA yields expanded lattices and softened bonds in relation to the LDA, but the SCAN meta-GGA systematically improves the agreement with experiment. Our study suggests the efficacy of the SCAN functionalmore » for accurate modeling of electronic structures of layered materials in high-throughput calculations more generally.« less

Characterization of Thin Film Materials using SCAN meta-GGA, an Accurate Nonempirical Density Functional

DOE PAGES

Buda, I. G.; Lane, C.; Barbiellini, B.; ...

2017-03-23

We discuss self-consistently obtained ground-state electronic properties of monolayers of graphene and a number of ’beyond graphene’ compounds, including films of transition-metal dichalcogenides (TMDs), using the recently proposed strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) to the density functional theory. The SCAN meta-GGA results are compared with those based on the local density approximation (LDA) as well as the generalized gradient approximation (GGA). As expected, the GGA yields expanded lattices and softened bonds in relation to the LDA, but the SCAN meta-GGA systematically improves the agreement with experiment. Our study suggests the efficacy of the SCAN functionalmore » for accurate modeling of electronic structures of layered materials in high-throughput calculations more generally.« less

Thermodynamic properties of OsB under high temperature and high pressure

NASA Astrophysics Data System (ADS)

Chen, Hai-Hua; Li, Zuo; Cheng, Yan; Bi, Yan; Cai, Ling-Cang

2011-09-01

The energy-volume curves of OsB have been obtained using the first-principles plane-wave ultrasoft-pseudopotential density functional theory (DFT) within the generalized gradient approximation (GGA) and local density approximation (LDA). Using the quasi-harmonic Debye model we first analyze the specific heat, the coefficients of thermal expansion as well as the thermodynamic Grüneisen parameter of OsB in a wide temperature range at high pressure. At temperature 300 K, the coefficients of thermal expansion αV by LDA and GGA calculations are 1.67×10 -5 1/K and 2.01×10 -5 1/K, respectively. The specific heat of OsB at constant pressure (volume) is also calculated. Meanwhile, we find that the Debye temperature of OsB increases monotonically with increasing pressure. The present study leads to a better understanding of how the OsB materials respond to pressure and temperature.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, Prashant; Harbola, Manoj K.; Johnson, Duane D.

Here, this work constitutes a comprehensive and improved account of electronic-structure and mechanical properties of silicon-nitride (more » $${\\rm Si}_{3}$$ $${\\rm N}_{4}$$ ) polymorphs via van Leeuwen and Baerends (LB) exchange-corrected local density approximation (LDA) that enforces the exact exchange potential asymptotic behavior. The calculated lattice constant, bulk modulus, and electronic band structure of $${\\rm Si}_{3}$$ $${\\rm N}_{4}$$ polymorphs are in good agreement with experimental results. We also show that, for a single electron in a hydrogen atom, spherical well, or harmonic oscillator, the LB-corrected LDA reduces the (self-interaction) error to exact total energy to ~10%, a factor of three to four lower than standard LDA, due to a dramatically improved representation of the exchange-potential.« less

Long-range-corrected Rung 3.5 density functional approximations

NASA Astrophysics Data System (ADS)

Janesko, Benjamin G.; Proynov, Emil; Scalmani, Giovanni; Frisch, Michael J.

2018-03-01

Rung 3.5 functionals are a new class of approximations for density functional theory. They provide a flexible intermediate between exact (Hartree-Fock, HF) exchange and semilocal approximations for exchange. Existing Rung 3.5 functionals inherit semilocal functionals' limitations in atomic cores and density tails. Here we address those limitations using range-separated admixture of HF exchange. We present three new functionals. LRC-ωΠLDA combines long-range HF exchange with short-range Rung 3.5 ΠLDA exchange. SLC-ΠLDA combines short- and long-range HF exchange with middle-range ΠLDA exchange. LRC-ωΠLDA-AC incorporates a combination of HF, semilocal, and Rung 3.5 exchange in the short range, based on an adiabatic connection. We test these in a new Rung 3.5 implementation including up to analytic fourth derivatives. LRC-ωΠLDA and SLC-ΠLDA improve atomization energies and reaction barriers by a factor of 8 compared to the full-range ΠLDA. LRC-ωΠLDA-AC brings further improvement approaching the accuracy of standard long-range corrected schemes LC-ωPBE and SLC-PBE. The new functionals yield highest occupied orbital energies closer to experimental ionization potentials and describe correctly the weak charge-transfer complex of ethylene and dichlorine and the hole-spin distribution created by an Al defect in quartz. This study provides a framework for more flexible range-separated Rung 3.5 approximations.

Calculation of phonon dispersion relation using new correlation functional

NASA Astrophysics Data System (ADS)

Jitropas, Ukrit; Hsu, Chung-Hao

2017-06-01

To extend the use of Local Density Approximation (LDA), a new analytical correlation functional is introduced. Correlation energy is an essential ingredient within density functional theory and used to determine ground state energy and other properties including phonon dispersion relation. Except for high and low density limit, the general expression of correlation energy is unknown. The approximation approach is therefore required. The accuracy of the modelling system depends on the quality of correlation energy approximation. Typical correlation functionals used in LDA such as Vosko-Wilk-Nusair (VWN) and Perdew-Wang (PW) were obtained from parameterizing the near-exact quantum Monte Carlo data of Ceperley and Alder. These functionals are presented in complex form and inconvenient to implement. Alternatively, the latest published formula of Chachiyo correlation functional provides a comparable result for those much more complicated functionals. In addition, it provides more predictive power based on the first principle approach, not fitting functionals. Nevertheless, the performance of Chachiyo formula for calculating phonon dispersion relation (a key to the thermal properties of materials) has not been tested yet. Here, the implementation of new correlation functional to calculate phonon dispersion relation is initiated. The accuracy and its validity will be explored.

Electron interference effects in energetic photoelectrons from C60@C240 probed by the Fourier spectroscopy

NASA Astrophysics Data System (ADS)

McCreary, Meghan; Chakraborty, Himadri

2013-05-01

The ground state structure of the simplest two-fullerene onion system, the C60@C240 molecule, is solved in the Kohn-Sham framework of local density approximation (LDA). Calculations are carried out with delocalized carbon valence electrons after modeling the onion ion-core of sixty C4+ ions from C60 and two hundred and forty of those from C240 in a smeared out jellium-type double-shell structure. Ionization cross sections of all the levels are then calculated in both independent particle LDA and many-particle time dependent LDA approaches at photon energies above the plasmon resonances. These high-energy results exhibit rich structures of energy dependent oscillations from the quantum interference of electron waves produced at the edges of the fullerene layers. A detailed scrutiny of these structures is conducted by Fourier transforming the spectra to the configuration space that relates the oscillations to the onion geometry. Supported by NSF and DOE.

The half-metallicity of Co2FeGe full Heusler alloy in (001) thin film: First principles study

NASA Astrophysics Data System (ADS)

Hyun, Jung-Min; Kim, Miyoung

2018-01-01

The electronic and magnetic properties of the Co2FeGe full Heusler alloy in (001) thin film are investigated using the first-principles electronic structure calculations within the density functional theory. We employ various exchange correlation functionals including the local density approximation (LDA), the generalized gradient approximation (GGA), and the additional + U corrections for strong on-site Coulomb interaction of transition metal 3d states, aiming to examine the correlation effect on the electronic structures which determine the spin gap and thus the half-metallicity. Our results reveal that the Co2FeGe thin film is metallic in both LDA and GGA, while the + U correction opens up the spin gap for spin minority channel in GGA+ U but not in LDA+U in contrast to its bulk alloy which is predicted to be half-metallic in both LDA+ U and GGA+ U approaches with total spin magnetic moment of 6 μ B . It is found that the surface states developed around the Fermi level and the enhanced 3d e g - t 2 g band splitting for the spin minority channel due to the correlation effect play critical roles to determine the emergence of the half-metallicity.

Structural, electronic, and vibrational properties of high-density amorphous silicon: a first-principles molecular-dynamics study.

PubMed

Morishita, Tetsuya

2009-05-21

We report a first-principles study of the structural, electronic, and dynamical properties of high-density amorphous (HDA) silicon, which was found to be formed by pressurizing low-density amorphous (LDA) silicon (a normal amorphous Si) [T. Morishita, Phys. Rev. Lett. 93, 055503 (2004); P. F. McMillan, M. Wilson, D. Daisenberger, and D. Machon, Nature Mater. 4, 680 (2005)]. Striking structural differences between HDA and LDA are revealed. The LDA structure holds a tetrahedral network, while the HDA structure contains a highly distorted tetrahedral network. The fifth neighboring atom in HDA tends to be located at an interstitial position of a distorted tetrahedron composed of the first four neighboring atoms. Consequently, the coordination number of HDA is calculated to be approximately 5 unlike that of LDA. The electronic density of state (EDOS) shows that HDA is metallic, which is consistent with a recent experimental measurement of the electronic resistance of HDA Si. We find from local EDOS that highly distorted tetrahedral configurations enhance the metallic nature of HDA. The vibrational density of state (VDOS) also reflects the structural differences between HDA and LDA. Some of the characteristic vibrational modes of LDA are dematerialized in HDA, indicating the degradation of covalent bonds. The overall profile of the VDOS for HDA is found to be an intermediate between that for LDA and liquid Si under pressure (high-density liquid Si).

Methodological study of computational approaches to address the problem of strong correlations

NASA Astrophysics Data System (ADS)

Lee, Juho

The main focus of this thesis is the detailed investigation of computational methods to tackle strongly correlated materials in which a rich variety of exotic phenomena are found. A many-body problem with sizable electronic correlations can no longer be explained by independent-particle approximations such as density functional theory (DFT) or tight-binding approaches. The influence of an electron to the others is too strong for each electron to be treated as an independent quasiparticle and consequently those standard band-structure methods fail even at a qualitative level. One of the most powerful approaches for strong correlations is the dynamical mean-field theory (DMFT), which has enlightened the understanding of the Mott transition based on the Hubbard model. For realistic applications, the dynamical mean-field theory is combined with various independent-particles approaches. The most widely used one is the DMFT combined with the DFT in the local density approximation (LDA), so-called LDA+DMFT. In this approach, the electrons in the weakly correlated orbitals are calculated by LDA while others in the strongly correlated orbitals are treated by DMFT. Recently, the method combining DMFT with Hedin's GW approximation was also developed, in which the momentum-dependent self-energy is also added. In this thesis, we discuss the application of those methodologies based on DMFT. First, we apply the dynamical mean-field theory to solve the 3-dimensional Hubbard model in Chap. 3. In this application, we model the interface between the thermodynamically coexisting metal and Mott insulator. We show how to model the required slab geometry and extract the electronic spectra. We construct an effective Landau free energy and compute the variation of its parameters across the phase diagram. Finally, using a linear mixture of the density and double-occupancy, we identify a natural Ising order parameter which unifies the treatment of the bandwidth and filling controlled Mott transitions. Secondly, we study the double-counting problem, a subtle issue that arises in LDA+DMFT. We propose a highly precise double-counting functional, in which the intersection of LDA and DMFT is calculated exactly, and implement a parameter-free version of the LDA+DMFT that is tested on one of the simplest strongly correlated systems, the H2 molecule. We show that the exact double-counting treatment along with a good DMFT projector leads to very accurate and total energy and excitation spectrum of H2 molecule. Finally, we implement various versions of GW+DMFT, in its fully self-consistent way, one shot GW approximation, and quasiparticle self-consistent scheme, and studied how well these combined methods perform on H2 molecule as compared to more established methods such as LDA+DMFT. We found that most flavors of GW+DMFT break down in strongly correlated regime due to causality violation. Among GW+DMFT methods, only the self-consistent quasiparticle GW+DMFT with static double-counting, and a new method with causal double-counting, correctly recover the atomic limit at large H-atom separation. While some flavors of GW+DMFT improve the single-electron spectra of LDA+DMFT, the total energy is best predicted by LDA+DMFT, for which the exact double-counting is known, and is static.

Structural and electronic properties of GaAs and GaP semiconductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rani, Anita; Kumar, Ranjan

2015-05-15

The Structural and Electronic properties of Zinc Blende phase of GaAs and GaP compounds are studied using self consistent SIESTA-code, pseudopotentials and Density Functional Theory (DFT) in Local Density Approximation (LDA). The Lattice Constant, Equillibrium Volume, Cohesive Energy per pair, Compressibility and Band Gap are calculated. The band gaps calcultated with DFT using LDA is smaller than the experimental values. The P-V data fitted to third order Birch Murnaghan equation of state provide the Bulk Modulus and its pressure derivatives. Our Structural and Electronic properties estimations are in agreement with available experimental and theoretical data.

Vibrational mode frequencies of H2S and H2O adsorbed on Ge(0 0 1)-(2 × 1) surfaces

NASA Astrophysics Data System (ADS)

Hartnett, M.; Fahy, S.

2015-02-01

The equilibrium geometry and vibrational modes of H2S and H2O-terminated Ge(0 0 1)-(2 × 1) surfaces are calculated in a supercell approach using first-principles density functional theory in the local density (LDA), generalized gradient (GGA) approximations and van der Waals (vdW) interactions. Mode frequencies are found using the frozen phonon method. For the H2S-passivated surface, the calculated frequencies in LDA (GGA) are 2429 cm-1 (2490) for the Hsbnd S stretch mode, 712 cm-1 (706) for the Hsbnd S bond bending mode, 377 cm-1 (36) for the Gesbnd S stretch mode and 328 cm-1 (337) for Hsbnd S wag mode. Frequencies for the H2O passivated surface are 3590 cm-1 (3600) for the Hsbnd O stretch mode, 921 cm-1 (947) for the bending mode, 609 cm-1 (559) for the Gesbnd O stretch, 1995 cm-1 (1991) for the Gesbnd H stretch mode, 498 cm-1 (478) for the Gesbnd H bending mode and 342 cm-1 (336) for the Hsbnd O wag mode. The differences between the functionals including vdW terms and the LDA or GGA are less than the differences between LDA and GGA for the vibrational mode frequencies.

First-principles energy band calculation of Ruddlesden–Popper compound Sr{sub 3}Sn{sub 2}O{sub 7} using modified Becke–Johnson exchange potential

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kamimura, Sunao, E-mail: kamimura-sunao@che.kyutech.ac.jp; National Institute of Advanced Industrial Science and Technology; Department of Molecular and Material Sciences, Interdisciplinary Graduate School of Engineering Science, Kyushu University, 6-1 Kasuga Kouen, Kasuga, Fukuoka 816-8580 Japan

The electronic structure of Sr{sub 3}Sn{sub 2}O{sub 7} is evaluated by the scalar-relativistic full potential linearized augmented plane wave (FLAPW+lo) method using the modified Becke–Johnson potential (Tran–Blaha potential) combined with the local density approximation correlation (MBJ–LDA). The fundamental gap between the valence band (VB) and conduction band (CB) is estimated to be 3.96 eV, which is close to the experimental value. Sn 5s states and Sr 4d states are predominant in the lower and upper CB, respectively. On the other hand, the lower VB is mainly composed of Sn 5s, 5p, and O 2p states, while the upper VB mainlymore » consists of O 2p states. These features of the DOS are well reflected by the optical transition between the upper VB and lower CB, as seen in the energy dependence of the dielectric function. Furthermore, the absorption coefficient estimated from the MBJ–LDA is similar to the experimental result. - Graphical abstract: Calculated energy band structure along the symmetry lines of the first BZ of Sr{sub 3}Sn{sub 2}O{sub 7} crystal obtained using the MBJ potential. - Highlights: • Electronic structure of Sr{sub 3}Sn{sub 2}O{sub 7} is calculated on the basis of MBJ–LDA method for the first time. • Band gap of Sr{sub 3}Sn{sub 2}O{sub 7} is determined accurately on the basis of MBJ–LDA method. • The experimental absorption spectrum of Sr{sub 3}Sn{sub 2}O{sub 7} produced by MBJ–LDA is more accurate than that obtained by GGA method.« less

Simple many-body based screening mixing ansatz for improvement of G W /Bethe-Salpeter equation excitation energies of molecular systems

NASA Astrophysics Data System (ADS)

Ziaei, Vafa; Bredow, Thomas

2017-11-01

We propose a simple many-body based screening mixing strategy to considerably enhance the performance of the Bethe-Salpeter equation (BSE) approach for prediction of excitation energies of molecular systems. This strategy enables us to closely reproduce results of highly correlated equation of motion coupled cluster singles and doubles (EOM-CCSD) through optimal use of cancellation effects. We start from the Hartree-Fock (HF) reference state and take advantage of local density approximation (LDA) based random phase approximation (RPA) screening, denoted as W0-RPA@LDA with W0 as the dynamically screened interaction built upon LDA wave functions and energies. We further use this W0-RPA@LDA screening as an initial screening guess for calculation of quasiparticle energies in the framework of G0W0 @HF. The W0-RPA@LDA screening is further injected into the BSE. By applying such an approach on a set of 22 molecules for which the traditional G W /BSE approaches fail, we observe good agreement with respect to EOM-CCSD references. The reason for the observed good accuracy of this mixing ansatz (scheme A) lies in an optimal damping of HF exchange effect through the W0-RPA@LDA strong screening, leading to substantial decrease of typically overestimated HF electronic gap, and hence to better excitation energies. Further, we present a second multiscreening ansatz (scheme B), which is similar to scheme A with the exception that now the W0-RPA@HF screening is used in the BSE in order to further improve the overestimated excitation energies of carbonyl sulfide (COS) and disilane (Si2H6 ). The reason for improvement of the excitation energies in scheme B lies in the fact that W0-RPA@HF screening is less effective (and weaker than W0-RPA@LDA), which gives rise to stronger electron-hole effects in the BSE.

Better band gaps for wide-gap semiconductors from a locally corrected exchange-correlation potential that nearly eliminates self-interaction errors

DOE PAGES

Singh, Prashant; Harbola, Manoj K.; Johnson, Duane D.

2017-09-08

Here, this work constitutes a comprehensive and improved account of electronic-structure and mechanical properties of silicon-nitride (more » $${\\rm Si}_{3}$$ $${\\rm N}_{4}$$ ) polymorphs via van Leeuwen and Baerends (LB) exchange-corrected local density approximation (LDA) that enforces the exact exchange potential asymptotic behavior. The calculated lattice constant, bulk modulus, and electronic band structure of $${\\rm Si}_{3}$$ $${\\rm N}_{4}$$ polymorphs are in good agreement with experimental results. We also show that, for a single electron in a hydrogen atom, spherical well, or harmonic oscillator, the LB-corrected LDA reduces the (self-interaction) error to exact total energy to ~10%, a factor of three to four lower than standard LDA, due to a dramatically improved representation of the exchange-potential.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castaño-González, E.-E.; Seña, N.; Mendoza-Estrada, V.

In this paper, we carried out first-principles calculations in order to investigate the structural and electronic properties of the binary compound gallium antimonide (GaSb). This theoretical study was carried out using the Density Functional Theory within the plane-wave pseudopotential method. The effects of exchange and correlation (XC) were treated using the functional Local Density Approximation (LDA), generalized gradient approximation (GGA): Perdew–Burke–Ernzerhof (PBE), Perdew-Burke-Ernzerhof revised for solids (PBEsol), Perdew-Wang91 (PW91), revised Perdew–Burke–Ernzerhof (rPBE), Armiento–Mattson 2005 (AM05) and meta-generalized gradient approximation (meta-GGA): Tao–Perdew–Staroverov–Scuseria (TPSS) and revised Tao–Perdew–Staroverov–Scuseria (RTPSS) and modified Becke-Johnson (MBJ). We calculated the densities of state (DOS) and band structuremore » with different XC potentials identified and compared them with the theoretical and experimental results reported in the literature. It was discovered that functional: LDA, PBEsol, AM05 and RTPSS provide the best results to calculate the lattice parameters (a) and bulk modulus (B{sub 0}); while for the cohesive energy (E{sub coh}), functional: AM05, RTPSS and PW91 are closer to the values obtained experimentally. The MBJ, Rtpss and AM05 values found for the band gap energy is slightly underestimated with those values reported experimentally.« less

Fundamental gaps with approximate density functionals: The derivative discontinuity revealed from ensemble considerations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kraisler, Eli; Kronik, Leeor

2014-05-14

The fundamental gap is a central quantity in the electronic structure of matter. Unfortunately, the fundamental gap is not generally equal to the Kohn-Sham gap of density functional theory (DFT), even in principle. The two gaps differ precisely by the derivative discontinuity, namely, an abrupt change in slope of the exchange-correlation energy as a function of electron number, expected across an integer-electron point. Popular approximate functionals are thought to be devoid of a derivative discontinuity, strongly compromising their performance for prediction of spectroscopic properties. Here we show that, in fact, all exchange-correlation functionals possess a derivative discontinuity, which arises naturallymore » from the application of ensemble considerations within DFT, without any empiricism. This derivative discontinuity can be expressed in closed form using only quantities obtained in the course of a standard DFT calculation of the neutral system. For small, finite systems, addition of this derivative discontinuity indeed results in a greatly improved prediction for the fundamental gap, even when based on the most simple approximate exchange-correlation density functional – the local density approximation (LDA). For solids, the same scheme is exact in principle, but when applied to LDA it results in a vanishing derivative discontinuity correction. This failure is shown to be directly related to the failure of LDA in predicting fundamental gaps from total energy differences in extended systems.« less

Computational materials design of attractive Fermion system with large negative effective Ueff in the hole-doped Delafossite of CuAlO2, AgAlO2 and AuAlO2: Charge-excitation induced Ueff < 0

NASA Astrophysics Data System (ADS)

Nakanishi, A.; Fukushima, T.; Uede, H.; Katayama-Yoshida, H.

2015-12-01

On the basis of general design rules for negative effective U(Ueff) systems by controlling purely-electronic and attractive Fermion mechanisms, we perform computational materials design (CMD®) for the negative Ueff system in hole-doped two-dimensional (2D) Delafossite CuAlO2, AgAlO2 and AuAlO2 by ab initio calculations with local density approximation (LDA) and self-interaction corrected-LDA (SIC-LDA). It is found that the large negative Ueff in the hole-doped attractive Fermion systems for CuAlO2 (UeffLDA = - 4.53 eV and UeffSIC-LDA = - 4.20 eV), AgAlO2 (UeffLDA = - 4.88 eV and UeffSIC-LDA = - 4.55 eV) and AuAlO2 (UeffLDA = - 4.14 eV and UeffSIC-LDA = - 3.55 eV). These values are 10 times larger than that in hole-doped three-dimensional (3D) CuFeS2 (Ueff = - 0.44 eV). For future calculations of Tc and phase diagram by quantum Monte Carlo simulations, we propose the negative Ueff Hubbard model with the anti-bonding single π-band model for CuAlO2, AgAlO2 and AuAlO2 using the mapped parameters obtained from ab initio electronic structure calculations. Based on the theory of negative Ueff Hubbard model (Noziéres and Schmitt-Rink, 1985), we discuss |Ueff| dependence of superconducting critical temperature (Tc) in the 2D Delafossite of CuAlO2, AgAlO2 and AuAlO2 and 3D Chalcopyrite of CuFeS2, which shows the interesting chemical trend, i.e., Tc increases exponentially (Tc ∝ exp [ - 1 / | Ueff | ]) in the weak coupling regime | Ueff(- 0.44 eV) | < W(∼ 2 eV) (where W is the band width of the negative Ueff Hubbard model) for the hole-doped CuFeS2, and then Tc goes through a maximum when | Ueff(- 4.88 eV , - 4.14 eV) | ∼ W(2.8 eV , 3.5 eV) for the hole-doped AgAlO2 and AuAlO2, and finally Tc decreases with increasing |Ueff| in the strong coupling regime, where | Ueff(- 4.53 eV) | > W(1.7 eV) , for the hole-doped CuAlO2.

Ultra-sensitive pressure dependence of bandgap of rutile-GeO2 revealed by many body perturbation theory.

PubMed

Samanta, Atanu; Jain, Manish; Singh, Abhishek K

2015-08-14

The reported values of bandgap of rutile GeO2 calculated by the standard density functional theory within local-density approximation (LDA)/generalized gradient approximation (GGA) show a wide variation (∼2 eV), whose origin remains unresolved. Here, we investigate the reasons for this variation by studying the electronic structure of rutile-GeO2 using many-body perturbation theory within the GW framework. The bandgap as well as valence bandwidth at Γ-point of rutile phase shows a strong dependence on volume change, which is independent of bandgap underestimation problem of LDA/GGA. This strong dependence originates from a change in hybridization among O-p and Ge-(s and p) orbitals. Furthermore, the parabolic nature of first conduction band along X-Γ-M direction changes towards a linear dispersion with volume expansion.

Structural, electronic and elastic properties of heavy fermion YbRh2 Laves phase compound

NASA Astrophysics Data System (ADS)

Pawar, Harsha; Shugani, Mani; Aynyas, Mahendra; Sanyal, Sankar P.

2018-05-01

The structural, electronic and elastic properties of YbRh2 Laves phase intermetallic compound which crystallize in cubic (MgCu2-type) structure have been investigated using ab-initio full potential linearized augmented plane wave (FP- LAPW) method with LDA and LDA+U approximation. The calculated ground state properties such as lattice parameter (a0), bulk modulus (B) and its pressure derivative (B') are in good agreement with available experimental and theoretical data. The electronic properties are analyzed from band structures and density of states. Elastic constants are predicted first time for this compound which obeys the stability criteria for cubic system.

Electronic structure of Ag7GeS5I superionic compound

NASA Astrophysics Data System (ADS)

Bletskan, Dmytro; Studenyak, Ihor; Bletskan, Mykhailo; Vakulchak, Vasyl

2018-05-01

This paper presents the originally results of ab initio calculations of electronic structure, total and partial densities of electronic states as well as electronic charge density distribution of Ag7GeS5I crystal performed within the density functional theory (DFT) in the local density approximation (LDA) for exchange-correlation potential. According to performed calculations, Ag7GeS5I is the direct-gap semiconductor with the valence band top and the conductivity band bottom in the Γ point of Brillouin zone. The band gap width calculated in the LDA-approximation is Egd = 0.73 eV. The analysis of total and partial densities of electronic states allow us to identify the atomic orbital contributions into the crystal orbitals as well as the formation data of chemical bond in the studied crystal. In the top part of Ag7GeS5I valence band it was revealed the considerable mixing (hybridization) of the occupied d-states of Ag noble metal and the delocalized p-states of sulfur and iodine, which is undoubtedly associated with the covalent character of chemical bond between S, I atoms and noble metal atom.

Density of states, optical and thermoelectric properties of perovskite vanadium fluorides Na3VF6

NASA Astrophysics Data System (ADS)

Reshak, A. H.; Azam, Sikander

2014-05-01

The electronic structure, charge density and Fermi surface of Na3VF6 compound have been examined with the support of density functional theory (DFT). Using the full potential linear augmented plane wave method, we employed the local density approximation (LDA), generalized gradient approximation (GGA) and Engel-Vosko GGA (EVGGA) to treat the exchange correlation potential to solve Kohn-Sham equations. The calculation show that Na3VF6 compound has metallic nature and the Fermi energy (EF) is assessed by overlapping of V-d state. The calculated density of states at the EF are about 18.655, 51.932 and 13.235 states/eV, and the bare linear low-temperature electronic specific heat coefficient (γ) is found to be 3.236 mJ/mol-K2, 9.008 mJ/mol-K2 and 2.295 mJ/mol-K2 for LDA, GGA and EVGGA, respectively. The Fermi surface is composed of two sheets. The chemical bonding of Na3VF6 compound is analyzed through the electronic charge density in the (1 1 0) crystallographic plane. The optical constants and thermal properties were also calculated and discussed.

High resistivity in undoped CdTe: carrier compensation of Te antisites and Cd vacancies

NASA Astrophysics Data System (ADS)

Lindström, A.; Mirbt, S.; Sanyal, B.; Klintenberg, M.

2016-01-01

In this paper, we focus on the high resistivity of intentionally undoped CdTe, where the most prevalent defects are Cd vacancies and Te antisites. Our calculated formation energies lead to the conclusion that the Fermi energy of undoped CdTe is at midgap due to carrier compensation of Te antisites and Cd vacancies, which explains the experimentally observed high resistivity. We use density functional theory with the hybrid functional of Heyd, Scuseria and Ernzerhof (HSE06) and show that the proper description of the native defects in general fails using the local density approximation (LDA) instead of HSE06. We conclude that LDA is insufficient to understand the high resistivity of undoped CdTe. We calculate the neutral and double acceptor state of the Te antisite to be intrinsic DX-centers.

X-ray photoelectron spectrum and electronic properties of a noncentrosymmetric chalcopyrite compound HgGa(2)S(4): LDA, GGA, and EV-GGA.

PubMed

Reshak, Ali Hussain; Khenata, R; Kityk, I V; Plucinski, K J; Auluck, S

2009-04-30

An all electron full potential linearized augmented plane wave method has been applied for a theoretical study of the band structure, density of states, and electron charge density of a noncentrosymmetric chalcopyrite compound HgGa(2)S(4) using three different approximations for the exchange correlation potential. Our calculations show that the valence band maximum (VBM) and conduction band minimum (CBM) are located at Gamma resulting in a direct energy gap of about 2.0, 2.2, and 2.8 eV for local density approximation (LDA), generalized gradient approximation (GGA), and Engel-Vosko (EVGGA) compared to the experimental value of 2.84 eV. We notice that EVGGA shows excellent agreement with the experimental data. This agreement is attributed to the fact that the Engel-Vosko GGA formalism optimizes the corresponding potential for band structure calculations. We make a detailed comparison of the density of states deduced from the X-ray photoelectron spectra with our calculations. We find that there is a strong covalent bond between the Hg and S atoms and Ga and S atoms. The Hg-Hg, Ga-Ga, and S-S bonds are found to be weaker than the Hg-S and Ga-S bonds showing that a covalent bond exists between Hg and S atoms and Ga and S atoms.

Ultra-sensitive pressure dependence of bandgap of rutile-GeO{sub 2} revealed by many body perturbation theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Samanta, Atanu; Singh, Abhishek K.; Jain, Manish

2015-08-14

The reported values of bandgap of rutile GeO{sub 2} calculated by the standard density functional theory within local-density approximation (LDA)/generalized gradient approximation (GGA) show a wide variation (∼2 eV), whose origin remains unresolved. Here, we investigate the reasons for this variation by studying the electronic structure of rutile-GeO{sub 2} using many-body perturbation theory within the GW framework. The bandgap as well as valence bandwidth at Γ-point of rutile phase shows a strong dependence on volume change, which is independent of bandgap underestimation problem of LDA/GGA. This strong dependence originates from a change in hybridization among O-p and Ge-(s and p)more » orbitals. Furthermore, the parabolic nature of first conduction band along X-Γ-M direction changes towards a linear dispersion with volume expansion.« less

Applications of the First-principles LDA+Usc Method to Spin-crossover Minerals: the NAL Phase and (Mg,Fe)CO3 ferromagnesite

NASA Astrophysics Data System (ADS)

Hsu, H.

2016-12-01

Spin crossover (SCO) in iron-bearing minerals has attracted tremendous attention in recent years, as SCO usually leads to anomalous changes of the elastic, conducting, and thermodynamic properties of these minerals. Possible geophysical effects of SCO have been anticipated as well. With the development of the local density approximation + self-consistent Hubbard U (LDA+Usc) method, first-principles calculations have elucidated SCO in many lower-mantle minerals. The success of LDA+Usc lies in its capability to correctly identify the ground state in a wide pressure range and to accurately determine the mechanism of SCO, including the transition pressure PT. In this talk, two recent LDA+Usc studies of SCO minerals are presented: the "new aluminous (NAL) phase" [1] and (Mg,Fe)CO3 ferromagnesite [2]. The former is considered as a main host of aluminum in the subducted basalt and may be related to the seismic heterogeneities, and the latter is believed to be the major carbon carrier in the Earth's lower mantle and play a key role in the deep carbon cycle. For both minerals, the abrupt change of iron quadrupole splitting and the volume/elastic anomalies accompanying the SCO obtained in our calculations are in great agreement with experiments. Our calculations also suggest that the spin transition pressure PT in the NAL phase is not very sensitive to temperature, due to its nearly degenerate low-spin (LS) states, in contrast with (Mg,Fe)O ferropericlase and (Mg,Fe)CO3 systems, in which PT significantly increases with temperature. By examining the overall performance of the LDA+Usc method in the NAL phase and ferromagnesite, along with our previous calculations for ferropericlase and Fe-bearing MgSiO3 bridgmanite [3-5], we have established LDA+Usc a highly reliable method to study iron-bearing minerals and related materials under high pressure. [1] H. Hsu, in preparation. [2] S.-C. Huang and H. Hsu, Phys. Rev. B (Rapid Comm.), in press. [3] H. Hsu and R. M. Wentzcovitch, Phys. Rev. B 90, 195205 (2014). [4] H. Hsu et al., Earth Planet. Sci. Lett. 359-360, 34 (2012). [5] H. Hsu et al., Phys. Rev. Lett. 106, 118501 (2011).

Structural, Electronic and Elastic Properties of Heavy Fermion YbTM2 (TM= Ir and Pt) Laves Phase Compounds

NASA Astrophysics Data System (ADS)

Pawar, H.; Shugani, M.; Aynyas, M.; Sanyal, S. P.

2018-02-01

The structural, electronic and elastic properties of YbTM2 (TM = Ir and Pt) Laves phase intermetallic compounds which crystallize in cubic (MgCu2-type) structure, have been investigated using ab-initio full potential linearized augmented plane wave (FP-LAPW) method with LDA and LDA+U approximation. The calculated ground state properties such as lattice parameter (a0), bulk modulus (B) and its pressure derivative (B‧) are in good agreement with available experimental and theoretical data. The electronic properties are analyzed from band structures and density of states. Elastic constants are predicted first time for these compounds which obey the stability criteria for cubic system.

Assessment of band gaps for alkaline-earth chalcogenides using improved Tran Blaha-modified Becke Johnson potential

NASA Astrophysics Data System (ADS)

Yedukondalu, N.; Kunduru, Lavanya; Roshan, S. C. Rakesh; Sainath, M.

2018-04-01

Assessment of band gaps for nine alkaline-earth chalcogenides namely MX (M = Ca, Sr, Ba and X = S, Se Te) compounds are reported using Tran Blaha-modified Becke Johnson (TB-mBJ) potential and its new parameterization. From the computed electronic band structures at the equilibrium lattice constants, these materials are found to be indirect band gap semiconductors at ambient conditions. The calculated band gaps are improved using TB-mBJ and its new parameterization when compared to local density approximation (LDA) and Becke Johnson potentials. We also observe that TB-mBJ new parameterization for semiconductors below 7 eV reproduces the experimental trends very well for the small band gap semiconducting alkaline-earth chalcogenides. The calculated band profiles look similar for MX compounds (electronic band structures are provided for BaS for representation purpose) using LDA and new parameterization of TB-mBJ potentials.

Electronic Correlation and Magnetism in the Ferromagnetic Metal Fe 3GeTe 2

DOE PAGES

Zhu, Jian-Xin; Janoschek, Marc; Chaves, D. S.; ...

2016-04-05

Motivated by the search for design principles of rare-earth-free strong magnets, we present a study of electronic structure and magnetic properties of the ferromagnetic metal Fe3GeTe2 within local density approximation (LDA) of the density functional theory, and its combination with dynamical mean-field theory (DMFT). For comparison to these calculations, we have measured magnetic and thermodynamic properties as well as X-ray magnetic circular dichroism and the photoemission spectrum of single crystal Fe3GeTe2. We find that the experimentally determined Sommerfeld coefficient is enhanced by an order of magnitude with respect to the LDA value. This enhancement can be partially explained by LDA+DMFT.more » Additionally, the inclusion of dynamical electronic correlation effects provides the experimentally observed magnetic moments, and the spectral density is in better agreement with photoemission data. Lastly, these results establish the importance of electronic correlations in this ferromagnet.« less

AB INITIO STUDY OF OPTOELECTRONIC PROPERTIES OF SPINEL ZnAl2O4 BEYOND GGA AND LDA

NASA Astrophysics Data System (ADS)

Yousaf, Masood; Saeed, M. A.; Isa, Ahmad Radzi Mat; Rahnamaye Aliabad, H. A.; Noor, N. A.

2012-12-01

Electronic band structure and optical parameters of ZnAl2O4 are investigated by first-principles technique based on a new potential approximation, known as modified Becke-Johnson (mBJ). This method describes the excited states of insulators and semiconductors more accurately The recent direct band gap result by EV-GGA is underestimated by about 15% compared to our band gap value using mBJ-GGA. The value of the band gap of ZnAl2O4 decreases as follows: Eg(mBJ-GGA/LDA) > Eg(GGA) > Eg(LDA). The band structure base optical parametric quantities (dielectric constant, index of refraction, reflectivity and optical conductivity) are also calculated, and their variations with energy range are discussed. The first critical point (optical absorption's edge) in ZnAl2O4 occurs at about 5.26 eV in case of mBJ. This study about the optoelectronic properties indicates that ZnAl2O4 can be used in optical devices.

First-principles calculations for elastic properties of OsB 2 under pressure

NASA Astrophysics Data System (ADS)

Yang, Jun-Wei; Chen, Xiang-Rong; Luo, Fen; Ji, Guang-Fu

2009-11-01

The structure, elastic properties and elastic anisotropy of orthorhombic OsB 2 are investigated by density functional theory method with the ultrasoft pseudopotential scheme in the frame of the generalized gradient approximation (GGA) as well as local density approximation (LDA). The obtained structural parameters, elastic constants, elastic anisotropy and Debye temperature for OsB 2 under pressure are consistent with the available experimental data and other theoretical results. It is found that the elastic constants, bulk modulus and Debye temperature of OsB 2 tend to increase with increasing pressure. It is predicted that OsB 2 is not a superhard material from our calculations.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daga, Avinash; Sharma, Smita

First principle study of band structure calculations in the local density approximations (LDA) as well as in the generalized gradient approximations (GGA) have been used to determine the electronic structure of SrMO{sub 3} where M stands for Ti, Zr and Mo. Occurrence of band gap proves SrTiO{sub 3} and SrZrO{sub 3} to be insulating. A small band gap is observed in SrMoO{sub 3} perovskite signifies it to be metallic. Band structures are found to compare well with the available data in the literature showing the relevance of this approach. ABINIT computer code has been used to carry out all themore » calculations.« less

Systematic approach for simultaneously correcting the band-gap and p - d separation errors of common cation III-V or II-VI binaries in density functional theory calculations within a local density approximation

DOE PAGES

Wang, Jianwei; Zhang, Yong; Wang, Lin-Wang

2015-07-31

We propose a systematic approach that can empirically correct three major errors typically found in a density functional theory (DFT) calculation within the local density approximation (LDA) simultaneously for a set of common cation binary semiconductors, such as III-V compounds, (Ga or In)X with X = N,P,As,Sb, and II-VI compounds, (Zn or Cd)X, with X = O,S,Se,Te. By correcting (1) the binary band gaps at high-symmetry points , L, X, (2) the separation of p-and d-orbital-derived valence bands, and (3) conduction band effective masses to experimental values and doing so simultaneously for common cation binaries, the resulting DFT-LDA-based quasi-first-principles methodmore » can be used to predict the electronic structure of complex materials involving multiple binaries with comparable accuracy but much less computational cost than a GW level theory. This approach provides an efficient way to evaluate the electronic structures and other material properties of complex systems, much needed for material discovery and design.« less

Systematic approach for simultaneously correcting the band-gap and p -d separation errors of common cation III-V or II-VI binaries in density functional theory calculations within a local density approximation

NASA Astrophysics Data System (ADS)

Wang, Jianwei; Zhang, Yong; Wang, Lin-Wang

2015-07-01

We propose a systematic approach that can empirically correct three major errors typically found in a density functional theory (DFT) calculation within the local density approximation (LDA) simultaneously for a set of common cation binary semiconductors, such as III-V compounds, (Ga or In)X with X =N ,P ,As ,Sb , and II-VI compounds, (Zn or Cd)X , with X =O ,S ,Se ,Te . By correcting (1) the binary band gaps at high-symmetry points Γ , L , X , (2) the separation of p -and d -orbital-derived valence bands, and (3) conduction band effective masses to experimental values and doing so simultaneously for common cation binaries, the resulting DFT-LDA-based quasi-first-principles method can be used to predict the electronic structure of complex materials involving multiple binaries with comparable accuracy but much less computational cost than a GW level theory. This approach provides an efficient way to evaluate the electronic structures and other material properties of complex systems, much needed for material discovery and design.

Electronic properties of excess Cr at Fe site in FeCr{sub 0.02}Se alloy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, Sandeep, E-mail: sandeepk.iitb@gmail.com; Singh, Prabhakar P.

2015-06-24

We have studied the effect of substitution of transition-metal chromium (Cr) in excess on Fe sub-lattice in the electronic structure of iron-selenide alloys, FeCr{sub 0.02}Se. In our calculations, we used Korringa-Kohn-Rostoker coherent potential approximation method in the atomic sphere approximation (KKR-ASA-CPA). We obtained different band structure of this alloy with respect to the parent FeSe and this may be reason of changing their superconducting properties. We did unpolarized calculations for FeCr{sub 0.02}Se alloy in terms of density of states (DOS) and Fermi surfaces. The local density approximation (LDA) is used in terms of exchange correlation potential.

First-principles modeling of localized d states with the GW@LDA+U approach

NASA Astrophysics Data System (ADS)

Jiang, Hong; Gomez-Abal, Ricardo I.; Rinke, Patrick; Scheffler, Matthias

2010-07-01

First-principles modeling of systems with localized d states is currently a great challenge in condensed-matter physics. Density-functional theory in the standard local-density approximation (LDA) proves to be problematic. This can be partly overcome by including local Hubbard U corrections (LDA+U) but itinerant states are still treated on the LDA level. Many-body perturbation theory in the GW approach offers both a quasiparticle perspective (appropriate for itinerant states) and an exact treatment of exchange (appropriate for localized states), and is therefore promising for these systems. LDA+U has previously been viewed as an approximate GW scheme. We present here a derivation that is simpler and more general, starting from the static Coulomb-hole and screened exchange approximation to the GW self-energy. Following our previous work for f -electron systems [H. Jiang, R. I. Gomez-Abal, P. Rinke, and M. Scheffler, Phys. Rev. Lett. 102, 126403 (2009)10.1103/PhysRevLett.102.126403] we conduct a systematic investigation of the GW method based on LDA+U(GW@LDA+U) , as implemented in our recently developed all-electron GW code FHI-gap (Green’s function with augmented plane waves) for a series of prototypical d -electron systems: (1) ScN with empty d states, (2) ZnS with semicore d states, and (3) late transition-metal oxides (MnO, FeO, CoO, and NiO) with partially occupied d states. We show that for ZnS and ScN, the GW band gaps only weakly depend on U but for the other transition-metal oxides the dependence on U is as strong as in LDA+U . These different trends can be understood in terms of changes in the hybridization and screening. Our work demonstrates that GW@LDA+U with “physical” values of U provides a balanced and accurate description of both localized and itinerant states.

Ab-initio Computation of the Electronic, transport, and Bulk Properties of Calcium Oxide.

NASA Astrophysics Data System (ADS)

Mbolle, Augustine; Banjara, Dipendra; Malozovsky, Yuriy; Franklin, Lashounda; Bagayoko, Diola

We report results from ab-initio, self-consistent, local Density approximation (LDA) calculations of electronic and related properties of calcium oxide (CaO) in the rock salt structure. We employed the Ceperley and Alder LDA potential and the linear combination of atomic orbitals (LCAO) formalism. Our calculations are non-relativistic. We implemented the LCAO formalism following the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF). The BZW-EF method involves a methodical search for the optimal basis set that yields the absolute minima of the occupied energies, as required by density functional theory (DFT). Our calculated, indirect band gap of 6.91eV, from towards the L point, is in excellent agreement with experimental value of 6.93-7.7eV, at room temperature (RT). We have also calculated the total (DOS) and partial (pDOS) densities of states as well as the bulk modulus. Our calculated bulk modulus is in excellent agreement with experiment. Work funded in part by the US Department of Energy (DOE), National Nuclear Security Administration (NNSA) (Award No.DE-NA0002630), the National Science Foundation (NSF) (Award No, 1503226), LaSPACE, and LONI-SUBR.

Theoretical calculation of electron-positron momentum density in YBa 2Cu 3O 7-δ

NASA Astrophysics Data System (ADS)

Massidda, S.

1990-07-01

We present calculations of the electron-positron momentum density for the high- Tc superconductor YBa 2Cu 3O 7-δ for δ=0 and for the insulating parent compound YBa 2Cu 3O 6, based on first-principle electronic structure calculations performed within the local density approximation (LDA) using the full potential linearized augmented plane wave (FLAPW) method. Our results indicate a small overlap of the positron wave function with the CuO 2 plane electrons and, as a consequence, relatively small signals due to the related Fermi surfaces. By contrast, the present calculations show, after the folding of Umklapp terms according to Lock, Crisp and West, clear Fermi surface breaks arising from the Cu-O chain bands. No general agreement with existing experiments allows a clear definition of Fermi surface structures in the latter. A comparison of the calculated momentum with the experimental two-dimensional angular correlation of annihilation radiation (2D-ACAR) recently measured in Geneva shows an overall agreement for the insulating compound, despite the spurious LDA metallic state, and possibly suggests the importance of O vacancies in experiments performed on non-stoichiometric YBa 2Cu 3O 7-δ samples.

Ab initio calculations of the magnetic properties of TM (Ti, V)-doped zinc-blende ZnO

NASA Astrophysics Data System (ADS)

Goumrhar, F.; Bahmad, L.; Mounkachi, O.; Benyoussef, A.

2018-01-01

In order to promote suitable material to be used in spintronics devices, this study purposes to evaluate the magnetic properties of the titanium and vanadium-doped zinc-blende ZnO from first-principles. The calculations of these properties are based on the Korringa-Kohn-Rostoker (KKR) method combined with the coherent potential approximation (CPA), using the local density approximation (LDA). We have calculated and discussed the density of states (DOSs) in the energy phase diagrams for different concentration values, of the dopants. We have also investigated the magnetic and half-metallic properties of this doped compound. Additionally, we showed the mechanism of the exchange coupling interaction. Finally, we estimated and studied the Curie temperature for different concentrations.

Electronic-structure theory of plutonium chalcogenides

NASA Astrophysics Data System (ADS)

Shick, Alexander; Havela, Ladislav; Gouder, Thomas; Rebizant, Jean

2009-03-01

The correlated band theory methods, the around-mean-field LDA + U and dynamical LDA + HIA (Hubbard-I), are applied to investigate the electronic structure of Pu chalcogenides. The LDA + U calculations for PuX (X = S, Se, Te) provide non-magnetic ground state in agreement with the experimental data. Non-integer filling of 5 f-manifold (from approx. 5.6 in PuS to 5.7 PuTe). indicates a mixed valence ground state which combines f5 and f6 multiplets. Making use of the dynamical LDA+HIA method the photoelectron spectra are calculated in good agreement with experimental data. The three-peak feature near EF attributed to 5 f-manifold is well reproduced by LDA + HIA, and follows from mixed valence character of the ground state.

First principles and Debye model study of the thermodynamic, electronic and optical properties of MgO under high-temperature and pressure

NASA Astrophysics Data System (ADS)

Miao, Yurun; Li, Huayang; Wang, Hongjuan; He, Kaihua; Wang, Qingbo

2018-02-01

First principles and quasi-harmonic Debye model have been used to study the thermodynamic properties, enthalpies, electronic and optical properties of MgO up to the core-mantle boundary (CMB) condition (137 GPa and 3700 K). Thermodynamic properties calculation includes thermal expansion coefficient and capacity, which have been studied up to the CMB pressure (137 GPa) and temperature (3700 K) by the Debye model with generalized gradient approximation (GGA) and local-density approximation (LDA). First principles with hybrid functional method (PBE0) has been used to calculate the electronic and optical properties under pressure up to 137 GPa and 0 K. Our results show the Debye model with LDA and first principles with PBE0 can provide accurate thermodynamic properties, enthalpies, electronic and optical properties. Calculated enthalpies show that MgO keep NaCl (B1) structure up to 137 GPa. And MgO is a direct bandgap insulator with a 7.23 eV calculated bandgap. The bandgap increased with increasing pressure, which will induce a blue shift of optical properties. We also calculated the density of states (DOS) and discussed the relation between DOS and band, optical properties. Equations were used to fit the relations between pressure and bandgaps, absorption coefficient (α(ω)) of MgO. The equations can be used to evaluate pressure after careful calibration. Our calculations can not only be used to identify some geological processes, but also offer a reference to the applications of MgO in the future.

Learning topic models by belief propagation.

PubMed

Zeng, Jia; Cheung, William K; Liu, Jiming

2013-05-01

Latent Dirichlet allocation (LDA) is an important hierarchical Bayesian model for probabilistic topic modeling, which attracts worldwide interest and touches on many important applications in text mining, computer vision and computational biology. This paper represents the collapsed LDA as a factor graph, which enables the classic loopy belief propagation (BP) algorithm for approximate inference and parameter estimation. Although two commonly used approximate inference methods, such as variational Bayes (VB) and collapsed Gibbs sampling (GS), have gained great success in learning LDA, the proposed BP is competitive in both speed and accuracy, as validated by encouraging experimental results on four large-scale document datasets. Furthermore, the BP algorithm has the potential to become a generic scheme for learning variants of LDA-based topic models in the collapsed space. To this end, we show how to learn two typical variants of LDA-based topic models, such as author-topic models (ATM) and relational topic models (RTM), using BP based on the factor graph representations.

Use of density functional theory orbitals in the GVVPT2 variant of second-order multistate multireference perturbation theory.

PubMed

Hoffmann, Mark R; Helgaker, Trygve

2015-03-05

A new variation of the second-order generalized van Vleck perturbation theory (GVVPT2) for molecular electronic structure is suggested. In contrast to the established procedure, in which CASSCF or MCSCF orbitals are first obtained and subsequently used to define a many-electron model (or reference) space, the use of an orbital space obtained from the local density approximation (LDA) variant of density functional theory is considered. Through a final, noniterative diagonalization of an average Fock matrix within orbital subspaces, quasicanonical orbitals that are otherwise indistinguishable from quasicanonical orbitals obtained from a CASSCF or MCSCF calculation are obtained. Consequently, all advantages of the GVVPT2 method are retained, including use of macroconfigurations to define incomplete active spaces and rigorous avoidance of intruder states. The suggested variant is vetted on three well-known model problems: the symmetric stretching of the O-H bonds in water, the dissociation of N2, and the stretching of ground and excited states C2 to more than twice the equilibrium bond length of the ground state. It is observed that the LDA-based GVVPT2 calculations yield good results, of comparable quality to conventional CASSCF-based calculations. This is true even for the C2 model problem, in which the orbital space for each state was defined by the LDA orbitals. These results suggest that GVVPT2 can be applied to much larger problems than previously accessible.

Understanding density functional theory (DFT) and completing it in practice

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bagayoko, Diola

2014-12-15

We review some salient points in the derivation of density functional theory (DFT) and of the local density approximation (LDA) of it. We then articulate an understanding of DFT and LDA that seems to be ignored in the literature. We note the well-established failures of many DFT and LDA calculations to reproduce the measured energy gaps of finite systems and band gaps of semiconductors and insulators. We then illustrate significant differences between the results from self consistent calculations using single trial basis sets and those from computations following the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma andmore » Franklin (BZW-EF). Unlike the former, the latter calculations verifiably attain the absolute minima of the occupied energies, as required by DFT. These minima are one of the reasons for the agreement between their results and corresponding, experimental ones for the band gap and a host of other properties. Further, we note predictions of DFT BZW-EF calculations that have been confirmed by experiment. Our subsequent description of the BZW-EF method ends with the application of the Rayleigh theorem in the selection, among the several calculations the method requires, of the one whose results have a full, physics content ascribed to DFT. This application of the Rayleigh theorem adds to or completes DFT, in practice, to preserve the physical content of unoccupied, low energy levels. Discussions, including implications of the method, and a short conclusion follow the description of the method. The successive augmentation of the basis set in the BZW-EF method, needed for the application of the Rayleigh theorem, is also necessary in the search for the absolute minima of the occupied energies, in practice.« less

Electronic properties of Fe3O4: LCAO calculations and Compton spectroscopy

NASA Astrophysics Data System (ADS)

Panwar, Kalpana; Tiwari, Shailja; Heda, N. L.

2018-04-01

We report the Compton profile (CP) measurements of Fe3O4 using 100 mCi241Am Compton spectrometer at momentum resolution of 0.55 a.u. The experimental CP has been compared with the linear combination of atomic orbitals (LCAO) data within density functional theory (DFT). The local density and generalized gradient approximation (LDA and GGA, respectively) have been used under the framework of DFT scheme. It is found that the DFT-GGA scheme gives the better agreement than to DFT-LDA. In addition, we have also computed the M ulliken's population (M P) and density of states (DOS) using the DFT scheme. M P data predicts the charge transfer from Fe to O atoms while DOS have confirmed the half metallic character of the compound.

Hyperfine field, electric field gradient, quadrupole coupling constant and magnetic properties of challenging actinide digallide

NASA Astrophysics Data System (ADS)

Khan, Sajid; Yazdani-Kachoei, M.; Jalali-Asadabadi, S.; Ahmad, Iftikhar

2017-12-01

In this paper, we explore the structural and magnetic properties as well as electric field gradient (EFG), hyperfine field (HFF) and quadrupole coupling constant in actinide digallide AcGa2 (Ac = U, Np, Pu) using LDA, GGA, LDA+U, GGA+U and hybrid functional with Wu-Cohen Generalized Gradient approximation HF-WC. Relativistic effects of the electrons are considered by including spin-orbit coupling. The comparison of the calculated structural parameters and magnetic properties with the available experimental results confirms the consistency and hence effectiveness of our theoretical tools. The calculated magnetic moments demonstrate that UGa2 and NpGa2 are ferromagnetic while PuGa2 is antiferromagnetic in nature. The EFG of AcGa2 is reported for the first time. The HFF, EFG and quadrupole coupling constant in AcGa2 (Ac = U, Np, Pu) are mainly originated from f-f and p-p contributions of Ac atom and p-p contribution of Ga atom.

Actinide electronic structure and atomic forces

NASA Astrophysics Data System (ADS)

Albers, R. C.; Rudin, Sven P.; Trinkle, Dallas R.; Jones, M. D.

2000-07-01

We have developed a new method[1] of fitting tight-binding parameterizations based on functional forms developed at the Naval Research Laboratory.[2] We have applied these methods to actinide metals and report our success using them (see below). The fitting procedure uses first-principles local-density-approximation (LDA) linear augmented plane-wave (LAPW) band structure techniques[3] to first calculate an electronic-structure band structure and total energy for fcc, bcc, and simple cubic crystal structures for the actinide of interest. The tight-binding parameterization is then chosen to fit the detailed energy eigenvalues of the bands along symmetry directions, and the symmetry of the parameterization is constrained to agree with the correct symmetry of the LDA band structure at each eigenvalue and k-vector that is fit to. By fitting to a range of different volumes and the three different crystal structures, we find that the resulting parameterization is robust and appears to accurately calculate other crystal structures and properties of interest.

Raman vibrational spectra of bulk to monolayer Re S 2 with lower symmetry

DOE PAGES

Feng, Yanqing; Zhou, Wei; Wang, Yaojia; ...

2015-08-26

Lattice structure and symmetry of two-dimensional (2D) layered materials are of key importance to their fundamental mechanical, thermal, electronic and optical properties. Raman spectroscopy, as a convenient and nondestructive tool, however has its limitations on identifying all symmetry allowing Raman modes and determining the corresponding crystal structure of 2D layered materials with high symmetry like graphene and MoS 2. Due to lower structural symmetry and extraordinary weak interlayer coupling of ReS 2, we successfully identified all 18 first-order Raman active modes for bulk and monolayer ReS 2. Without van der Waals (vdW) correction, our local density approximation (LDA) calculations successfullymore » reproduce all the Raman modes. Our calculations also suggest no surface reconstruction effect and the absence of low frequency rigid-layer Raman modes below 100 cm -1. As a result, combining with Raman and LDA thus provides a general approach for studying the vibrational and structural properties of 2D layered materials with lower symmetry.« less

First-principles studies of electronic, transport and bulk properties of pyrite FeS2

NASA Astrophysics Data System (ADS)

Banjara, Dipendra; Malozovsky, Yuriy; Franklin, LaShounda; Bagayoko, Diola

2018-02-01

We present results from first principle, local density approximation (LDA) calculations of electronic, transport, and bulk properties of iron pyrite (FeS2). Our non-relativistic computations employed the Ceperley and Alder LDA potential and the linear combination of atomic orbitals (LCAO) formalism. The implementation of the LCAO formalism followed the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF). We discuss the electronic energy bands, total and partial densities of states, electron effective masses, and the bulk modulus. Our calculated indirect band gap of 0.959 eV (0.96), using an experimental lattice constant of 5.4166 Å, at room temperature, is in agreement with the measured indirect values, for bulk samples, ranging from 0.84 eV to 1.03 ± 0.05 eV. Our calculated bulk modulus of 147 GPa is practically in agreement with the experimental value of 145 GPa. The calculated, partial densities of states reproduced the splitting of the Fe d bands to constitute the dominant upper most valence and lower most conduction bands, separated by the generally accepted, indirect, experimental band gap of 0.95 eV.

A study on native defects and magnetic properties in undoped rutile TiO2 using LDA and LDA+UO p+UTi d methods

NASA Astrophysics Data System (ADS)

Shi, Li-Bin; Wang, Yong Ping

2016-05-01

The native defects and magnetic properties in undoped rutile TiO2 are studied using local density approximation (LDA) and LDA adding Hubbard parameters (U) schemes. The band gap is adjusted to experimental value of 3.0 eV by combination of UTi d=4.2 eV and UO p=4.8 eV. This LDA+U methodology overcomes the band-gap problem and renders the approach more predictive. The formation energies of oxygen vacancy (VO), oxygen interstitial (Oi), titanium vacancy (VTi), titanium interstitial (Tii), oxygen anti-sites (OTi), and titanium anti-sites (TiO) are investigated by the LDA and LDA+U methods. In addition, some ground state configurations can be obtained by optimization of total spin. It is found that native defects can induce spin polarization and produce magnetic moment.

Including screening in van der Waals corrected density functional theory calculations: the case of atoms and small molecules physisorbed on graphene.

PubMed

Silvestrelli, Pier Luigi; Ambrosetti, Alberto

2014-03-28

The Density Functional Theory (DFT)/van der Waals-Quantum Harmonic Oscillator-Wannier function (vdW-QHO-WF) method, recently developed to include the vdW interactions in approximated DFT by combining the quantum harmonic oscillator model with the maximally localized Wannier function technique, is applied to the cases of atoms and small molecules (X=Ar, CO, H2, H2O) weakly interacting with benzene and with the ideal planar graphene surface. Comparison is also presented with the results obtained by other DFT vdW-corrected schemes, including PBE+D, vdW-DF, vdW-DF2, rVV10, and by the simpler Local Density Approximation (LDA) and semilocal generalized gradient approximation approaches. While for the X-benzene systems all the considered vdW-corrected schemes perform reasonably well, it turns out that an accurate description of the X-graphene interaction requires a proper treatment of many-body contributions and of short-range screening effects, as demonstrated by adopting an improved version of the DFT/vdW-QHO-WF method. We also comment on the widespread attitude of relying on LDA to get a rough description of weakly interacting systems.

Benchmarking the GW Approximation and Bethe–Salpeter Equation for Groups IB and IIB Atoms and Monoxides

DOE PAGES

Hung, Linda; Bruneval, Fabien; Baishya, Kopinjol; ...

2017-04-07

Energies from the GW approximation and the Bethe–Salpeter equation (BSE) are benchmarked against the excitation energies of transition-metal (Cu, Zn, Ag, and Cd) single atoms and monoxide anions. We demonstrate that best estimates of GW quasiparticle energies at the complete basis set limit should be obtained via extrapolation or closure relations, while numerically converged GW-BSE eigenvalues can be obtained on a finite basis set. Calculations using real-space wave functions and pseudopotentials are shown to give best-estimate GW energies that agree (up to the extrapolation error) with calculations using all-electron Gaussian basis sets. We benchmark the effects of a vertex approximationmore » (ΓLDA) and the mean-field starting point in GW and the BSE, performing computations using a real-space, transition-space basis and scalar-relativistic pseudopotentials. Here, while no variant of GW improves on perturbative G0W0 at predicting ionization energies, G0W0Γ LDA-BSE computations give excellent agreement with experimental absorption spectra as long as off-diagonal self-energy terms are included. We also present G0W0 quasiparticle energies for the CuO –, ZnO –, AgO –, and CdO – anions, in comparison to available anion photoelectron spectra.« less

Benchmarking the GW Approximation and Bethe–Salpeter Equation for Groups IB and IIB Atoms and Monoxides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hung, Linda; Bruneval, Fabien; Baishya, Kopinjol

Energies from the GW approximation and the Bethe–Salpeter equation (BSE) are benchmarked against the excitation energies of transition-metal (Cu, Zn, Ag, and Cd) single atoms and monoxide anions. We demonstrate that best estimates of GW quasiparticle energies at the complete basis set limit should be obtained via extrapolation or closure relations, while numerically converged GW-BSE eigenvalues can be obtained on a finite basis set. Calculations using real-space wave functions and pseudopotentials are shown to give best-estimate GW energies that agree (up to the extrapolation error) with calculations using all-electron Gaussian basis sets. We benchmark the effects of a vertex approximationmore » (ΓLDA) and the mean-field starting point in GW and the BSE, performing computations using a real-space, transition-space basis and scalar-relativistic pseudopotentials. Here, while no variant of GW improves on perturbative G0W0 at predicting ionization energies, G0W0Γ LDA-BSE computations give excellent agreement with experimental absorption spectra as long as off-diagonal self-energy terms are included. We also present G0W0 quasiparticle energies for the CuO –, ZnO –, AgO –, and CdO – anions, in comparison to available anion photoelectron spectra.« less

OsB 2 and RuB 2, ultra-incompressible, hard materials: First-principles electronic structure calculations

NASA Astrophysics Data System (ADS)

Chiodo, S.; Gotsis, H. J.; Russo, N.; Sicilia, E.

2006-07-01

Recently it has been reported that osmium diboride has an unusually large bulk modulus combined with high hardness, and consequently is a most interesting candidate as an ultra-incompressible and hard material. The electronic and structural properties of the transition metal diborides OsB 2 and RuB 2 have been calculated within the local density approximation (LDA). It is shown that the high hardness is the result of covalent bonding between transition metal d states and boron p states in the orthorhombic structure.

First-principles study of low-spin LaCoO3 with structurally consistent Hubbard U

NASA Astrophysics Data System (ADS)

Hsu, H.; Umemoto, K.; Cococcioni, M.; Wentzcovitch, R.

2008-12-01

We use the local density approximation + Hubbard U (LDA+U) method to calculate the structural and electronic properties of low-spin LaCoO3. The Hubbard U is obtained by first principles and consistent with each fully-optimized atomic structure at different pressures. With structurally consistent U, the fully-optimized atomic structure agrees with experimental data better than the calculations with fixed or vanishing U. A discussion on how the Hubbard U affects the electronic and atomic structure of LaCoO3 is also given.

Nonlinear electronic excitations in crystalline solids using meta-generalized gradient approximation and hybrid functional in time-dependent density functional theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sato, Shunsuke A.; Taniguchi, Yasutaka; Department of Medical and General Sciences, Nihon Institute of Medical Science, 1276 Shimogawara, Moroyama-Machi, Iruma-Gun, Saitama 350-0435

2015-12-14

We develop methods to calculate electron dynamics in crystalline solids in real-time time-dependent density functional theory employing exchange-correlation potentials which reproduce band gap energies of dielectrics; a meta-generalized gradient approximation was proposed by Tran and Blaha [Phys. Rev. Lett. 102, 226401 (2009)] (TBm-BJ) and a hybrid functional was proposed by Heyd, Scuseria, and Ernzerhof [J. Chem. Phys. 118, 8207 (2003)] (HSE). In time evolution calculations employing the TB-mBJ potential, we have found it necessary to adopt the predictor-corrector step for a stable time evolution. We have developed a method to evaluate electronic excitation energy without referring to the energy functionalmore » which is unknown for the TB-mBJ potential. For the HSE functional, we have developed a method for the operation of the Fock-like term in Fourier space to facilitate efficient use of massive parallel computers equipped with graphic processing units. We compare electronic excitations in silicon and germanium induced by femtosecond laser pulses using the TB-mBJ, HSE, and a simple local density approximation (LDA). At low laser intensities, electronic excitations are found to be sensitive to the band gap energy: they are close to each other using TB-mBJ and HSE and are much smaller in LDA. At high laser intensities close to the damage threshold, electronic excitation energies do not differ much among the three cases.« less

Carbon diffusion in molten uranium: an ab initio molecular dynamics study

NASA Astrophysics Data System (ADS)

Garrett, Kerry E.; Abrecht, David G.; Kessler, Sean H.; Henson, Neil J.; Devanathan, Ram; Schwantes, Jon M.; Reilly, Dallas D.

2018-04-01

In this work we used ab initio molecular dynamics within the framework of density functional theory and the projector-augmented wave method to study carbon diffusion in liquid uranium at temperatures above 1600 K. The electronic interactions of carbon and uranium were described using the local density approximation (LDA). The self-diffusion of uranium based on this approach is compared with literature computational and experimental results for liquid uranium. The temperature dependence of carbon and uranium diffusion in the melt was evaluated by fitting the resulting diffusion coefficients to an Arrhenius relationship. We found that the LDA calculated activation energy for carbon was nearly twice that of uranium: 0.55 ± 0.03 eV for carbon compared to 0.32 ± 0.04 eV for uranium. Structural analysis of the liquid uranium-carbon system is also discussed.

A density functional theory study of the influence of exchange-correlation functionals on the properties of FeAs.

PubMed

Griffin, Sinéad M; Spaldin, Nicola A

2017-06-01

We use density functional theory within the local density approximation (LDA), LDA  +  U, generalised gradient approximation (GGA), GGA  +  U, and hybrid-functional methods to calculate the properties of iron monoarsenide. FeAs, which forms in the MnP structure, is of current interest for potential spintronic applications as well as being the parent compound for the pnictide superconductors. We compare the calculated structural, magnetic and electronic properties obtained using the different functionals to each other and to experiment, and investigate the origin of a recently reported magnetic spiral. Our results indicate the appropriateness or otherwise of the various functionals for describing FeAs and the related Fe-pnictide superconductors.

DFT-BASED AB INITIO STUDY OF THE ELECTRONIC AND OPTICAL PROPERTIES OF CESIUM BASED FLUORO-PEROVSKITE CsMF3 (M = Ca AND Sr)

NASA Astrophysics Data System (ADS)

Harmel, M.; Khachai, H.; Ameri, M.; Khenata, R.; Baki, N.; Haddou, A.; Abbar, B.; UǦUR, Ş.; Omran, S. Bin; Soyalp, F.

2012-12-01

Density functional theory (DFT) is performed to study the structural, electronic and optical properties of cubic fluoroperovskite AMF3 (A = Cs; M = Ca and Sr) compounds. The calculations are based on the total-energy calculations within the full-potential linearized augmented plane wave (FP-LAPW) method. The exchange-correlation potential is treated by local density approximation (LDA) and generalized gradient approximation (GGA). The structural properties, including lattice constants, bulk modulus and their pressure derivatives are in very good agreement with the available experimental and theoretical data. The calculations of the electronic band structure, density of states and charge density reveal that compounds are both ionic insulators. The optical properties (namely: the real and the imaginary parts of the dielectric function ɛ(ω), the refractive index n(ω) and the extinction coefficient k(ω)) were calculated for radiation up to 40.0 eV.

An ab initio density functional study of the optical functions of 9-Methyl-3-Thiophen-2-YI-Thieno [3,2e] [1,2,4] Thriazolo [4,3c] Pyrimidine-8-Carboxylic Acid Ethyl Ester crystals.

PubMed

Reshak, Ali H; Kityk, I V; Khenata, R; Al-Douri, Y; Auluck, S

2012-09-01

An ab initio investigation of the optical constants of 9-Methyl-3-Thiophen-2-YI-Thieno [3,2e] [1,2,4] Thriazolo [4,3c] Pyrimidine-8-Carboxylic Acid Ethyl Ester crystal is performed within a framework of local density approximation (LDA), and the Engel-Vosko generalized gradient approximation (EV-GGA) exchange correlation potentials. It is established that there are two independent molecules (A and B) exhibiting different intra-molecular interactions: C-H⋯O (A) and C-H⋯N (B). These intra-molecular interactions favor stabilization of the crystal structure for molecules A and B. It should be emphasized that there exist remarkable π-π interactions between the pyrimidine rings of the two neighbors B molecules giving extra strengths and stabilizations to the superamolecular structure. These different intra-molecular interactions C-H⋯O (A) and C-H⋯N (B) and the π-π interaction between the pyrimidine rings of the two neighbors B molecules give principal contribution to dispersion of optical properties. With a view to seek deeper insight into the electronic structure, the optical properties were investigated. Our calculations show that the optical constants are very anisotropic. The EVGGA calculation shows a blue spectral shift of around 0.024 eV with significant changes in the spectra compared to the LDA calculation. The observed spectral shifts are in agreement with the calculated band structure and corresponding electron density of states. Copyright © 2012 Elsevier B.V. All rights reserved.

Physical Meaning of Virtual Kohn-Sham Orbitals and Orbital Energies: An Ideal Basis for the Description of Molecular Excitations.

PubMed

van Meer, R; Gritsenko, O V; Baerends, E J

2014-10-14

In recent years, several benchmark studies on the performance of large sets of functionals in time-dependent density functional theory (TDDFT) calculations of excitation energies have been performed. The tested functionals do not approximate exact Kohn-Sham orbitals and orbital energies closely. We highlight the advantages of (close to) exact Kohn-Sham orbitals and orbital energies for a simple description, very often as just a single orbital-to-orbital transition, of molecular excitations. Benchmark calculations are performed for the statistical average of orbital potentials (SAOP) functional for the potential [J. Chem. Phys. 2000, 112, 1344; 2001, 114, 652], which approximates the true Kohn-Sham potential much better than LDA, GGA, mGGA, and hybrid potentials do. An accurate Kohn-Sham potential does not only perform satisfactorily for calculated vertical excitation energies of both valence and Rydberg transitions but also exhibits appealing properties of the KS orbitals including occupied orbital energies close to ionization energies, virtual-occupied orbital energy gaps very close to excitation energies, realistic shapes of virtual orbitals, leading to straightforward interpretation of most excitations as single orbital transitions. We stress that such advantages are completely lost in time-dependent Hartree-Fock and partly in hybrid approaches. Many excitations and excitation energies calculated with local density, generalized gradient, and hybrid functionals are spurious. There is, with an accurate KS, or even the LDA or GGA potentials, nothing problematic about the "band gap" in molecules: the HOMO-LUMO gap is close to the first excitation energy (the optical gap).

Ab-initio calculation for cation vacancy formation energy in anti-fluorite structure

NASA Astrophysics Data System (ADS)

Saleel, V. P. Saleel Ahammad; Chitra, D.; Veluraja, K.; Eithiraj, R. D.

2018-04-01

Lithium oxide (Li2O) has been suggested as a suitable breeder blanket material for fusion reactors. Li+ vacancies are created by neutron irradiation, forming bulk defect complex whose extra character is experimentally unclear. We present a theoretical study of Li2O using density functional theory (DFT) with a plane-wave basis set. The generalized gradient approximation (GGA) and local-density approximation (LDA) were used for exchange and correlation. Here we address the total energy for defect free, cation defect, cation vacancy and vacancy formation energy in Li2O crystal in anti-fluorite structure.

Electronic structure of LiGaS 2

NASA Astrophysics Data System (ADS)

Atuchin, V. V.; Isaenko, L. I.; Kesler, V. G.; Lobanov, S.; Huang, H.; Lin, Z. S.

2009-04-01

X-ray photoelectron spectroscopy (XPS) measurement has been performed to determine the valence band structure of LiGaS 2 crystals. The experimental measurement is compared with the electronic structure obtained from the density functional calculations. It is found that the Ga 3d states in the XPS spectrum are much higher than the calculated results. In order to eliminate this discrepancy, the LDA+ U method is employed and reasonable agreement is achieved. Further calculations show that the difference of the linear and nonlinear optical coefficients between LDA and LDA+ U calculations is negligibly small, indicating that the Ga 3d states are actually independent of the excited properties of LiGaS 2 crystals since they are located at a very deep position in the valence bands.

Density-functional expansion methods: evaluation of LDA, GGA, and meta-GGA functionals and different integral approximations.

PubMed

Giese, Timothy J; York, Darrin M

2010-12-28

We extend the Kohn-Sham potential energy expansion (VE) to include variations of the kinetic energy density and use the VE formulation with a 6-31G* basis to perform a "Jacob's ladder" comparison of small molecule properties using density functionals classified as being either LDA, GGA, or meta-GGA. We show that the VE reproduces standard Kohn-Sham DFT results well if all integrals are performed without further approximation, and there is no substantial improvement in using meta-GGA functionals relative to GGA functionals. The advantages of using GGA versus LDA functionals becomes apparent when modeling hydrogen bonds. We furthermore examine the effect of using integral approximations to compute the zeroth-order energy and first-order matrix elements, and the results suggest that the origin of the short-range repulsive potential within self-consistent charge density-functional tight-binding methods mainly arises from the approximations made to the first-order matrix elements.

Calculation of strained BaTiO3 with different exchange correlation functionals examined with criterion by Ginzburg-Landau theory, uncovering expressions by crystallographic parameters

NASA Astrophysics Data System (ADS)

Watanabe, Yukio

2018-05-01

In the calculations of tetragonal BaTiO3, some exchange-correlation (XC) energy functionals such as local density approximation (LDA) have shown good agreement with experiments at room temperature (RT), e.g., spontaneous polarization (PS), and superiority compared with other XC functionals. This is due to the error compensation of the RT effect and, hence, will be ineffective in the heavily strained case such as domain boundaries. Here, ferroelectrics under large strain at RT are approximated as those at 0 K because the strain effect surpasses the RT effects. To find effective XC energy functionals for strained BaTiO3, we propose a new comparison, i.e., a criterion. This criterion is the properties at 0 K given by the Ginzburg-Landau (GL) theory because GL theory is a thermodynamic description of experiments working under the same symmetry-constraints as ab initio calculations. With this criterion, we examine LDA, generalized gradient approximations (GGA), meta-GGA, meta-GGA + local correlation potential (U), and hybrid functionals, which reveals the high accuracy of some XC functionals superior to XC functionals that have been regarded as accurate. This result is examined directly by the calculations of homogenously strained tetragonal BaTiO3, confirming the validity of the new criterion. In addition, the data points of theoretical PS vs. certain crystallographic parameters calculated with different XC functionals are found to lie on a single curve, despite their wide variations. Regarding these theoretical data points as corresponding to the experimental results, analytical expressions of the local PS using crystallographic parameters are uncovered. These expressions show the primary origin of BaTiO3 ferroelectricity as oxygen displacements. Elastic compliance and electrostrictive coefficients are estimated. For the comparison of strained results, we show that the effective critical temperature TC under strain <-0.01 is >1000 K from an approximate method combining ab initio results with GL theory. In addition, in a definite manner, the present results show much more enhanced ferroelectricity at large strain than the previous reports.

Electronic and magnetic properties of TiO2 (co)-doped with (V, Mn)

NASA Astrophysics Data System (ADS)

Rami, R.; Rkhioui, N.; Ahl Laamara, R.; Drissi, L. B.

2017-12-01

The effect of dopage and co-dopage with vanadium and manganese on the structural, the electronic and the magnetic properties of TiO2 is studied using ab initio calculations. The calculations are based on the Korringa-Kohn-Rostoker method combined with the coherent potential approach, employing the local density approximation (LDA). The density of states are plotted in the energy diagram for different concentrations of dopants. The magnetic moments and half-metallic character of the doped compounds are investigated and the mechanism of exchange interaction is determined. In addition, the Curie temperature is given for different concentrations.

First-principles study of electronic properties of Si doped FeSe{sub 0.9} alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, Sandeep, E-mail: sandeep@phy.iitb.ac.in; Singh, Prabhakar P.

2016-05-23

We have performed first-principles study of electronic and superconducting properties of FeSe{sub 0.9-x}Si{sub x} (x = 0.0, 0.05) alloys using Korringa-Kohn-Rostoker Atomic Sphere Approximation within the coherent potential approximation (KKR-ASA-CPA). In our calculations, we used the local density approximation (LDA) for the exchange correlation potential. Our calculations show that these alloys are nonmagnetic in nature. We found that the substitution of Si at Se site into FeSe{sub 0.9} made subtle affects in the electronic structure with respect to the parent FeSe. The results have been analyzed in terms of changes in the density of states (DOS), band structures, Fermi surfacesmore » and the superconducting transition temperature of FeSe{sub 0.9} and FeSe{sub 0.85}Si{sub 0.05} alloys.« less

Performance of exchange-correlation functionals in density functional theory calculations for liquid metal: A benchmark test for sodium.

PubMed

Han, Jeong-Hwan; Oda, Takuji

2018-04-14

The performance of exchange-correlation functionals in density-functional theory (DFT) calculations for liquid metal has not been sufficiently examined. In the present study, benchmark tests of Perdew-Burke-Ernzerhof (PBE), Armiento-Mattsson 2005 (AM05), PBE re-parameterized for solids, and local density approximation (LDA) functionals are conducted for liquid sodium. The pair correlation function, equilibrium atomic volume, bulk modulus, and relative enthalpy are evaluated at 600 K and 1000 K. Compared with the available experimental data, the errors range from -11.2% to 0.0% for the atomic volume, from -5.2% to 22.0% for the bulk modulus, and from -3.5% to 2.5% for the relative enthalpy depending on the DFT functional. The generalized gradient approximation functionals are superior to the LDA functional, and the PBE and AM05 functionals exhibit the best performance. In addition, we assess whether the error tendency in liquid simulations is comparable to that in solid simulations, which would suggest that the atomic volume and relative enthalpy performances are comparable between solid and liquid states but that the bulk modulus performance is not. These benchmark test results indicate that the results of liquid simulations are significantly dependent on the exchange-correlation functional and that the DFT functional performance in solid simulations can be used to roughly estimate the performance in liquid simulations.

Performance of exchange-correlation functionals in density functional theory calculations for liquid metal: A benchmark test for sodium

NASA Astrophysics Data System (ADS)

Han, Jeong-Hwan; Oda, Takuji

2018-04-01

The performance of exchange-correlation functionals in density-functional theory (DFT) calculations for liquid metal has not been sufficiently examined. In the present study, benchmark tests of Perdew-Burke-Ernzerhof (PBE), Armiento-Mattsson 2005 (AM05), PBE re-parameterized for solids, and local density approximation (LDA) functionals are conducted for liquid sodium. The pair correlation function, equilibrium atomic volume, bulk modulus, and relative enthalpy are evaluated at 600 K and 1000 K. Compared with the available experimental data, the errors range from -11.2% to 0.0% for the atomic volume, from -5.2% to 22.0% for the bulk modulus, and from -3.5% to 2.5% for the relative enthalpy depending on the DFT functional. The generalized gradient approximation functionals are superior to the LDA functional, and the PBE and AM05 functionals exhibit the best performance. In addition, we assess whether the error tendency in liquid simulations is comparable to that in solid simulations, which would suggest that the atomic volume and relative enthalpy performances are comparable between solid and liquid states but that the bulk modulus performance is not. These benchmark test results indicate that the results of liquid simulations are significantly dependent on the exchange-correlation functional and that the DFT functional performance in solid simulations can be used to roughly estimate the performance in liquid simulations.

Carbon diffusion in molten uranium: an ab initio molecular dynamics study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garrett, Kerry E.; Abrecht, David G.; Kessler, Sean H.

In this work we used ab initio molecular dynamics (AIMD) within the framework of density functional theory (DFT) and the projector-augmented wave (PAW) method to study carbon diffusion in liquid uranium at temperatures above 1600 K. The electronic interactions of carbon and uranium were described using the local density approximation (LDA). The self-diffusion of uranium based on this approach is compared with literature computational and experimental results for liquid uranium. The temperature dependence of carbon and uranium diffusion in the melt was evaluated by fitting the resulting diffusion coefficients to an Arrhenius relationship. We found that the LDA calculated activationmore » energy for carbon was nearly twice that of uranium: 0.55±0.03 eV for carbon compared to 0.32±0.04 eV for uranium. Structural analysis of the liquid uranium-carbon system is also discussed.« less

First principles calculation of thermo-mechanical properties of thoria using Quantum ESPRESSO

NASA Astrophysics Data System (ADS)

Malakkal, Linu; Szpunar, Barbara; Zuniga, Juan Carlos; Siripurapu, Ravi Kiran; Szpunar, Jerzy A.

2016-05-01

In this work, we have used Quantum ESPRESSO (QE), an open source first principles code, based on density-functional theory, plane waves, and pseudopotentials, along with quasi-harmonic approximation (QHA) to calculate the thermo-mechanical properties of thorium dioxide (ThO2). Using Python programming language, our group developed qe-nipy-advanced, an interface to QE, which can evaluate the structural and thermo-mechanical properties of materials. We predicted the phonon contribution to thermal conductivity (kL) using the Slack model. We performed the calculations within local density approximation (LDA) and generalized gradient approximation (GGA) with the recently proposed version for solids (PBEsol). We employed a Monkhorst-Pack 5 × 5 × 5 k-points mesh in reciprocal space with a plane wave cut-off energy of 150 Ry to obtain the convergence of the structure. We calculated the dynamical matrices of the lattice on a 4 × 4 × 4 mesh. We have predicted the heat capacity, thermal expansion and the phonon contribution to thermal conductivity, as a function of temperature up to 1400K, and compared them with the previous work and known experimental results.

From clusters to bulk: A relativistic density functional investigation on a series of gold clusters Aun, n=6,…,147

NASA Astrophysics Data System (ADS)

Häberlen, Oliver D.; Chung, Sai-Cheong; Stener, Mauro; Rösch, Notker

1997-03-01

A series of gold clusters spanning the size range from Au6 through Au147 (with diameters from 0.7 to 1.7 nm) in icosahedral, octahedral, and cuboctahedral structure has been theoretically investigated by means of a scalar relativistic all-electron density functional method. One of the main objectives of this work was to analyze the convergence of cluster properties toward the corresponding bulk metal values and to compare the results obtained for the local density approximation (LDA) to those for a generalized gradient approximation (GGA) to the exchange-correlation functional. The average gold-gold distance in the clusters increases with their nuclearity and correlates essentially linearly with the average coordination number in the clusters. An extrapolation to the bulk coordination of 12 yields a gold-gold distance of 289 pm in LDA, very close to the experimental bulk value of 288 pm, while the extrapolated GGA gold-gold distance is 297 pm. The cluster cohesive energy varies linearly with the inverse of the calculated cluster radius, indicating that the surface-to-volume ratio is the primary determinant of the convergence of this quantity toward bulk. The extrapolated LDA binding energy per atom, 4.7 eV, overestimates the experimental bulk value of 3.8 eV, while the GGA value, 3.2 eV, underestimates the experiment by almost the same amount. The calculated ionization potentials and electron affinities of the clusters may be related to the metallic droplet model, although deviations due to the electronic shell structure are noticeable. The GGA extrapolation to bulk values yields 4.8 and 4.9 eV for the ionization potential and the electron affinity, respectively, remarkably close to the experimental polycrystalline work function of bulk gold, 5.1 eV. Gold 4f core level binding energies were calculated for sites with bulk coordination and for different surface sites. The core level shifts for the surface sites are all positive and distinguish among the corner, edge, and face-centered sites; sites in the first subsurface layer show still small positive shifts.

Cobalt spin states and hyperfine interactions in LaCoO3 investigated by LDA+U calculations

NASA Astrophysics Data System (ADS)

Hsu, Han; Blaha, Peter; Wentzcovitch, Renata M.; Leighton, C.

2010-09-01

With a series of local-density approximation plus Hubbard U calculations, we have demonstrated that for lanthanum cobaltite (LaCoO3) , the electric field gradient at the cobalt nucleus can be used as a fingerprint to identify the spin state of the cobalt ion. Therefore, in principle, the spin state of the cobalt ion can be unambiguously determined from nuclear magnetic resonance spectra. Our calculations also suggest that a crossover from the low-spin to intermediate-spin state in the temperature range of 0-90 K is unlikely, based on the half-metallic band structure associated with isolated IS Co ions, which is incompatible with the measured conductivity.

A theoretical study of perovskite CsXCl3 (X=Pb, Cd) within first principles calculations

NASA Astrophysics Data System (ADS)

Ilyas, Bahaa M.; Elias, Badal H.

2017-04-01

The structural, elastic, electronic, optical acoustic and thermodynamic properties of the cubic perovskite CsPbCl3 and CsCdCl3 unit cell, were studied using an ultra-soft pseudopotential plane wave, the Trouiller-Martins-Functional was utilized to perform these calculations. The study was implemented within both the Local Density Approximation (LDA) and the Generalized Gradient Approximation (GGA). the Generalized Gradient Approximation (GGA) scheme proposed by van Leeuwen-Baerends which is the same as the Perdew-Wang 92 functional have been carried out to preform our calculations. As for the Local Density Approximation (LDA) the Teter-Pade parametrization (4/93) was implemented which is the same as Perdew-Wang that in its turn reproduces the Ceperley-Alder-Functional. The computed GGA/LDA-lattice parameter for both CsCdCl3 and CsPbCl3 is in an exquisite agreement with the experimental and theoretical results. The energy band structure shows that CsCdCl3 is Γ-R indirect band gap insulator, while CsPbCl3 is an insulator with a direct band gap Γ-Γ separating the valence bands from the conduction bands, which shows metallic nature after pressure 30 GPa. A hybridization exists between Pb-p states and Cl-p states for CsPbCl3, and Cd-p states and Cs-p states for the CsCdCl3 in the valence bonding region. Optimization of both cell shape (geometry) volume were investigated as pressure of 0-20 GPa and 0-40 GPa for the CsCdCl3 and CsPbCl3 respectively. The Pressure dependence of cubic perovskite elastic constants, Young modulus, bulk and shear moduli, Lame's constants, elastic anisotropy factor, elastic wave velocities, phonon dispersion, Debye temperature and the density of states of CsXCl3 (X=Pb, Cd) were theoretically calculated and compared with the other available theoretical results. The above elastic constants reveal the fact that both compounds are stable and show nature of ductility. For the optical properties, both the static refractive index and dielectric constant are found to be related proportionally to the indirect band gap of CsCdCl3. The refractive index, extinction coefficient, complex dielectric function, energy loss function, optical conductivity, reflectivity and absorption coefficient for 0-25 eV incident photon energies have been predicted. The phonon properties were investigated using response functions to predict the phonon lattice dispersion and the density of states. The thermal effect on the heat capacities, entropy, enthalpy and Free energy were predicted and compared using both the quasi-harmonic Debye model and response functions, the latter provided far better results. To the best of the authors' knowledge, most of the studied properties have not been experimentally reported so far. Generally, the computed results for both CsCdCl3 and CsPbCl3 are very satisfactory and show good agreement with other calculations.

Quantum Monte Carlo Simulations of the Quartz to Stishovite Transition in SiO2

NASA Astrophysics Data System (ADS)

Cohen, R. E.; Towler, Mike; Lopez Rios, Pablo; Drummond, Neil; Needs, Richard

2007-03-01

The quartz-stishovite transition has been a long standing problem for density functional theory (DFT). Although conventional DFT computations within the local density approximation (LDA) give reasonably good properties of silica phases individually, they do not give the energy difference between quartz and stishovite accurately. The LDA gives stishovite as a lower energy structure than quartz at zero pressure, which is incorrect. The generalized gradient approximation (GGA) has been shown to give the correct energy difference between quartz and stishovite (about 0.5 eV/formula unit) (Hamann, PRL 76, 660, 1996; Zupan et al., PRB 58, 11266, 1998), and it was generally thought that the GGA was simply a better approximation than the LDA. However, closer inspection shows that other properties are not better for the GGA than the LDA, so there is room for improvement. A new density functional that is an improvement for most materials unfortunately does not improve the quartz-stishovite transition (Wu and Cohen, PRB 73, 235116, 2006). We are performing QMC computations using the CASINO code to obtain the accurate energy difference between quartz and stishovite to obtain more accurate high pressure properties, and to better understand the errors on DFT and how DFT can be improved.

Electronic Structure of the Kitaev Material α-RuCl3 Probed by Photoemission and Inverse Photoemission Spectroscopies

NASA Astrophysics Data System (ADS)

Sinn, Soobin; Kim, Choong Hyun; Kim, Beom Hyun; Lee, Kyung Dong; Won, Choong Jae; Oh, Ji Seop; Han, Moonsup; Chang, Young Jun; Hur, Namjung; Sato, Hitoshi; Park, Byeong-Gyu; Kim, Changyoung; Kim, Hyeong-Do; Noh, Tae Won

2016-12-01

Recently, α-RuCl3 has attracted much attention as a possible material to realize the honeycomb Kitaev model of a quantum-spin-liquid state. Although the magnetic properties of α-RuCl3 have been extensively studied, its electronic structure, which is strongly related to its Kitaev physics, is poorly understood. Here, the electronic structure of α-RuCl3 was investigated by photoemission (PE) and inverse-photoemission (IPE) spectroscopies. The band gap was directly measured from the PE and IPE spectra and was found to be 1.9 eV, much larger than previously estimated values. Local density approximation (LDA) calculations showed that the on-site Coulomb interaction U could open the band gap without spin-orbit coupling (SOC). However, the SOC should also be incorporated to reproduce the proper gap size, indicating that the interplay between U and SOC plays an essential role. Several features of the PE and IPE spectra could not be explained by the results of LDA calculations. To explain such discrepancies, we performed configuration-interaction calculations for a RuCl63- cluster. The experimental data and calculations demonstrated that the 4d compound α-RuCl3 is a Jeff = 1/2 Mott insulator rather than a quasimolecular-orbital insulator. Our study also provides important physical parameters required for verifying the proposed Kitaev physics in α-RuCl3.

Electronic structure properties of UO2 as a Mott insulator

NASA Astrophysics Data System (ADS)

Sheykhi, Samira; Payami, Mahmoud

2018-06-01

In this work using the density functional theory (DFT), we have studied the structural, electronic and magnetic properties of uranium dioxide with antiferromagnetic 1k-, 2k-, and 3k-order structures. Ordinary approximations in DFT, such as the local density approximation (LDA) or generalized gradient approximation (GGA), usually predict incorrect metallic behaviors for this strongly correlated electron system. Using Hubbard term correction for f-electrons, LDA+U method, as well as using the screened Heyd-Scuseria-Ernzerhof (HSE) hybrid functional for the exchange-correlation (XC), we have obtained the correct ground-state behavior as an insulator, with band gaps in good agreement with experiment.

Glass polymorphism in glycerol-water mixtures: I. A computer simulation study.

PubMed

Jahn, David A; Wong, Jessina; Bachler, Johannes; Loerting, Thomas; Giovambattista, Nicolas

2016-04-28

We perform out-of-equilibrium molecular dynamics (MD) simulations of water-glycerol mixtures in the glass state. Specifically, we study the transformations between low-density (LDA) and high-density amorphous (HDA) forms of these mixtures induced by compression/decompression at constant temperature. Our MD simulations reproduce qualitatively the density changes observed in experiments. Specifically, the LDA-HDA transformation becomes (i) smoother and (ii) the hysteresis in a compression/decompression cycle decreases as T and/or glycerol content increase. This is surprising given the fast compression/decompression rates (relative to experiments) accessible in MD simulations. We study mixtures with glycerol molar concentration χ(g) = 0-13% and find that, for the present mixture models and rates, the LDA-HDA transformation is detectable up to χ(g) ≈ 5%. As the concentration increases, the density of the starting glass (i.e., LDA at approximately χ(g) ≤ 5%) rapidly increases while, instead, the density of HDA remains practically constant. Accordingly, the LDA state and hence glass polymorphism become inaccessible for glassy mixtures with approximately χ(g) > 5%. We present an analysis of the molecular-level changes underlying the LDA-HDA transformation. As observed in pure glassy water, during the LDA-to-HDA transformation, water molecules within the mixture approach each other, moving from the second to the first hydration shell and filling the first interstitial shell of water molecules. Interestingly, similar changes also occur around glycerol OH groups. It follows that glycerol OH groups contribute to the density increase during the LDA-HDA transformation. An analysis of the hydrogen bond (HB)-network of the mixtures shows that the LDA-HDA transformation is accompanied by minor changes in the number of HBs of water and glycerol. Instead, large changes in glycerol and water coordination numbers occur. We also perform a detailed analysis of the effects that the glycerol force field (FF) has on our results. By comparing MD simulations using two different glycerol models, we find that glycerol conformations indeed depend on the FF employed. Yet, the thermodynamic and microscopic mechanisms accompanying the LDA-HDA transformation and hence, our main results, do not. This work is accompanied by an experimental report where we study the glass polymorphism in glycerol-water mixtures prepared by isobaric cooling at 1 bar.

Importance of conduction electron correlation in a Kondo lattice, Ce₂CoSi₃.

PubMed

Patil, Swapnil; Pandey, Sudhir K; Medicherla, V R R; Singh, R S; Bindu, R; Sampathkumaran, E V; Maiti, Kalobaran

2010-06-30

Kondo systems are usually described by the interaction of the correlation induced local moments with the highly itinerant conduction electrons. Here, we study the role of electron correlations among conduction electrons in the electronic structure of a Kondo lattice compound, Ce₂CoSi₃, using high resolution photoemission spectroscopy and ab initio band structure calculations, where Co 3d electrons contribute in the conduction band. High energy resolution employed in the measurements helped to reveal the signatures of Ce 4f states derived Kondo resonance features at the Fermi level and the dominance of Co 3d contributions at higher binding energies in the conduction band. The lineshape of the experimental Co 3d band is found to be significantly different from that obtained from the band structure calculations within the local density approximations, LDA. Consideration of electron-electron Coulomb repulsion, U, among Co 3d electrons within the LDA + U method leads to a better representation of experimental results. The signature of an electron correlation induced satellite feature is also observed in the Co 2p core level spectrum. These results clearly demonstrate the importance of the electron correlation among conduction electrons in deriving the microscopic description of such Kondo systems.

Electronic structure of Mott-insulator CaCu3Ti4O12: Photoemission and inverse photoemission study

NASA Astrophysics Data System (ADS)

Im, H. J.; Iwataki, M.; Yamazaki, S.; Usui, T.; Adachi, S.; Tsunekawa, M.; Watanabe, T.; Takegahara, K.; Kimura, S.; Matsunami, M.; Sato, H.; Namatame, H.; Taniguchi, M.

2015-09-01

We have performed the photoemission and inverse photoemission experiments to elucidate the origin of Mott insulating states in A-site ordered perovskite CaCu3Ti4O12 (CCTO). Experimental results have revealed that Cu 3d-O 2p hybridized bands, which are located around the Fermi level in the prediction of the local-density approximation (LDA) band calculations, are actually separated into the upper Hubbard band at ~1.5 eV and the lower Hubbard band at ~-1.7 eV with a band gap of ~1.5-1.8 eV. We also observed that Cu 3d peak at ~-3.8 eV and Ti 3d peak at ~3.8 eV are further away from each other than as indicated in the LDA calculations. In addition, it is found that the multiplet structure around -9 eV includes a considerable number of O 2p states. These observations indicate that the Cu 3d and Ti 3d electrons hybridized with the O 2p states are strongly correlated, which originates in the Mott-insulating states of CCTO.

Phase stability of transition metals and alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hixson, R.S.; Schiferl, D.; Wills, J.M.

1997-06-01

This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). This project was focused on resolving unexplained differences in calculated and measured phase transition pressures in transition metals. Part of the approach was to do new, higher accuracy calculations of transmission pressures for group 4B and group 6B metals. Theory indicates that the transition pressures for these baseline metals should change if alloyed with a d-electron donor metal, and calculations done using the Local Density Approximation (LDA) and the Virtual Crystal Approximation (VCA) indicate that this is true. Alloymore » systems were calculated for Ti, Zr and Hf based alloys with various solute concentrations. The second part of the program was to do new Diamond Anvil Cell (DAC) measurements to experimentally verify calculational results. Alloys were prepared for these systems with grain size suitable for Diamond Anvil Cell experiments. Experiments were done on pure Ti as well as Ti-V and Ti-Ta alloys. Measuring unambiguous transition pressures for these systems proved difficult, but a new technique developed yielded good results.« less

Structural, electronic, and elastic properties of CuFeS2: first-principles study

NASA Astrophysics Data System (ADS)

Zhou, Meng; Gao, Xiang; Cheng, Yan; Chen, Xiangrong; Cai, Lingcang

2015-03-01

The structural, electronic, and elastic properties of CuFeS2 have been investigated by using the generalized gradient approximation (GGA), GGA + U (on-site Coulomb repulsion energy), the local density approximation (LDA), and the LDA + U approach in the frame of density functional theory. It is shown that when the GGA + U formalism is selected with a U value of 3 eV for the 3d state of Fe, the calculated lattice constants agree well with the available experimental and other theoretical data. Our GGA + U calculations indicate that CuFeS2 is a semiconductor with a band gap of 0.552 eV and with a magnetic moment of 3.64 µB per Fe atom, which are well consistent with the experimental results. Combined with the density of states, the band structure characteristics of CuFeS2 have been analyzed and their origins have been specified, which reveals a hybridization existing between Fe-3d, Cu-3s, and S-3p, respectively. The charge and Mulliken population analyses indicate that CuFeS2 is a covalent crystal. Moreover, the calculated elastic constants prove that CuFeS2 is mechanically stable but anisotropic. The bulk modulus obtained from elastic constants is 87.1 GPa, which agrees well with the experimental value of 91 ± 15 GPa and better than the theoretical bulk modulus 74 GPa obtained from GGA method by Lazewski et al. The obtained shear modulus and Debye temperature are 21.0 GPa and 287 K, respectively, and the latter accords well with the available experimental value. It is expected that our work can provide useful information to further investigate CuFeS2 from both the experimental and theoretical sides.

An Anonymous Referee Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tobin, J. G.

2015-06-08

This is a combined experimental and theoretical study of the compound UO 2, UO 2(NO 3) 2(H 20) 6 and UO 0.75Pu 0.25O 2, using resonant inelastic x-ray scattering (RXIS), high resolution x-ray absorption (XAS) and LDA and LDA-U calculations.

An LDA+U study of the photoemission spectra of ground state phase of americium and curium

NASA Astrophysics Data System (ADS)

Islam, Md; Ray, Asok

2009-03-01

We have investigated the photoemission spectra and other ground state properties such as equilibrium volume and bulk modulus of dhcp americium and the density of states and magnetic properties of dhcp curium using LDA+U method. Our calculations show that spin polarized americium is energetically favorable but spin degenerate configuration produces experimental quantities much better than that calculated using spin polarized configuration. The DOS calculated using LDA+U with both non-magnetic and spin polarized configurations is compared and the non-magnetic DOS is shown to be in good agreement with experimental photoemission spectra when U=4.5 eV. In spin polarized case, U is observed to increase the splitting between occupied and unoccupied bands by enhancing Stoner parameter. The results are shown to be in good agreement with that calculated using dynamical mean field theory for these two heavy actinides. For curium, exchange interaction appears to play the dominant role in its magnetic stability.

Electronic and mechanical properties of ZnX (X = S, Se and Te)—An ab initio study

NASA Astrophysics Data System (ADS)

Verma, Ajay Singh; Sharma, Sheetal; Sarkar, Bimal Kumar; Jindal, Vijay Kumar

2011-12-01

Zinc chalcogenides (ZnX, X = S, Se and Te) have been increasing attention as wide and direct band gap semiconductor for blue and ultraviolet optical devices. This paper analyzes electronic and mechanical properties of these materials by ab initio pseudo-potential method that uses non conserving pseudopotentials in fully nonlocal form, as implemented in SIESTA code. In this approach the local density approximation (LDA) is used for the exchange-correlation (XC) potential. The calculations are given for band gap, elastic constants (C11, C12 and C44), shear modulus, and Young's modulus. The results are in very good agreement with previous theoretical calculations and available experimental data.

Combined hybrid functional and DFT+U calculations for metal chalcogenides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aras, Mehmet; Kılıç, Çetin, E-mail: cetin-kilic@gyte.edu.tr

2014-07-28

In the density-functional studies of materials with localized electronic states, the local/semilocal exchange-correlation functionals are often either combined with a Hubbard parameter U as in the LDA+U method or mixed with a fraction of exactly computed (Fock) exchange energy yielding a hybrid functional. Although some inaccuracies of the semilocal density approximations are thus fixed to a certain extent, the improvements are not sufficient to make the predictions agree with the experimental data. Here, we put forward the perspective that the hybrid functional scheme and the LDA+U method should be treated as complementary, and propose to combine the range-separated Heyd-Scuseria-Ernzerhof (HSE)more » hybrid functional with the Hubbard U. We thus present a variety of HSE+U calculations for a set of II-VI semiconductors, consisting of zinc and cadmium monochalcogenides, along with comparison to the experimental data. Our findings imply that an optimal value U{sup *} of the Hubbard parameter could be determined, which ensures that the HSE+U{sup *} calculation reproduces the experimental band gap. It is shown that an improved description not only of the electronic structure but also of the crystal structure and energetics is obtained by adding the U{sup *} term to the HSE functional, proving the utility of HSE+U{sup *} approach in modeling semiconductors with localized electronic states.« less

Temperature dependence of the symmetry energy and neutron skins in Ni, Sn, and Pb isotopic chains

NASA Astrophysics Data System (ADS)

Antonov, A. N.; Kadrev, D. N.; Gaidarov, M. K.; Sarriguren, P.; de Guerra, E. Moya

2017-02-01

The temperature dependence of the symmetry energy for isotopic chains of even-even Ni, Sn, and Pb nuclei is investigated in the framework of the local density approximation (LDA). The Skyrme energy density functional with two Skyrme-class effective interactions, SkM* and SLy4, is used in the calculations. The temperature-dependent proton and neutron densities are calculated through the hfbtho code that solves the nuclear Skyrme-Hartree-Fock-Bogoliubov problem by using the cylindrical transformed deformed harmonic-oscillator basis. In addition, two other density distributions of 208Pb, namely the Fermi-type density determined within the extended Thomas-Fermi (TF) method and symmetrized-Fermi local density obtained within the rigorous density functional approach, are used. The kinetic energy densities are calculated either by the hfbtho code or, for a comparison, by the extended TF method up to second order in temperature (with T2 term). Alternative ways to calculate the symmetry energy coefficient within the LDA are proposed. The results for the thermal evolution of the symmetry energy coefficient in the interval T =0 -4 MeV show that its values decrease with temperature. The temperature dependence of the neutron and proton root-mean-square radii and corresponding neutron skin thickness is also investigated, showing that the effect of temperature leads mainly to a substantial increase of the neutron radii and skins, especially in the more neutron-rich nuclei, a feature that may have consequences on astrophysical processes and neutron stars.

Electronic Structure of the Kitaev Material α-RuCl3 Probed by Photoemission and Inverse Photoemission Spectroscopies.

PubMed

Sinn, Soobin; Kim, Choong Hyun; Kim, Beom Hyun; Lee, Kyung Dong; Won, Choong Jae; Oh, Ji Seop; Han, Moonsup; Chang, Young Jun; Hur, Namjung; Sato, Hitoshi; Park, Byeong-Gyu; Kim, Changyoung; Kim, Hyeong-Do; Noh, Tae Won

2016-12-21

Recently, α-RuCl 3 has attracted much attention as a possible material to realize the honeycomb Kitaev model of a quantum-spin-liquid state. Although the magnetic properties of α-RuCl 3 have been extensively studied, its electronic structure, which is strongly related to its Kitaev physics, is poorly understood. Here, the electronic structure of α-RuCl 3 was investigated by photoemission (PE) and inverse-photoemission (IPE) spectroscopies. The band gap was directly measured from the PE and IPE spectra and was found to be 1.9 eV, much larger than previously estimated values. Local density approximation (LDA) calculations showed that the on-site Coulomb interaction U could open the band gap without spin-orbit coupling (SOC). However, the SOC should also be incorporated to reproduce the proper gap size, indicating that the interplay between U and SOC plays an essential role. Several features of the PE and IPE spectra could not be explained by the results of LDA calculations. To explain such discrepancies, we performed configuration-interaction calculations for a RuCl 6 3- cluster. The experimental data and calculations demonstrated that the 4d compound α-RuCl 3 is a J eff  = 1/2 Mott insulator rather than a quasimolecular-orbital insulator. Our study also provides important physical parameters required for verifying the proposed Kitaev physics in α-RuCl 3 .

Electronic Structure of the Kitaev Material α-RuCl3 Probed by Photoemission and Inverse Photoemission Spectroscopies

PubMed Central

Sinn, Soobin; Kim, Choong Hyun; Kim, Beom Hyun; Lee, Kyung Dong; Won, Choong Jae; Oh, Ji Seop; Han, Moonsup; Chang, Young Jun; Hur, Namjung; Sato, Hitoshi; Park, Byeong-Gyu; Kim, Changyoung; Kim, Hyeong-Do; Noh, Tae Won

2016-01-01

Recently, α-RuCl3 has attracted much attention as a possible material to realize the honeycomb Kitaev model of a quantum-spin-liquid state. Although the magnetic properties of α-RuCl3 have been extensively studied, its electronic structure, which is strongly related to its Kitaev physics, is poorly understood. Here, the electronic structure of α-RuCl3 was investigated by photoemission (PE) and inverse-photoemission (IPE) spectroscopies. The band gap was directly measured from the PE and IPE spectra and was found to be 1.9 eV, much larger than previously estimated values. Local density approximation (LDA) calculations showed that the on-site Coulomb interaction U could open the band gap without spin-orbit coupling (SOC). However, the SOC should also be incorporated to reproduce the proper gap size, indicating that the interplay between U and SOC plays an essential role. Several features of the PE and IPE spectra could not be explained by the results of LDA calculations. To explain such discrepancies, we performed configuration-interaction calculations for a RuCl63− cluster. The experimental data and calculations demonstrated that the 4d compound α-RuCl3 is a Jeff = 1/2 Mott insulator rather than a quasimolecular-orbital insulator. Our study also provides important physical parameters required for verifying the proposed Kitaev physics in α-RuCl3. PMID:28000731

Surface optical properties calculated from first principles: The influence of defects, self-energy and excitonic effects

NASA Astrophysics Data System (ADS)

Gero Schmidt, Wolf

2002-03-01

Optical spectroscopies are emerging as powerful tools to probe surfaces, since they allow for the real-time monitoring under challenging conditions as may be encountered, e.g., during material growth. However, their full potential can only be realised if it becomes possible to calculate surface optical spectra accurately and with true predictive power. Such calculations have been difficult, however, due to the large numerical expense involved. Based on a massively parallel, real-space multigrid implementation of DFT-LDA we have calculated reflectance anisotropy spectra for a wide range of group-IV materials and III-V compounds. Transitions between surface states give rise to specific, fingerprint-like spectral features. In addition, the anisotropic surface potential, the electric field at the surface of the sample and, to some extent, surface induced strain and relaxation may cause optical anisotropies in the layers underneath the surface. Surface defects have to be taken into account in order to explain some experimental results. Our DFT-LDA results explain very well the stoichiometric trends and qualitative features of the measured spectra. Quantitative agreement with the measured data is achieved by taking many-body effects into account. We include electronic self-energy corrections in the GW approximation using a model dielectric function to describe the screening. An efficient algorithm for solving the Bethe-Salpeter equation allows us to study the influence of electron-hole attraction and local-field effects on the surface optical properties.

Location of the valence band maximum in the band structure of anisotropic 1 T'-ReSe2

NASA Astrophysics Data System (ADS)

Eickholt, P.; Noky, J.; Schwier, E. F.; Shimada, K.; Miyamoto, K.; Okuda, T.; Datzer, C.; Drüppel, M.; Krüger, P.; Rohlfing, M.; Donath, M.

2018-04-01

Transition-metal dichalcogenides (TMDCs) are a focus of current research due to their fascinating optical and electronic properties with possible technical applications. ReSe2 is an interesting material of the TMDC family, with unique anisotropic properties originating from its distorted 1 T structure (1 T '). To develop a fundamental understanding of the optical and electric properties, we studied the underlying electronic structure with angle-resolved photoemission (ARPES) as well as band-structure calculations within the density functional theory (DFT)-local density approximation (LDA) and GdW approximations. We identified the Γ ¯M¯1 direction, which is perpendicular to the a axis, as a distinct direction in k space with the smallest bandwidth of the highest valence band. Using photon-energy-dependent ARPES, two valence band maxima are identified within experimental limits of about 50 meV: one at the high-symmetry point Z , and a second one at a non-high-symmetry point in the Brillouin zone. Thus, the position in k space of the global valence band maximum is undecided experimentally. Theoretically, an indirect band gap is predicted on a DFT-LDA level, while quasiparticle corrections lead to a direct band gap at the Z point.

Liquid Aluminum: Atomic diffusion and viscosity from ab initio molecular dynamics

PubMed Central

Jakse, Noel; Pasturel, Alain

2013-01-01

We present a study of dynamic properties of liquid aluminum using density-functional theory within the local-density (LDA) and generalized gradient (GGA) approximations. We determine the temperature dependence of the self-diffusion coefficient as well the viscosity using direct methods. Comparisons with experimental data favor the LDA approximation to compute dynamic properties of liquid aluminum. We show that the GGA approximation induce more important backscattering effects due to an enhancement of the icosahedral short range order (ISRO) that impact directly dynamic properties like the self-diffusion coefficient. All these results are then used to test the Stokes-Einstein relation and the universal scaling law relating the diffusion coefficient and the excess entropy of a liquid. PMID:24190311

First principles predictions of electronic and elastic properties of BaPb2As2 in the ThCr2Si2-type structure

NASA Astrophysics Data System (ADS)

Bourourou, Y.; Amari, S.; Yahiaoui, I. E.; Bouhafs, B.

2018-01-01

A first-principles approach is used to predicts the electronic and elastic properties of BaPb2As2 superconductor compound, using full-potential linearized augmented plane wave plus local orbitals (FP-L/APW+lo) scheme within the local density approximation LDA. The calculated equilibrium structural parameter a agree well with the experiment while the c/a ratio is far away from the experimental result. The band structure, density of states, together with the charge density and chemical bonding are discussed. The calculated elastic constants for our compound indicate that it is mechanically stable at ambient pressure. Polycrystalline elastic moduli (Young's, Bulk, shear Modulus and the Poisson's ratio) were calculated according to the Voigte-Reusse-Hill (VRH) average.

High-resolution Compton scattering study of the electron momentum density in Al

NASA Astrophysics Data System (ADS)

Ohata, T.; Itou, M.; Matsumoto, I.; Sakurai, Y.; Kawata, H.; Shiotani, N.; Kaprzyk, S.; Mijnarends, P. E.; Bansil, A.

2000-12-01

We report high-resolution Compton profiles (CP's) of Al along the three principal symmetry directions at a photon energy of 59.38 keV, together with corresponding highly accurate theoretical profiles obtained within the local-density approximation (LDA) based band-theory framework. A good accord between theory and experiment is found with respect to the overall shapes of the CP's and their first and second derivatives, as well as the anisotropies in the CP's defined as differences between pairs of various CP's. There are, however, discrepancies in that, in comparison to the LDA predictions, the measured profiles are lower at low momenta, show a Fermi cutoff that is broader, and display a tail that is higher at momenta above the Fermi momentum. A number of simple model calculations are carried out in order to gain insight into the nature of the underlying 3D momentum density in Al and the role of the Fermi surface in inducing fine structure in the CP's. The present results when compared with those on Li show clearly that the size of discrepancies between theoretical and experimental CP's is markedly smaller in Al than in Li. This indicates that, with increasing electron density, the conventional picture of the electron gas becomes more representative of the momentum density and that shortcomings of the LDA framework in describing the electron correlation effects become less important.

Structural and electronic properties of Sr{sub x}Ba{sub 1-x}SnO{sub 3} from first principles calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moreira, E.; Henriques, J.M.; Azevedo, D.L.

2012-03-15

Neutron diffraction data for Sr{sub x}Ba{sub 1-x}SnO{sub 3} (x=0.0, 0.2, 0.4, 0.6, 0.8 and 1.0) solid solutions were used as inputs to obtain optimized geometries and electronic properties using the density functional theory (DFT) formalism considering both the local density and generalized gradient approximations, LDA and GGA, respectively. The crystal structures and SnO{sub 6} octahedra tilting angles found after total energy minimization agree well with experiment, specially for the GGA data. Elastic constants were also obtained and compared with theoretical and experimental results for cubic BaSnO{sub 3}. While the alloys with cubic unit cell have an indirect band gap, tetragonalmore » and orthorhombic alloys exhibit direct band gaps (exception made to x=1.0). The Kohn-Sham minimum electronic band gap oscillates from 1.52 eV (cubic x=0.0, LDA) to 2.61 eV (orthorhombic x=1.0, LDA), and from 0.74 eV (cubic BaSnO{sub 3}, GGA) to 1.97 eV (orthorhombic SrSnO{sub 3}, GGA). Parabolic interpolation of bands has allowed us to estimate the effective masses for charge carriers, which are shown to be anisotropic and larger for holes. - Graphical Abstract: Highlights: Black-Right-Pointing-Pointer DFT calculations were performed on Sr{sub x}Ba{sub 1-x}SnO{sub 3} solid solutions. Black-Right-Pointing-Pointer Calculated crystal structures agree well with experiment. Black-Right-Pointing-Pointer Alloys have direct or indirect gaps depending on the Sr molar fraction. Black-Right-Pointing-Pointer The Kohn-Sham gap variation from x=0.0 to x=1.0 is close to the experimental value. Black-Right-Pointing-Pointer Carrier effective masses are very anisotropic, specially for holes.« less

Application of Tight-Binding Method in Atomistic Simulation of Covalent Materials

NASA Astrophysics Data System (ADS)

Isik, Ahmet

1994-05-01

The primary goal of this thesis is to develop and apply molecular dynamics simulation methods to elemental and binary covalent materials (Si, C, SiC) based on the tight-binding (TB) model of atomic cohesion in studies of bulk and deformation properties far from equilibrium. A second purpose is to compare results with those obtained using empirical interatomic potential functions in order to elucidate the applicability of models of interatomic interactions which do not take into account explicitly electronic structure effects. We have calculated the former by using a basis set consisting of four atomic orbitals, one for the s state and three for the p states, constructing a TB Hamiltonian in the usual Slater-Koster parametrization, and diagonalizing the Hamiltonian matrix at the origin of the Brillouin zone. For the repulsive part of the energy we employ a function in the form of inverse power law with screening which is then fitted to the bulk modulus and lattice parameter of several stable polytypes, results calculated by ab initio methods in the literature. Three types of applications have been investigated to demonstrate the utility of the present TB models and their advantages relative to empirical potentials. In the case of Si we show the calculated cohesive energy agrees to within a few percent with the ab initio local-density approximation (LDA) results. In addition, for clusters up to 10 atoms we find most of the energies and equilibrium structures to be in good agreement with LDA results (the failure of the empirical potential of Stillinger and Weber (SW) is well known). In the case of C clusters our TB model gives ring and chain structures which have been found both experimentally and by LDA calculations. In the second application we have applied our TB model of Si to investigate the core structure and energetics of partial dislocations on the glide plane and reconstruction antiphase defect (APD). For the 90^circ partial we show that the TB description gives the correct asymetric reconstruction previously found by LDA. For the 30^circ partial, TB gives better bond angles in the dislocation core. For the APD we have obtained a binding energy and activation for migration which are somewhat larger than the SW values, but the conclusion remains that APD is a low-energy defect which should be quite mobile. In the third application we formulate a simple TB model for SiC where the coefficients of the two-center integrals in Si-C interactions are taken to be simple averages of Si-Si and C-C integrals. Fitting is done on two polytypes, zincblende and rocksalt structures, and a simulated annealing procedure is used. The TB results are found in good agreement with LDA and experimental results in the cohesive energy, acoustic phonon modes, and elastic constants. (Abstract shortened by UMI.).

Pseudogap in normal underdoped phase of Bi2212: LDA + DMFT + Σk

NASA Astrophysics Data System (ADS)

Nekrasov, I. A.; Kuchinskii, E. Z.; Pchelkina, Z. V.; Sadovskii, M. V.

2007-09-01

Pseudogap phenomena are observed for normal underdoped phase of different high- Tc cuprates. Among others Bi 2Sr 2CaCu 2O 8- δ (Bi2212) compound is one of the most studied experimentally [A. Damascelli, Z. Hussain, Z.-X. Shen, Rev. Mod. Phys. 75 (2003) 473; J.C. Campuzano, M.R. Norman, M. Randeria, in: K.H. Bennemann, J.B. Ketterson (Eds.), Physics of Superconductors, vol. 2, Springer, Berlin, 2004, p. 167; J. Fink et al., cond-mat/0512307; X.J. Zhou et al., cond-mat/0604284]. To describe pseudogap regime in Bi2212, we employ novel generalized DMFT + Σk approach [E.Z. Kuchinskii, I.A. Nekrasov, M.V. Sadovskii, JETP Lett. 82 (2005) 198; M.V. Sadovskii et al., Phys. Rev. B 72 (2005) 155105, and these proceedings, doi:10.1016/j.physc.2007.03.367]. This approach gives possibility to preserve conventional dynamical mean-field theory (DMFT) equations [A. Georges et al., Rev. Mod. Phys. 68 (1996) 13] and include an additional (momentum dependent) self-energy Σk. In the present case, Σk describes non-local dynamical correlations induced by short-ranged collective Heisenberg-like antiferromagnetic spin fluctuations [M.V. Sadovskii, Physics-Uspekhi 44 (2001) 515, cond-mat/0408489]. The effective single impurity problem in the DMFT + Σk is solved by numerical renormalization group (NRG) [R. Bulla, A.C. Hewson, Th. Pruschke, J. Phys. Cond. Mat. 10 (1998) 8365; R. Bulla, Phys. Rev. Lett. 83 (1999) 136]. To take into account material specific properties of two neighboring CuO 2 layers of Bi2212 we employ local density approximation (LDA) to calculate necessary model parameters, e.g. the values of intra- and interlayer hopping integrals between Cu-sites. Onsite Coulomb interaction U for x2- y2 orbital was calculated in constrained LDA method [O. Gunnarsson et al., Phys. Rev. B 39 (1989) 1708]. The value of pseudogap potential Δ was obtained within DMFT(NRG) [E.Z. Kuchinskii, I.A. Nekrasov, M.V. Sadovskii, JETP Lett. 82 (2005) 198; M.V. Sadovskii et al., Phys. Rev. B 72 (2005) 155105, and these proceedings, doi:10.1016/j.physc.2007.03.367]. Here, we report theoretical LDA + DMFT + Σk quasiparticle bands dispersion, Fermi surface (FS) and angular resolved photoemission (ARPES) spectra accounting for pseudogap and bilayer splitting effects for normal underdoped Bi2212 ( δ = 0.15). We show that LDA-calculated value of bilayer splitting (BS) is too small to describe experimentally observed peak-dip-hump structure. Fermi surface in presence of the pseudogap fluctuations is almost insensitive to the BS value. Results obtained are in good agreement with recent ARPES experiments.

Large Band Gap of alpha-RuCl3 Probed by Photoemission and Inverse Photoemission Spectroscopy

NASA Astrophysics Data System (ADS)

Sinn, Soobin; Kim, Choong Hyun; Sandilands, Luke; Lee, Kyungdong; Won, Choongjae; Oh, Ji Seop; Han, Moonsup; Chang, Young Jun; Hur, Namjung; Sato, Hitoshi; Park, Byeong-Gyu; Kim, Changyoung; Kim, Hyeong-Do; Noh, Tae Won

The Kitaev honeycomb lattice model has attracted great attention because of its possibility to stabilize a quantum spin liquid ground state. Recently, it was proposed that alpha-RuCl3 is its material realization and the first 4 d relativistic Mott insulator from an optical spectrum and LDA + U + SO calculations. Here, we present photoemission and inverse photoemission spectra of alpha-RuCl3. The observed band gap is about 1.8 eV, which suggests that the previously assigned optical gap of 0.3 eV is misinterpreted, and that the strong peak at about 1.2 eV in the optical spectrum may be associated with an actual optical gap. Assuming a strong excitonic effect of 0.6 eV in the optical spectrum, all the structures except for the peak at 0.3 eV are consistent with our electronic spectra. When compared with LDA + U + SO calculations, the value of U should be considerably larger than the previous one, which implies that the spin-orbit coupling is not a necessary ingredient for the insulating mechanism of alpha-RuCl3. We also present angle-resolved photoemission spectra to be compared with LDA + U + SO and LDA +DMFT calculations.

Ground state of a confined Yukawa plasma including correlation effects

NASA Astrophysics Data System (ADS)

Henning, C.; Ludwig, P.; Filinov, A.; Piel, A.; Bonitz, M.

2007-09-01

The ground state of an externally confined one-component Yukawa plasma is derived analytically using the local density approximation (LDA). In particular, the radial density profile is computed. The results are compared with the recently obtained mean-field (MF) density profile [Henning , Phys. Rev. E 74, 056403 (2006)]. While the MF results are more accurate for weak screening, the LDA with correlations included yields the proper description for large screening. By comparison with first-principles simulations for three-dimensional spherical Yukawa crystals, we demonstrate that the two approximations complement each other. Together they accurately describe the density profile in the full range of screening parameters.

Insight into the optoelectronic and thermoelectric properties of Ca-based Zintl phase CaCd2X2 (X = P, As) from first principles calculation

NASA Astrophysics Data System (ADS)

Belfarh, T.; Batouche, M.; Seddik, T.; Uğur, G.; Omran, S. Bin; Bouhemadou, A.; Sandeep; Wang, Xiaotian; Sun, Xiao-Wei; Khenata, R.

2018-06-01

We have studied the structural, optical, electronic and thermoelectric properties of the CaCd2X2 (X = P, As) compounds by using the full-potential augmented plane wave plus local orbitals method (FP-APW + lo). The exchange-correlation potential was treated using both the gradient generalized approximation (WC-GGA) and local density approximation (LDA). The estimated structural parameters, including the lattice parameters and internal coordinates agree well with the available experimental data. Our computed band structure shows that both studied compounds are semiconductors, with direct band gaps (Γ-Γ) of approximately 1.78 eV and 1.2 eV for CaCd2P2 and CaCd2As2, respectively, using GGA-TB-mBJ approach. The calculated optical spectra reveal a strong response of these materials in the energy range between the visible light and extreme UV regions, making them a good candidate for optoelectronic devices. Thermoelectric parameters, such as thermal conductivity, electrical conductivity, Seebeck coefficient, power factor and figure of merit were calculated. We note that both the CaCd2P2 and CaCd2As2 compounds show promising thermoelectric properties.

A LDA + U study of the photoemission spectra of the double hexagonal close packed phases of Am and Cm

NASA Astrophysics Data System (ADS)

Islam, M. Fhokrul; Ray, Asok K.

2010-05-01

We have investigated the photoemission spectra and other electronic structure properties such as equilibrium volume and bulk modulus of double hexagonal close packed (dhcp) americium and the density of states (DOS) and magnetic properties of dhcp curium using the LDA+U method. Our calculations show that spin polarized americium is energetically favorable but spin degenerate configuration produces experimental quantities significantly better than those calculated using the spin polarized configuration. The density of states calculated using LDA+U with both non-magnetic and spin polarized configurations is compared and the non-magnetic DOS is shown to be in good agreement with experimental photoemission spectra when U=4.5 eV. In spin polarized case, the onsite interaction parameter, U, is observed to increase the splitting between occupied and unoccupied bands by enhancing the Stoner parameter. The DOS of both non-magnetic americium and anti-ferromagnetic curium are shown to be in good agreement with that calculated using dynamical mean field theory for these two heavy actinides. For curium exchange interaction appears to play a dominant role in magnetic stability.

X-Ray Absorption Spectra of Amorphous Ices from GW Quasiparticle Calculation

NASA Astrophysics Data System (ADS)

Kong, Lingzhu; Car, Roberto

2013-03-01

We use a GW approach[2] to compute the x-ray absorption spectra of model low- and high-density amorphous ice structures(LDA and HDA)[3]. We include the structural effects of quantum zero point motion using colored-noise Langevin molecular dynamics[4]. The calculated spectra differences in the main and post edge region between LDA and HDA agree well with experimental observations. We attribute these differences to the presence of interstitial molecules within the first coordination shell range in HDA. This assignment is further supported by a calculation of the spectrum of ice VIII, a high-pressure structure that maximizes the number of interstitial molecules and, accordingly, shows a much weaker post-edge feature. We further rationalize the spectral similarity between HDA and liquid water, and between LDA and ice Ih in terms of the respective similarities in the H-bond network topology and bond angle distributions. Supported by grants DOE-DE-SC0005180, DOE DE-SC0008626 and NSF-CHE-0956500.

Theoretical calculations of structural, electronic, and elastic properties of CdSe1-x Te x : A first principles study

NASA Astrophysics Data System (ADS)

M, Shakil; Muhammad, Zafar; Shabbir, Ahmed; Muhammad Raza-ur-rehman, Hashmi; M, A. Choudhary; T, Iqbal

2016-07-01

The plane wave pseudo-potential method was used to investigate the structural, electronic, and elastic properties of CdSe1-x Te x in the zinc blende phase. It is observed that the electronic properties are improved considerably by using LDA+U as compared to the LDA approach. The calculated lattice constants and bulk moduli are also comparable to the experimental results. The cohesive energies for pure CdSe and CdTe binary and their mixed alloys are calculated. The second-order elastic constants are also calculated by the Lagrangian theory of elasticity. The elastic properties show that the studied material has a ductile nature.

Ab initio MD simulations of Mg2SiO4 liquid at high pressures and temperatures relevant to the Earth's mantle

NASA Astrophysics Data System (ADS)

Martin, G. B.; Kirtman, B.; Spera, F. J.

2010-12-01

Computational studies implementing Density Functional Theory (DFT) methods have become very popular in the Materials Sciences in recent years. DFT codes are now used routinely to simulate properties of geomaterials—mainly silicates and geochemically important metals such as Fe. These materials are ubiquitous in the Earth’s mantle and core and in terrestrial exoplanets. Because of computational limitations, most First Principles Molecular Dynamics (FPMD) calculations are done on systems of only 100 atoms for a few picoseconds. While this approach can be useful for calculating physical quantities related to crystal structure, vibrational frequency, and other lattice-scale properties (especially in crystals), it would be useful to be able to compute larger systems especially for extracting transport properties and coordination statistics. Previous studies have used codes such as VASP where CPU time increases as N2, making calculations on systems of more than 100 atoms computationally very taxing. SIESTA (Soler, et al. 2002) is a an order-N (linear-scaling) DFT code that enables electronic structure and MD computations on larger systems (N 1000) by making approximations such as localized numerical orbitals. Here we test the applicability of SIESTA to simulate geosilicates in the liquid and glass state. We have used SIESTA for MD simulations of liquid Mg2SiO4 at various state points pertinent to the Earth’s mantle and congruous with those calculated in a previous DFT study using the VASP code (DeKoker, et al. 2008). The core electronic wave functions of Mg, Si, and O were approximated using pseudopotentials with a core cutoff radius of 1.38, 1.0, and 0.61 Angstroms respectively. The Ceperly-Alder parameterization of the Local Density Approximation (LDA) was used as the exchange-correlation functional. Known systematic overbinding of LDA was corrected with the addition of a pressure term, P 1.6 GPa, which is the pressure calculated by SIESTA at the experimental zero-pressure volume of forsterite under static conditions (Stixrude and Lithgow-Bertollini 2005). Results are reported here that show SIESTA calculations of T and P on densities in the range of 2.7 - 5.0 g/cc of liquid Mg2SiO4 are similar to the VASP calculations of DeKoker et al. (2008), which used the same functional. This opens the possibility of conducting fast /emph{ab initio} MD simulations of geomaterials with a hundreds of atoms.

Effects of inter-fullerene π-band mixings in the photoexcitation of hybrid plasmons in the C60@C240 molecule

NASA Astrophysics Data System (ADS)

de, Rume; Madjet, Mohamed; Chakraborty, Himadri

2013-05-01

We perform a detailed study of the ground state electronic structure of a two-layer fullerene onion molecule C60@C240. Calculations are carried out in a quantum mechanical framework of local density approximation (LDA) where the onion's ion-core of sixty C4+ ions from C60 and two hundred and forty of those from C240 is smeared into a classical jellium distribution. Significant inter-fullerene mixing between the bands of single-node radial symmetry, the π-bands, is found. We then compute the photoionization from all the levels of the system using a time-dependent version of LDA at photon energies where the ionization is dominated by the inter-layer hybridization of collective plasmon resonances. It is determined, by comparing the isolated fullerene cross sections with the cross section of the onion system for both π and σ (having nodeless radial waves) symmetry, that the π-band mixing is predominantly responsible for the production of plasmon hybrids. Supported by NSF and DOE.

From the Kohn-Sham band gap to the fundamental gap in solids. An integer electron approach.

PubMed

Baerends, E J

2017-06-21

It is often stated that the Kohn-Sham occupied-unoccupied gap in both molecules and solids is "wrong". We argue that this is not a correct statement. The KS theory does not allow to interpret the exact KS HOMO-LUMO gap as the fundamental gap (difference (I - A) of electron affinity (A) and ionization energy (I), twice the chemical hardness), from which it indeed differs, strongly in molecules and moderately in solids. The exact Kohn-Sham HOMO-LUMO gap in molecules is much below the fundamental gap and very close to the much smaller optical gap (first excitation energy), and LDA/GGA yield very similar gaps. In solids the situation is different: the excitation energy to delocalized excited states and the fundamental gap (I - A) are very similar, not so disparate as in molecules. Again the Kohn-Sham and LDA/GGA band gaps do not represent (I - A) but are significantly smaller. However, the special properties of an extended system like a solid make it very easy to calculate the fundamental gap from the ground state (neutral system) band structure calculations entirely within a density functional framework. The correction Δ from the KS gap to the fundamental gap originates from the response part v resp of the exchange-correlation potential and can be calculated very simply using an approximation to v resp . This affords a calculation of the fundamental gap at the same level of accuracy as other properties of crystals at little extra cost beyond the ground state bandstructure calculation. The method is based on integer electron systems, fractional electron systems (an ensemble of N- and (N + 1)-electron systems) and the derivative discontinuity are not invoked.

Electronic and optical properties of graphene-like InAs: An ab initio study

NASA Astrophysics Data System (ADS)

Sohrabi, Leila; Boochani, Arash; Ali Sebt, S.; Mohammad Elahi, S.

2018-03-01

The present work initially investigates structural, optical, and electronic properties of graphene-like InAs by using the full potential linear augmented plane wave method in the framework of density functional theory and is then compared with the bulk Indium Arsenide in the wurtzite phase. The lattice parameters are optimized with GGA-PBE and LDA approximations for both 2D- and 3D-InAs. In order to study the electronic properties of graphene-like InAs and bulk InAs in the wurtzite phase, the band gap is calculated by GGA-PBG and GGA-EV approximations. Moreover, optical parameters of graphene-like InAs and bulk InAs such as the real and imaginary parts of dielectric function, electron energy loss function, refractivity, extinction and absorption coefficients, and optical conductivity are investigated. Plasmonic frequencies of 2D- and 3D-InAs are also calculated by using maximum electron energy loss function and the roots of the real part of the dielectric function.

Structural, electronic and vibrational properties of LaF3 according to density functional theory and Raman spectroscopy

NASA Astrophysics Data System (ADS)

Oreshonkov, A. S.; Roginskii, E. M.; Krylov, A. S.; Ershov, A. A.; Voronov, V. N.

2018-06-01

Crystal structure of LaF3 single crystal is refined in tysonite-type trigonal unit cell P c1 using density functional theory calculations and Raman spectroscopy. It is shown that trigonal structure with P c1 space group is more energy-efficient than hexagonal structure with space group P63 cm. Simulated Raman spectra obtained using LDA approximation is in much better agreement with experimental data than that obtained with PBE and PBEsol functionals of GGA. The calculated frequency value of silent mode B 2 in case of hexagonal structure P63 cm was found to be imaginary (unstable mode), thus the energy surface obtains negative curvature with respect to the corresponding normal coordinates of the mode which leads to instability of the hexagonal structure in harmonic approximation. The A 1g line at 214 cm‑1 in Raman spectra of LaF3 related to the translation of F2 ions along c axis can be connected with F2 ionic conductivity.

Wave-function-based approach to quasiparticle bands: Insight into the electronic structure of c-ZnS

NASA Astrophysics Data System (ADS)

Stoyanova, A.; Hozoi, L.; Fulde, P.; Stoll, H.

2011-05-01

Ab initio wave-function-based methods are employed for the study of quasiparticle energy bands of zinc-blende ZnS, with focus on the Zn 3d “semicore” states. The relative energies of these states with respect to the top of the S 3p valence bands appear to be poorly described as compared to experimental values not only within the local density approximation (LDA), but also when many-body corrections within the GW approximation are applied to the LDA or LDA + U mean-field solutions [T. Miyake, P. Zhang, M. L. Cohen, and S. G. Louie, Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.74.245213 74, 245213 (2006)]. In the present study, we show that for the accurate description of the Zn 3d states a correlation treatment based on wave-function methods is needed. Our study rests on a local Hamiltonian approach which rigorously describes the short-range polarization and charge redistribution effects around an extra hole or electron placed into the valence respective conduction bands of semiconductors and insulators. The method also facilitates the computation of electron correlation effects beyond relaxation and polarization. The electron correlation treatment is performed on finite clusters cut off the infinite system. The formalism makes use of localized Wannier functions and embedding potentials derived explicitly from prior periodic Hartree-Fock calculations. The on-site and nearest-neighbor charge relaxation lead to corrections of several eV to the Hartree-Fock band energies and gap. Corrections due to long-range polarization are of the order of 1.0 eV. The dispersion of the Hartree-Fock bands is only slightly affected by electron correlations. We find the Zn 3d “semicore” states to lie ~9.0 eV below the top of the S 3p valence bands, in very good agreement with values from valence-band x-ray photoemission.

Structural, electronic, and thermodynamic properties of curium dioxide: Density functional theory calculations

NASA Astrophysics Data System (ADS)

Hou, Ling; Li, Wei-Dong; Wang, Fangwei; Eriksson, Olle; Wang, Bao-Tian

2017-12-01

We present a systematic investigation of the structural, magnetic, electronic, mechanical, and thermodynamic properties of CmO2 with the local density approximation (LDA)+U and the generalized gradient approximation (GGA)+U approaches. The strong Coulomb repulsion and the spin-orbit coupling (SOC) effects on the lattice structures, electronic density of states, and band gaps are carefully studied, and compared with other A O2 (A =U , Np, Pu, and Am). The ferromagnetic configuration with half-metallic character is predicted to be energetically stable while a charge-transfer semiconductor is predicted for the antiferromagnetic configuration. The elastic constants and phonon spectra show that the fluorite structure is mechanically and dynamically stable. Based on the first-principles phonon density of states, the lattice vibrational energy is calculated using the quasiharmonic approximation. Then, the Gibbs free energy, thermal expansion coefficient, specific heat, and entropy are obtained and compared with experimental data. The mode Grüneisen parameters are presented to analyze the anharmonic properties. The Slack relation is applied to obtain the lattice thermal conductivity in temperature range of 300-1600 K. The phonon group velocities are also calculated to investigate the heat transfer. For all these properties, if available, we compare the results of CmO2 with other A O2 .

Theoretical calculations of high-pressure phases of NiF2: An ab initio constant-pressure study

NASA Astrophysics Data System (ADS)

Kürkçü, Cihan; Merdan, Ziya; Öztürk, Hülya

2016-12-01

We have studied the structural properties of the antiferromagnetic NiF2 tetragonal structure with P42/ mnm symmetry using density functional theory (DFT) under rapid hydrostatic pressure up to 400 GPa. For the exchange correlation energy we used the local density approximation (LDA) of Ceperley and Alder (CA). Two phase transformations are successfully observed through the simulations. The structures of XF2-type compounds crystallize in rutile-type structure. NiF2 undergoes phase transformations from the tetragonal rutile-type structure with space group P42/ mnm to orthorhombic CaCl2-type structure with space group Pnnm and from this orthorhombic phase to monoclinic structure with space group C2/ m at 152 GPa and 360 GPa, respectively. These phase changes are also studied by total energy and enthalpy calculations. According to these calculations, we perdict these phase transformations at about 1.85 and 30 GPa.

Investigation of the electronic structure in La1-xCaxCoO3 (x = 0, 0.5) using full potential calculations

NASA Astrophysics Data System (ADS)

Sahnoun, M.; Daul, C.; Haas, O.; Wokaun, A.

2005-12-01

The electronic and magnetic properties of both LaCoO3 and La0.5Ca0.5CoO3 have been investigated by means of ab initio full-potential augmented plane wave plus local orbitals (APW+lo) calculations carried out with the Wien 2k code. The functional used is the local-density approximation LDA +U. Doping with Ca2+ introduces holes into the Co-O network. We analyse the densities of states and we confirm that the intermediate state (IS) is stabilized by the Ca2+ substitution. This intermediate state in our results turns out to be metallic, and has a large density of states at the Fermi energy. The calculated magnetic moment in La0.5Ca0.5CoO3 is found to be in good agreement with experiment.

Adsorption and Electronic Structure of Sr and Ag Atoms on Graphite Surfaces: a First-Principles Study

NASA Astrophysics Data System (ADS)

Luo, Xiao-Feng; Fang, Chao; Li, Xin; Lai, Wen-Sheng; Sun, Li-Feng; Liang, Tong-Xiang

2013-06-01

The adsorption behaviors of radioactive strontium and silver nuclides on the graphite surface in a high-temperature gas-cooled reactor are studied by first-principles theory using generalized gradient approximation (GGA) and local density approximation (LDA) pseudo-potentials. It turns out that Sr prefers to be absorbed at the hollow of the carbon hexagonal cell by 0.54 eV (GGA), while Ag likes to sit right above the carbon atom with an adsorption energy of almost zero (GGA) and 0.45 eV (LDA). Electronic structure analysis reveals that Sr donates its partial electrons of the 4p and 5s states to the graphite substrate, while Ag on graphite is a physical adsorption without any electron transfer.

Angle-resolved Photoemission of CeCoIn5: Detailed Comparison to LDA and LDA+DMFT

NASA Astrophysics Data System (ADS)

Allen, J. W.

2008-03-01

Highly-automated photon-dependent angle resolved photoemission spectroscopy (ARPES) in the energy range of 80-200 eV has been used to characterize the three dimensional (3D) Fermi surface (FS) topology and electronic band structure of cleaved single crystals of CeCoIn5. The sample temperature of 26K is well below the lattice coherence onset temperature of 45K found in a recent ``two fluid'' analysis of transport data. Detailed comparison of ARPES FS contours to LDA calculations for the Ce 4f electrons treated as itinerant or confined to the core reveals remarkable agreement to fine topological details of the f-core calculations. Also in agreement to the f-core calculations is the experimental absence of extra electron-like contours predicted in the f-itinerant calculation, originating from α and β bands re-entrant below EF along Z-A. Finally, the areas enclosed by FS contours for the α and β bands are significantly smaller than are found in very low temperature CeCoIn5 de Haas van Alphen data that agrees generally with the f-itinerant calculation. It is concluded that clear signatures of coherence in the transport data can develop at temperatures for which the f-electrons are not yet included in the FS. In this connection, comparison will also be made to recent T-dependent LDA+DMFT calculations for CeIrIn5. This work was done in collaboration with J. D. Denlinger, Feng Wang, R. S. Singh, K. Rossnagel, S. Elgazzar, P. M. Oppeneer, V. S. Zapf and M. B. Maple, and was supported by the U.S. DOE (DE-AC03-76SF00098 at the ALS, DE-FG02-07ER46379 at UM for current work, DE FG02-04ER-46105 at UCSD), by the U.S. NSF (DMR-03-02825 at UM for initial work, DMR-03-35173 at UCSD) and by the Swedish Research Council (VR) and the European Commission (JRC-ITU).

Electronic structure and magnetic properties of dilute U impurities in metals

NASA Astrophysics Data System (ADS)

Mohanta, S. K.; Cottenier, S.; Mishra, S. N.

2016-05-01

The electronic structure and magnetic moment of dilute U impurity in metallic hosts have been calculated from first principles. The calculations have been performed within local density approximation of the density functional theory using Augmented plane wave+local orbital (APW+lo) technique, taking account of spin-orbit coupling and Coulomb correlation through LDA+U approach. We present here our results for the local density of states, magnetic moment and hyperfine field calculated for an isolated U impurity embedded in hosts with sp-, d- and f-type conduction electrons. The results of our systematic study provide a comprehensive insight on the pressure dependence of 5f local magnetism in metallic systems. The unpolarized local density of states (LDOS), analyzed within the frame work of Stoner model suggest the occurrence of local moment for U in sp-elements, noble metals and f-block hosts like La, Ce, Lu and Th. In contrast, U is predicted to be nonmagnetic in most transition metal hosts except in Sc, Ti, Y, Zr, and Hf consistent with the results obtained from spin polarized calculation. The spin and orbital magnetic moments of U computed within the frame of LDA+U formalism show a scaling behavior with lattice compression. We have also computed the spin and orbital hyperfine fields and a detail analysis has been carried out. The host dependent trends for the magnetic moment, hyperfine field and 5f occupation reflect pressure induced change of electronic structure with U valency changing from 3+ to 4+ under lattice compression. In addition, we have made a detailed analysis of the impurity induced host spin polarization suggesting qualitatively different roles of f-band electrons on moment stability. The results presented in this work would be helpful towards understanding magnetism and spin fluctuation in U based alloys.

Spectral Learning for Supervised Topic Models.

PubMed

Ren, Yong; Wang, Yining; Zhu, Jun

2018-03-01

Supervised topic models simultaneously model the latent topic structure of large collections of documents and a response variable associated with each document. Existing inference methods are based on variational approximation or Monte Carlo sampling, which often suffers from the local minimum defect. Spectral methods have been applied to learn unsupervised topic models, such as latent Dirichlet allocation (LDA), with provable guarantees. This paper investigates the possibility of applying spectral methods to recover the parameters of supervised LDA (sLDA). We first present a two-stage spectral method, which recovers the parameters of LDA followed by a power update method to recover the regression model parameters. Then, we further present a single-phase spectral algorithm to jointly recover the topic distribution matrix as well as the regression weights. Our spectral algorithms are provably correct and computationally efficient. We prove a sample complexity bound for each algorithm and subsequently derive a sufficient condition for the identifiability of sLDA. Thorough experiments on synthetic and real-world datasets verify the theory and demonstrate the practical effectiveness of the spectral algorithms. In fact, our results on a large-scale review rating dataset demonstrate that our single-phase spectral algorithm alone gets comparable or even better performance than state-of-the-art methods, while previous work on spectral methods has rarely reported such promising performance.

Investigation of the spectral properties and magnetism of BiFeO3 by dynamical mean-field theory

NASA Astrophysics Data System (ADS)

Paul, Souvik; Iuşan, Diana; Thunström, Patrik; Kvashnin, Yaroslav O.; Hellsvik, Johan; Pereiro, Manuel; Delin, Anna; Knut, Ronny; Phuyal, Dibya; Lindblad, Andreas; Karis, Olof; Sanyal, Biplab; Eriksson, Olle

2018-03-01

Using the local density approximation plus dynamical mean-field theory (LDA+DMFT), we have computed the valence-band photoelectron spectra and magnetic excitation spectra of BiFeO3, one of the most studied multiferroics. Within the DMFT approach, the local impurity problem is tackled by the exact diagonalization solver. The solution of the impurity problem within the LDA+DMFT method for the paramagnetic and magnetically ordered phases produces result in agreement with the experimental data on electronic and magnetic structures. For comparison, we also present results obtained by the LDA +U approach which is commonly used to compute the physical properties of this compound. Our LDA+DMFT derived electronic spectra match adequately with the experimental hard x-ray photoelectron spectroscopy and resonant photoelectron spectroscopy for Fe 3 d states, whereas the LDA +U method fails to capture the general features of the measured spectra. This indicates the importance of accurately incorporating the dynamical aspect of electronic correlation among Fe 3 d orbitals to reproduce the experimental excitation spectra. Specifically, the LDA+DMFT derived density of states exhibits a significant amount of Fe 3 d states at the position of Bi lone pairs, implying that the latter are not alone in the spectral scenario. This fact might modify our interpretation about the origin of ferroelectric polarization in this material. Our study demonstrates that the combination of orbital cross sections for the constituent elements and broadening schemes for the spectral functions are crucial to explain the detailed structures of the experimental electronic spectra. Our magnetic excitation spectra computed from the LDA+DMFT result conform well with the inelastic neutron scattering data.

Effect of U on the electronic properties of neodymium gallate (NdGaO3): theoretical and experimental studies.

PubMed

Reshak, Ali Hussain; Piasecki, M; Auluck, S; Kityk, I V; Khenata, R; Andriyevsky, B; Cobet, C; Esser, N; Majchrowski, A; Swirkowicz, M; Diduszko, R; Szyrski, W

2009-11-19

We have performed a density functional calculation for the centrosymmetric neodymium gallate using a full-potential linear augmented plane wave method with the LDA and LDA+U exchange correlation. In particular, we explored the influence of U on the band dispersion and optical transitions. Our calculations show that U = 0.55 Ry gives the best agreement with our ellipsometry data taken in the VUV spectral range with a synchrotron source. Our LDA+U (U = 0.55) calculation shows that the valence band maximum (VBM) is located at T and the conduction band minimum (CBM) is located at the center of the Brillouin zone, resulting in a wide indirect energy band gap of about 3.8 eV in excellent agreement with our experiment. The partial density of states show that the upper valence band originates predominantly from Nd-f and O-p states, with a small admixture of Nd-s/p and Ga-p B-p states, while the lower conduction band prevailingly originates from the Nd-f and Nd-d terms with a small contribution of O-p-Ga-s/p states. The Nd-f states in the upper valence band and lower conduction band have a significant influence on the energy band gap dispersion which is illustrated by our calculations. The calculated frequency dependent optical properties show a small positive uniaxial anisotropy.

Effect of pressure on the Raman-active modes of zircon (ZrSiO4): a first-principles study

NASA Astrophysics Data System (ADS)

Sheremetyeva, Natalya; Cherniak, Daniele J.; Watson, E. Bruce; Meunier, Vincent

2018-02-01

Density-functional theory (DFT) was employed in a first-principles study of the effects of pressure on the Raman-active modes of zircon (ZrSiO4), using both the generalized gradient and local density approximations (GGA and LDA, respectively). Beginning with the equilibrium structure at zero pressure, we conducted a calibration of the effect of pressure in a manner procedurally similar to an experimental calibration. For pressures between 0 and 7 GPa, we find excellent qualitative agreement of frequency-pressure slopes partial ω /partial P calculated from GGA DFT with results of previous experimental studies. In addition, we were able to rationalize the ω vs. P behavior based on details of the vibrational modes and their atomic displacements. Most of the partial ω /partial P slopes are positive as expected, but the symmetry of the zircon lattice also results in two negative slopes for modes that involve slight shearing and rigid rotation of SiO4 tetrahedra. Overall, LDA yields absolute values of the frequencies of the Raman-active modes in good agreement with experimental values, while GGA reproduces the shift in frequency with pressure especially well.

High-temperature high-pressure properties of silica from Quantum Monte Carlo and Density Functional Perturbation Theory

NASA Astrophysics Data System (ADS)

Cohen, R. E.; Driver, K.; Wu, Z.; Militzer, B.; Rios, P. L.; Towler, M.; Needs, R.

2009-03-01

We have used diffusion quantum Monte Carlo (DMC) with the CASINO code with thermal free energies from phonons computed using density functional perturbation theory (DFPT) with the ABINIT code to obtain phase transition curves and thermal equations of state of silica phases under pressure. We obtain excellent agreement with experiments for the metastable phase transition from quartz to stishovite. The local density approximation (LDA) incorrectly gives stishovite as the ground state. The generalized gradient approximation (GGA) correctly gives quartz as the ground state, but does worse than LDA for the equations of state. DMC, variational quantum Monte Carlo (VMC), and DFT all give good results for the ferroelastic transition of stishovite to the CaCl2 structure, and LDA or the WC exchange correlation potentials give good results within a given silica phase. The δV and δH from the CaCl2 structure to α-PbO2 is small, giving uncertainly in the theoretical transition pressure. It is interesting that DFT has trouble with silica transitions, although the electronic structures of silica are insulating, simple closed-shell with ionic/covalent bonding. It seems like the errors in DFT are from not precisely giving the ion sizes.

Absence of B1-B2 structural transition in lithium halides under hydrostatic pressure

NASA Astrophysics Data System (ADS)

de Coss, Romeo; Murrieta, Gabriel

2005-03-01

We have investigated the B1-B2 structural transition in LiF, LiCl, LiBr, and LiI under hydrostatic pressure by means of first-principles total-energy calculations using the Full- Potential LAPW method. In order to analyze the gradient effects, we have performed calculations using the local density approximation (LDA) and the generalized gradient approximation (GGA), for the exchange and correlation potential. In agreement with the experimental observations, we find that even for pressures higher than 100 GPa, the Li halides do not present the B1-B2 structural transition. In order to understand this behavior, we have calculated the distribution of the electron densities. From the analysis of the distribution of electron densities for the Li halides in the B1 and B2 phases, we find that for this group of ionic compounds the B1 phase have a distribution of electron densities more homogeneous than in the B2 phase, preventing the B1-B2 structural transition. This work was partially supported by Consejo Nacional de Ciencia y Tecnolog'ia (CONACYT, M'exico) under Grant No. 43830-F.

[Study of cubic boron nitride crystal UV absorption spectroscopy].

PubMed

Liu, Hai-Bo; Jia, Gang; Chen, Gang; Meng, Qing-Ju; Zhang, Tie-Chen

2008-07-01

UV absorption spectroscopy of artificial cubic boron nitride (cBN) single crystal flake, synthesized under high-temperature and high-pressure, was studied in the present paper. UV WINLAB spectrometer was used in the experiments, and MOLECULAR SPECTROSCOPY software was used for data analysis. The UV-cBN limit of 198 nm was showed in this test by a special fixture quartz sample. We calculated the energy gap by virtue of the formula: lambda0 = 1.24/E(g) (microm). The energy gap is 6. 26 eV. There are many viewpoints about the gap of cBN. By using the first-principles theory to calculate energy band structure and density of electronic states of cBN, an indirect transition due to electronics in valence band jumping into conduction band by absorbing photon can be confirmed. That leads to UV absorption. The method of calculation was based on the quantum mechanics of CASTEP in the commercial software package of Cerius2 in the Co. Accerlrys in the United States. The theory of CASTEP is based on local density approximation or gradient corrected LDA. The crystal parameter of cBN was input to the quantum mechanics of CASTEP in order to construct the crystal parameter model of cBN. We calculated the energy gap of cBN by the method of gradient corrected LDA. The method underestimates the value of nonconductor by about 1 to 2 eV. We gaot some opinions as follows: cBN is indirect band semiconductor. The energy gap is 4.76 eV, less than our experiment. The reason may be defect that we ignored in calculating process. It was reported that the results by first principles method of calculation of the band generally was less than the experimental results. This paper shows good UV characteristics of cBN because of the good agreement of experimental results with the cBN band width. That is a kind of development prospect of UV photo-electronic devices and high-temperature semiconductor devices.

First-principles studies of electronic, transport and bulk properties of pyrite FeS2

NASA Astrophysics Data System (ADS)

Banjara, Dipendra; Mbolle, Augustine; Malozovsky, Yuriy; Franklin, Lashounda; Bagayoko, Diola

We present results of ab-initio, self-consistent density functional theory (DFT) calculations of electronic, transport, and bulk properties of pyrite FeS2. We employed a local density approximation (LDA) potential and the linear combination of atomic orbitals (LCAO) formalism, following the Bagayoko, Zhao and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF). The BZW-EF method requires successive, self consistent calculations with increasing basis sets to reach the ground state of the system under study. We report the band structure, the band gap, total and partial densities of states, effective masses, and the bulk modulus. Work funded in part by the US Department of Energy (DOE), National Nuclear Security Administration (NNSA) (Award No.DE-NA0002630), the National Science Foundation (NSF) (Award No, 1503226), LaSPACE, and LONI-SUBR.

Calculation of longitudinal polarizability and second hyperpolarizability of polyacetylene with the coupled perturbed Hartree-Fock/Kohn-Sham scheme: Where it is shown how finite oligomer chains tend to the infinite periodic polymer

NASA Astrophysics Data System (ADS)

Lacivita, Valentina; Rèrat, Michel; Orlando, Roberto; Ferrero, Mauro; Dovesi, Roberto

2012-03-01

The longitudinal polarizability, αxx, and second hyperpolarizability, γxxxx, of polyacetylene are evaluated by using the coupled perturbed Hartree-Fock/Kohn-Sham (HF/KS) scheme as implemented in the periodic CRYSTAL code and a split valence type basis set. Four different density functionals, namely local density approximation (LDA) (pure local), Perdew-Becke-Ernzerhof (PBE) (gradient corrected), PBE0, and B3LYP (hybrid), and the Hartree-Fock Hamiltonian are compared. It is shown that very tight computational conditions must be used to obtain well converged results, especially for γxxxx, that is, very sensitive to the number of k points in reciprocal space when the band gap is small (as for LDA and PBE), and to the extension of summations of the exact exchange series (HF and hybrids). The band gap in LDA is only 0.01 eV: at least 300 k points are required to obtain well converged total energy and equilibrium geometry, and 1200 for well converged optical properties. Also, the exchange series convergence is related to the band gap. The PBE0 band gap is as small as 1.4 eV and the exchange summation must extend to about 130 Å from the origin cell. Total energy, band gap, equilibrium geometry, polarizability, and second hyperpolarizability of oligomers -(C2H2)m-, with m up to 50 (202 atoms), and of the polymer have been compared. It turns out that oligomers of that length provide an extremely poor representation of the infinite chain polarizability and hyperpolarizability when the gap is smaller than 0.2 eV (that is, for LDA and PBE). Huge differences are observed on αxx and γxxxx of the polymer when different functionals are used, that is in connection to the well-known density functional theory (DFT) overshoot, reported in the literature about short oligomers: for the infinite model the ratio between LDA (or PBE) and HF becomes even more dramatic (about 500 for αxx and 1010 for γxxxx). On the basis of previous systematic comparisons of results obtained with various approaches including DFT, HF, Moller-Plesset (MP2) and coupled cluster for finite chains, we can argue that, for the infinite chain, the present HF results are the most reliable.

Tuning the thermoelectric properties of YNiBi half-Heusler alloy

NASA Astrophysics Data System (ADS)

Sharma, Sonu; Kumar, Pradeep

2018-04-01

A detail comparison between the results obtained for the electronic and transport properties of YNiBi half-Heusler alloy by local density approximation (LDA) and generalized gradient approximation (GGA) functionals with and without spin–orbit coupling (SOC) is presented. In the presence of SOC both functionals provide ∼30% smaller band gap. The transport coefficients computed without SOC confirm that YNiBi is a promising p-type thermoelectric material. However, with SOC at higher temperature, Seebeck coefficient was found to be negative because of the bipolar effects. Without SOC the computed power factor (PF) is found to be closer to the experimental value, while in the presence of SOC we have obtained comparatively smaller PF. No importance of SOC has been observed in the calculations of transport properties of the compound. The appropriate Ti doping in place of Y is predicted to significantly enhance the thermoelectric properties of YNiBi compound.

Structural, electronic, elastic, and thermal properties of CaNiH3 perovskite obtained from first-principles calculations

NASA Astrophysics Data System (ADS)

Benlamari, S.; Bendjeddou, H.; Boulechfar, R.; Amara Korba, S.; Meradji, H.; Ahmed, R.; Ghemid, S.; Khenata, R.; Omran, S. Bin

2018-03-01

A theoretical study of the structural, elastic, electronic, mechanical, and thermal properties of the perovskite-type hydride CaNiH3 is presented. This study is carried out via first-principles full potential (FP) linearized augmented plane wave plus local orbital (LAPW+lo) method designed within the density functional theory (DFT). To treat the exchange–correlation energy/potential for the total energy calculations, the local density approximation (LDA) of Perdew–Wang (PW) and the generalized gradient approximation (GGA) of Perdew–Burke–Ernzerhof (PBE) are used. The three independent elastic constants (C 11, C 12, and C 44) are calculated from the direct computation of the stresses generated by small strains. Besides, we report the variation of the elastic constants as a function of pressure as well. From the calculated elastic constants, the mechanical character of CaNiH3 is predicted. Pertaining to the thermal properties, the Debye temperature is estimated from the average sound velocity. To further comprehend this compound, the quasi-harmonic Debye model is used to analyze the thermal properties. From the calculations, we find that the obtained results of the lattice constant (a 0), bulk modulus (B 0), and its pressure derivative ({B}0^{\\prime }) are in good agreement with the available theoretical as well as experimental results. Similarly, the obtained electronic band structure demonstrates the metallic character of this perovskite-type hydride.

Structural, optoelectronic, infrared and Raman spectra of orthorhombic SrSnO{sub 3} from DFT calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moreira, E.; Henriques, J.M.; Azevedo, D.L.

2011-04-15

Orthorhombic SrSnO{sub 3} was investigated using density functional theory (DFT) considering both the local density and generalized gradient approximations, LDA and GGA, respectively. The electronic band structure, density of states, complex dielectric function, optical absorption, and the infrared and Raman spectra were computed. Calculated lattice parameters are close to the experimental measurements, and an indirect band gap E(S{yields}{Gamma})=1.97eV (2.27 eV) was obtained within the GGA (LDA) level of calculation. Effective masses for holes and electrons were estimated, being very anisotropic in comparison with similar results for orthorhombic CaSnO{sub 3}. The complex dielectric function and the optical absorption of SrSnO{sub 3}more » were shown to be sensitive to the plane of polarization of the incident light. The infrared spectrum between 100 and 600 cm{sup -1} was obtained, with its main peaks being assigned, and a nice agreement between experimental and theoretical peaks of the Raman spectrum of orthorhombic SrSnO{sub 3} was achieved. -- Graphical abstract: Orthorhombic SrSnO{sub 3}: a view of the unit cell (left) and plots showing the calculated and experimental Raman spectra (right). Display Omitted Research highlights: {yields} We have performed DFT calculations on orthorhombic SrSnO{sub 3} crystals, obtaining their structural, electronical and optical properties. {yields} An indirect band gap was obtained, and anisotropic effective masses were found for both electrons and holes. {yields} The complex dielectric function and the optical absorption of SrSnO{sub 3} were shown to be very sensitive to the plane of polarization of the incident light. {yields} The infrared spectrum between 100 and 600 cm{sup -1} was obtained, with its main peaks being assigned, and a nice agreement between experimental and theoretical peaks of the Raman spectrum was achieved.« less

First-principles study of SnS electronic properties using LDA, PBE and HSE06 functionals

NASA Astrophysics Data System (ADS)

Ibragimova, R.; Ganchenkova, M.; Karazhanov, S.; Marstein, E. S.

2018-03-01

Recently, tin sulphide (SnS) has emerged as a promising alternative to conventional CIGS and CZTC for use in solar cells, possessing such properties as non-toxicity, low cost and production stability. SnS has a high theoretically predicted efficiency above 20%, but the experimentally achieved efficiency so far is as low as 4.36%. The reason for the low achieved efficiency is unclear. One of the powerful tools to get deeper insights about the nature of the problem is first-principles calculation approaches. That is why SnS has become an attractive subject for first-principles calculations recently. Previously calculated data, however, show a widespread of such fundamental value as the bandgap varying from 0.26 to 1.26 eV. In order to understand a reason for that, in this work, we concentrate on a systematic study of calculation parameters effects on the resulting electronic structure, with the particular attention paid to the influence of the exchange-correlation functional chosen for calculations. Several exchange-correlation functionals (LDA, PBE and HSE06) were considered. The systematic analysis has shown that the bandgap variation can result from a tensile/compressive hydrostatic pressure introduced by non-equilibrium lattice parameters used for the calculations. The study of the applicability of three functionals has shown that HSE06 gives the best match to both experimentally obtained bandgap and the XPS valence band spectra. LDA underestimates the bandgap but qualitatively reproduces experimentally measured valence DOS similar to that of HSE06 in contrast to PBE. PBE underestimates the bandgap and does not match to the measured XPS spectra.

Pulse shape discrimination and classification methods for continuous depth of interaction encoding PET detectors.

PubMed

Roncali, Emilie; Phipps, Jennifer E; Marcu, Laura; Cherry, Simon R

2012-10-21

In previous work we demonstrated the potential of positron emission tomography (PET) detectors with depth-of-interaction (DOI) encoding capability based on phosphor-coated crystals. A DOI resolution of 8 mm full-width at half-maximum was obtained for 20 mm long scintillator crystals using a delayed charge integration linear regression method (DCI-LR). Phosphor-coated crystals modify the pulse shape to allow continuous DOI information determination, but the relationship between pulse shape and DOI is complex. We are therefore interested in developing a sensitive and robust method to estimate the DOI. Here, linear discriminant analysis (LDA) was implemented to classify the events based on information extracted from the pulse shape. Pulses were acquired with 2×2×20 mm(3) phosphor-coated crystals at five irradiation depths and characterized by their DCI values or Laguerre coefficients. These coefficients were obtained by expanding the pulses on a Laguerre basis set and constituted a unique signature for each pulse. The DOI of individual events was predicted using LDA based on Laguerre coefficients (Laguerre-LDA) or DCI values (DCI-LDA) as discriminant features. Predicted DOIs were compared to true irradiation depths. Laguerre-LDA showed higher sensitivity and accuracy than DCI-LDA and DCI-LR and was also more robust to predict the DOI of pulses with higher statistical noise due to low light levels (interaction depths further from the photodetector face). This indicates that Laguerre-LDA may be more suitable to DOI estimation in smaller crystals where lower collected light levels are expected. This novel approach is promising for calculating DOI using pulse shape discrimination in single-ended readout depth-encoding PET detectors.

Pulse Shape Discrimination and Classification Methods for Continuous Depth of Interaction Encoding PET Detectors

PubMed Central

Roncali, Emilie; Phipps, Jennifer E.; Marcu, Laura; Cherry, Simon R.

2012-01-01

In previous work we demonstrated the potential of positron emission tomography (PET) detectors with depth-of-interaction (DOI) encoding capability based on phosphor-coated crystals. A DOI resolution of 8 mm full-width at half-maximum was obtained for 20 mm long scintillator crystals using a delayed charge integration linear regression method (DCI-LR). Phosphor-coated crystals modify the pulse shape to allow continuous DOI information determination, but the relationship between pulse shape and DOI is complex. We are therefore interested in developing a sensitive and robust method to estimate the DOI. Here, linear discriminant analysis (LDA) was implemented to classify the events based on information extracted from the pulse shape. Pulses were acquired with 2 × 2 × 20 mm3 phosphor-coated crystals at five irradiation depths and characterized by their DCI values or Laguerre coefficients. These coefficients were obtained by expanding the pulses on a Laguerre basis set and constituted a unique signature for each pulse. The DOI of individual events was predicted using LDA based on Laguerre coefficients (Laguerre-LDA) or DCI values (DCI-LDA) as discriminant features. Predicted DOIs were compared to true irradiation depths. Laguerre-LDA showed higher sensitivity and accuracy than DCI-LDA and DCI-LR and was also more robust to predict the DOI of pulses with higher statistical noise due to low light levels (interaction depths further from the photodetector face). This indicates that Laguerre-LDA may be more suitable to DOI estimation in smaller crystals where lower collected light levels are expected. This novel approach is promising for calculating DOI using pulse shape discrimination in single-ended readout depth-encoding PET detectors. PMID:23010690

Prediction of Depression in Cancer Patients With Different Classification Criteria, Linear Discriminant Analysis versus Logistic Regression.

PubMed

Shayan, Zahra; Mohammad Gholi Mezerji, Naser; Shayan, Leila; Naseri, Parisa

2015-11-03

Logistic regression (LR) and linear discriminant analysis (LDA) are two popular statistical models for prediction of group membership. Although they are very similar, the LDA makes more assumptions about the data. When categorical and continuous variables used simultaneously, the optimal choice between the two models is questionable. In most studies, classification error (CE) is used to discriminate between subjects in several groups, but this index is not suitable to predict the accuracy of the outcome. The present study compared LR and LDA models using classification indices. This cross-sectional study selected 243 cancer patients. Sample sets of different sizes (n = 50, 100, 150, 200, 220) were randomly selected and the CE, B, and Q classification indices were calculated by the LR and LDA models. CE revealed the a lack of superiority for one model over the other, but the results showed that LR performed better than LDA for the B and Q indices in all situations. No significant effect for sample size on CE was noted for selection of an optimal model. Assessment of the accuracy of prediction of real data indicated that the B and Q indices are appropriate for selection of an optimal model. The results of this study showed that LR performs better in some cases and LDA in others when based on CE. The CE index is not appropriate for classification, although the B and Q indices performed better and offered more efficient criteria for comparison and discrimination between groups.

Elasticity of Pargasite Amphibole: A Hydrous Phase at Mid Lithospheric Discontinuity

NASA Astrophysics Data System (ADS)

Peng, Y.; Mookherjee, M.

2017-12-01

Mid Lithospheric Discontinuity (MLD) is characterized by a low shear wave velocity ( 3 to 10 %). In cratons, the depth of MLD varies between 80 and 100 km. The reduction of the shear wave velocity at MLD is similar to what is observed in the lithosphere-asthenosphere boundary (LAB). Such low velocity at MLD could be caused by partial melting, temperature induced grain boundary sliding, changes in the elastic anisotropy, and/or metasomatism which may lead to the formation of hydrous phases including mica and amphibole. Thus, it is clear that in order to assess the role of metasomatism at MLD, we need better constraints on the elasticity of hydrous phases. However, such elasticity data are scarce. In this study, we explore elasticity of pargasite amphibole [NaCa2(Mg4Al)(Si6Al2)O22(OH)2] using density functional theory (DFT) with local density approximation (LDA) and generalized gradient approximation (GGA). We find that the pressure-volume results can be adequately described by a finite strain equation with the bulk modulus, K0 being 102 and 85 GPa for LDA and GGA respectively. We also determined the full elastic constant tensor (Cij) using the finite difference method. The bulk modulus, K0 determined from the full elastic constant tensor is 104 GPa for LDA and 87 GPa for GGA. The shear modulus, G0 determined from the full elastic constant tensor is 64 GPa for LDA and 58 GPa for GGA. The bulk and shear moduli predicted with LDA are 5 and 1 % stiffer than the recent results [1]. In contrast, the bulk and shear moduli predicted with GGA are 12 and 10 % softer compared to the recent results [1]. The full elastic constant tensor for pargasite shows significant anisotropy. For instance, LDA predicts compressional (AVP) and shear (AVS) wave anisotropy of 22 and 20 % respectively. At higher pressure, elastic moduli stiffen. However, temperature is likely to have an opposite effect on the elasticity and this remains largely unknown for pargasite. Compared to the major mantle minerals, pargasite has softer elastic constants and significant anisotropy and may explain the reduction in shear wave velocity at MLD. Reference: [1] Brown, J. M., Abramson, E. H.,2016, Phys. Earth Planet. Int., 261, 161-171. Acknowledgement: This work is supported by US NSF award EAR 1639552.

Properties of real metallic surfaces: Effects of density functional semilocality and van der Waals nonlocality

PubMed Central

Patra, Abhirup; Bates, Jefferson E.; Sun, Jianwei; Perdew, John P.

2017-01-01

We have computed the surface energies, work functions, and interlayer surface relaxations of clean (111), (100), and (110) surfaces of Al, Cu, Ru, Rh, Pd, Ag, Pt, and Au. We interpret the surface energy from liquid metal measurements as the mean of the solid-state surface energies over these three lowest-index crystal faces. We compare experimental (and random phase approximation) reference values to those of a family of nonempirical semilocal density functionals, from the basic local density approximation (LDA) to our most advanced general purpose meta-generalized gradient approximation, strongly constrained and appropriately normed (SCAN). The closest agreement is achieved by the simplest density functional LDA, and by the most sophisticated one, SCAN+rVV10 (Vydrov–Van Voorhis 2010). The long-range van der Waals interaction, incorporated through rVV10, increases the surface energies by about 10%, and increases the work functions by about 3%. LDA works for metal surfaces through two known error cancellations. The Perdew–Burke–Ernzerhof generalized gradient approximation tends to underestimate both surface energies (by about 24%) and work functions (by about 4%), yielding the least-accurate results. The amount by which a functional underestimates these surface properties correlates with the extent to which it neglects van der Waals attraction at intermediate and long range. Qualitative arguments are given for the signs of the van der Waals contributions to the surface energy and work function. A standard expression for the work function in Kohn–Sham (KS) theory is shown to be valid in generalized KS theory. Interlayer relaxations from different functionals are in reasonable agreement with one another, and usually with experiment. PMID:29042509

G W (Γ ) method without the Bethe-Salpeter equation for photoabsorption energies of spin-polarized systems

NASA Astrophysics Data System (ADS)

Isobe, Tomoharu; Kuwahara, Riichi; Ohno, Kaoru

2018-06-01

The one-shot G W method, beginning with the local density approximation (LDA), enables one to calculate photoemission and inverse photoemission spectra. In order to calculate photoabsorption spectra, one had to additionally solve the Bethe-Salpeter equation (BSE) for the two-particle (electron-hole) Green's function, which doubly induces evaluation errors. It has been recently reported that the G W +BSE method significantly underestimates the experimental photoabsorption energies (PAEs) of small molecules. In order to avoid these problems, we propose to apply the G W (Γ ) method not to the neutral ground state but to the cationic state to calculate PAEs without solving the BSE, which allows a rigorous one-to-one correspondence between the photoabsorption peak and the "extended" quasiparticle level. We applied the self-consistent linearized G W Γ method including the vertex correction Γ to our method, and found that this method gives the PAEs of B, Na3, and Li3 to within 0.1 eV accuracy.

Theoretical investigation of structural, mechanical and electronic properties of GaAs1-xNx alloys under ambient and high pressure

NASA Astrophysics Data System (ADS)

Li, Jian; Han, Xiuxun; Dong, Chen; Fan, Changzeng

2017-12-01

Using first-principles total energy calculations, we have studied the structural, mechanical and electronic properties of GaAs1-xNx ternary semiconductor alloys with the zinc-blende crystal structure over the whole nitrogen concentration range (with x from 0 to 1) within density functional theory (DFT) framework. To obtain the ideal band gap, we employ the semi-empirical approach called local density approximation plus the multi-orbital mean-field Hubbard model (LDA+U). The calculated results illustrate the varying lattice constants and band gap in GaAs1-xNx alloys as functions of the nitrogen concentration x. According to the pressure dependence of the lattice constants and volume, the higher N concentration alloy exhibits the better anti-compressibility. In addition, an increasing band gap is predicted under 20 GPa pressure for GaAs1-xNx alloys.

On the difference between the pyroxenes LiFeSi2O6 and LiFeGe2O6 in their magnetic structures and spin orientations

NASA Astrophysics Data System (ADS)

Lee, Changhoon; Hong, Jisook; Shim, Ji Hoon; Whangbo, Myung-Hwan

2014-03-01

The clinopyroxenes LiFeSi2O6 and LiFeGe2O6, crystallizing in a monoclinic space group P21/c, are isostructural and isoelectronic Their crystal structures are made up of zigzag chains of edge-sharing FeO6 octahedra containing high-spin Fe3 + ions, which run along the c direction. Despite this structural similarity, the two have quite different magnetic structures and spin orientations. In LiFeSi2O6 the Fe spins have a ferromagnetic coupling within the zigzag chains along c and such FM chains have an antiferromagnetic coupling along a. In contrast, in LiFeGe2O6, the spins have an AFM coupling within the zigzag chains along c and such FM chains have an ↑ ↑ ↓ ↓ coupling along a. In addition, the spin orientation is parallel to c in LiFeSi2O6, but is perpendicular to c in LiFeGe2O6. To explain these differences in the magnetic structure and spin orientation, we evaluated the spin exchange parameters by performing energy mapping analysis based on LDA +U and GGA +U calculations and also by evaluating the magnetocrystalline anisotropy energies in terms of GGA +U +SOC and LDA +U +SOC calculations. Our study show that the magnetic structures and spin orientations of LiFeSi2O6 and LiFeGe2O6 are better described by LDA +U and LDA +U +SOC calculations. This research was supported by Basic Science Research Program through the National Research Foundation of Korea(NRF) funded by the Ministry of Education(2013R1A1A2060341).

Multigrid based First-Principles Molecular Dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fattebert, Jean-Luc; Osei-Kuffuor, Daniel; Dunn, Ian

2017-06-01

MGmol ls a First-Principles Molecular Dynamics code. It relies on the Born-Oppenheimer approximation and models the electronic structure using Density Functional Theory, either LDA or PBE. Norm-conserving pseudopotentials are used to model atomic cores.

A first-principles study of elastic and diffusion properties of magnesium based alloys

NASA Astrophysics Data System (ADS)

Ganeshan, Swetha

2011-12-01

In this thesis, the influence of alloying elements on the elastic and diffusion properties of Magnesium (Mg) has been studied based on first-principles density functional theory. The stress-strain method has been used to predict the elastic constants of the Mg based alloys studied herein. This method involves calculating the resultant change in stress due to application of strain. The validity of this method has been successfully tested for both 0K as well as at finite temperatures. The elastic constants predicted in this work have been correlated to ductility, fracture toughness, stiffness, elastic anisotropy and bond directionality, thus providing a better understanding of the influence of alloying elements on the mechanical and physical properties of Mg. Elastic constants, as a function of temperature have been predicted using first-principles quasi-static approximation. In this approach elastic stiffness coefficients calculated with respect to volume (cij( V)) have been correlated to the equilibrium volume as a function of temperature V(T) from phonon calculations to obtain temperature dependence of elastic stiffness coefficients cij(T). To compare our calculated temperature dependent elastic constants with that of experiments an isentropic correction term has been introduced. It is seen that the influence of this isentropic correction term on the elastic constants becomes significant at high temperatures. The quasi-static approximation has been primarily applied to calculate temperature dependent elastic constants of Mg2Ge, Mg2Si, Mg 2Sn and Mg2Pb. In the case of dilute Mg alloys, a 36 atom supercell with 35 atoms of Mg and one atom of the alloying impurity has been used for calculating the corresponding elastic constants. It is seen that there is a direct correspondence between the trends in the elastic constants and the lattice parameters of all the Mg based alloys studied herein. Elements that cause a decrease (increase) in the lattice constants result in an increase (decrease) in the bulk modulus. Self-diffusion calculations of Mg have been performed within both LDA and GGA. It is seen that, in the absence of surface corrections, while results of the two approximations (i.e. LDA and GGA) bound experimental data, better agreement is seen with respect to results from LDA, in comparison with experimental measurements. The effect of thermal expansion on the diffusivity of Mg has been studied using both HA and QHA. It is seen that the influence of anharmonicity on the diffusivity of Mg is negligible. Self-diffusion of Mg is faster in the basal plane than between adjacent basal planes. Partial correlation factors corresponding to the diffusion of a Mg atom from one basal plane to the adjacent basal plane, i.e. fBx and fBz, decrease with temperature whereas the partial correlation factor corresponding to the diffusion of Mg atom within the basal plane, i.e. fAx , increases with temperature. The ratio of jump frequencies w⊥/w∥ for self-diffusion of Mg increase with increase in temperature. The method used to calculate self-diffusion coefficients has been extended to compute impurity diffusion coefficients of Al, Ca, Sn and Zn in Mg. For these calculations, a 36 atom supercell with 1 vacant site and 1 impurity has been used. The 8-frequencey model has been implemented to obtain the different atom jump frequencies in order to calculate impurity diffusion coefficients in Mg. The trend in the impurity diffusion coefficients, with the exception of DZn-Mg is as follows: D Mg-Ca>DMg>DMg-Sn> DMg-Al. For impurity diffusion of Zn in Mg, at high temperatures DMg-Zn overlaps with that of DMg-Al , while at low temperatures it overlaps with that of D Mg-Sn. The different atom jump frequencies computed during the diffusion calculations are seen to be temperature dependent, increasing with increase in temperature. The correlation factors for all the alloy systems considered herein, is close to 1. This is expected to be due to the close packing of Mg lattice. (Abstract shortened by UMI.)

Wavelets in electronic structure calculations

NASA Astrophysics Data System (ADS)

Modisette, Jason Perry

1997-09-01

Ab initio calculations of the electronic structure of bulk materials and large clusters are not possible on today's computers using current techniques. The storage and diagonalization of the Hamiltonian matrix are the limiting factors in both memory and execution time. The scaling of both quantities with problem size can be reduced by using approximate diagonalization or direct minimization of the total energy with respect to the density matrix in conjunction with a localized basis. Wavelet basis members are much more localized than conventional bases such as Gaussians or numerical atomic orbitals. This localization leads to sparse matrices of the operators that arise in SCF multi-electron calculations. We have investigated the construction of the one-electron Hamiltonian, and also the effective one- electron Hamiltonians that appear in density-functional and Hartree-Fock theories. We develop efficient methods for the generation of the kinetic energy and potential matrices, the Hartree and exchange potentials, and the local exchange-correlation potential of the LDA. Test calculations are performed on one-electron problems with a variety of potentials in one and three dimensions.

Electronic Properties of Curved and Defective 2-D BN Nanostructures

NASA Astrophysics Data System (ADS)

Beach, Kory; Terrones, Humberto; Raeliarijaona, Aldo; Siegel, Ross; Florio, Fred

Density functional theory (DFT) with local density approximation (LDA) pseudopotentials is used to calculate the band structure and density of states of various novel 2-D BN nanostructures. Three types of systems are studied: Schwarzites, a Haeckelite, and an h-BN monolayer. Schwarzites are negatively curved structures in which the curvature is due to the introduction of octagonal rings of alternating boron and nitrogen atoms. In particular, three families of Schwarzites are analyzed: P, G and IWP. The Haeckelites on the other hand, are flat layers composed of squares and octagons of BN. It is found that all these BN allotropes are metastable in which the band gap is direct and smaller than the most stable system, h-BN. National Science Foundation (EFRI-1433311).

Calculation of longitudinal polarizability and second hyperpolarizability of polyacetylene with the coupled perturbed Hartree-Fock/Kohn-Sham scheme: where it is shown how finite oligomer chains tend to the infinite periodic polymer.

PubMed

Lacivita, Valentina; Rèrat, Michel; Orlando, Roberto; Ferrero, Mauro; Dovesi, Roberto

2012-03-21

The longitudinal polarizability, α(xx), and second hyperpolarizability, γ(xxxx), of polyacetylene are evaluated by using the coupled perturbed Hartree-Fock/Kohn-Sham (HF/KS) scheme as implemented in the periodic CRYSTAL code and a split valence type basis set. Four different density functionals, namely local density approximation (LDA) (pure local), Perdew-Becke-Ernzerhof (PBE) (gradient corrected), PBE0, and B3LYP (hybrid), and the Hartree-Fock Hamiltonian are compared. It is shown that very tight computational conditions must be used to obtain well converged results, especially for γ(xxxx), that is, very sensitive to the number of k(->) points in reciprocal space when the band gap is small (as for LDA and PBE), and to the extension of summations of the exact exchange series (HF and hybrids). The band gap in LDA is only 0.01 eV: at least 300 k(->) points are required to obtain well converged total energy and equilibrium geometry, and 1200 for well converged optical properties. Also, the exchange series convergence is related to the band gap. The PBE0 band gap is as small as 1.4 eV and the exchange summation must extend to about 130 Å from the origin cell. Total energy, band gap, equilibrium geometry, polarizability, and second hyperpolarizability of oligomers -(C(2)H(2))(m)-, with m up to 50 (202 atoms), and of the polymer have been compared. It turns out that oligomers of that length provide an extremely poor representation of the infinite chain polarizability and hyperpolarizability when the gap is smaller than 0.2 eV (that is, for LDA and PBE). Huge differences are observed on α(xx) and γ(xxxx) of the polymer when different functionals are used, that is in connection to the well-known density functional theory (DFT) overshoot, reported in the literature about short oligomers: for the infinite model the ratio between LDA (or PBE) and HF becomes even more dramatic (about 500 for α(xx) and 10(10) for γ(xxxx)). On the basis of previous systematic comparisons of results obtained with various approaches including DFT, HF, Moller-Plesset (MP2) and coupled cluster for finite chains, we can argue that, for the infinite chain, the present HF results are the most reliable. © 2012 American Institute of Physics

All-electron quasiparticle self-consistent GW band structures for SrTiO 3 including lattice polarization corrections in different phases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhandari, Churna; van Schilfgaarde, Mark; Kotani, Takao

The electronic band structure of SrTiO3 is investigated in the all-electron quasiparticle self-consistent GW (QSGW) approximation. Unlike previous pseudopotential-based QSGW or single-shot G0W0 calculations, the gap is found to be significantly overestimated compared to experiment. After putting in a correction for the underestimate of the screening by the random phase approximation in terms of a 0.8Σ approach, the gap is still overestimated. The 0.8Σ approach is discussed and justified in terms of various recent literature results including electron-hole corrections. Adding a lattice polarization correction (LPC) in the q→0 limit for the screening of W, agreement with experiment is recovered. Themore » LPC is alternatively estimated using a polaron model. Here, we apply our approach to the cubic and tetragonal phases as well as a hypothetical layered postperovskite structure and find that the local density approximation (LDA) to GW gap correction is almost independent of structure.« less

All-electron quasiparticle self-consistent GW band structures for SrTiO 3 including lattice polarization corrections in different phases

DOE PAGES

Bhandari, Churna; van Schilfgaarde, Mark; Kotani, Takao; ...

2018-01-23

The electronic band structure of SrTiO3 is investigated in the all-electron quasiparticle self-consistent GW (QSGW) approximation. Unlike previous pseudopotential-based QSGW or single-shot G0W0 calculations, the gap is found to be significantly overestimated compared to experiment. After putting in a correction for the underestimate of the screening by the random phase approximation in terms of a 0.8Σ approach, the gap is still overestimated. The 0.8Σ approach is discussed and justified in terms of various recent literature results including electron-hole corrections. Adding a lattice polarization correction (LPC) in the q→0 limit for the screening of W, agreement with experiment is recovered. Themore » LPC is alternatively estimated using a polaron model. Here, we apply our approach to the cubic and tetragonal phases as well as a hypothetical layered postperovskite structure and find that the local density approximation (LDA) to GW gap correction is almost independent of structure.« less

Magnetic properties and stability of Cu3V2O8 compound in the different phases

NASA Astrophysics Data System (ADS)

Jezierski, Andrzej

2016-11-01

The magnetic and thermodynamic properties of Cu3V2O8 compound in four structures (P-1, P21/c, P21/m and Cmca) are reported. The calculations are performed by using the Full-Potential Local Orbital Minimum Basis (FPLO) and Vienna ab initio Simulation Package (VASP) methods. We have applied the local density approximation (LDA) with the generalized gradient corrections (GGA). The effect of electron correlations was also included in GGA+U approximation. The thermodynamic properties were obtained in the quasi-harmonic Debye-Grüneisen model using the equation of states (EOS) in the form of Poirier-Tarantola. Our ab-intio results indicate that α (P-1) phase is stable below 1.87 GPa, β (P21/c) exists in the region 1.87

Efficient and accurate approach to modeling the microstructure and defect properties of LaCoO3

NASA Astrophysics Data System (ADS)

Buckeridge, J.; Taylor, F. H.; Catlow, C. R. A.

2016-04-01

Complex perovskite oxides are promising materials for cathode layers in solid oxide fuel cells. Such materials have intricate electronic, magnetic, and crystalline structures that prove challenging to model accurately. We analyze a wide range of standard density functional theory approaches to modeling a highly promising system, the perovskite LaCoO3, focusing on optimizing the Hubbard U parameter to treat the self-interaction of the B-site cation's d states, in order to determine the most appropriate method to study defect formation and the effect of spin on local structure. By calculating structural and electronic properties for different magnetic states we determine that U =4 eV for Co in LaCoO3 agrees best with available experiments. We demonstrate that the generalized gradient approximation (PBEsol +U ) is most appropriate for studying structure versus spin state, while the local density approximation (LDA +U ) is most appropriate for determining accurate energetics for defect properties.

Influence of warfarin and low-dose aspirin on the outcomes of geriatric patients with traumatic intracranial hemorrhage resulting from ground-level fall.

PubMed

Inamasu, Joji; Nakatsukasa, Masashi; Miyatake, Satoru; Hirose, Yuichi

2012-10-01

Ground-level fall is the most common cause of traumatic intracranial hemorrhage (TICH) in the elderly, and is a major cause of morbidity and mortality in that population. A retrospective study was carried out to evaluate whether the use of warfarin/low-dose aspirin (LDA) is predictive of unfavorable outcomes in geriatric patients who sustain a fall-induced TICH. Charts of 76 geriatric patients (≥ 65 years-of-age) with fall-induced TICH were reviewed. The number of patients taking warfarin and LDA was 12 and 21, respectively, whereas the other 43 took neither medication (non-user group). The frequency of patients with unfavorable outcomes (Glasgow Outcome Scale score of 1-3) at discharge was calculated. Furthermore, variables predictive of unfavorable outcomes were identified by logistic regression analysis. The frequency of patients with unfavorable outcomes was 75% in the warfarin group, 33% in the LDA group and 27% in the non-user group, respectively. The risk of having unfavorable outcomes was significantly higher in the warfarin group compared with the LDA group (P = 0.03) and non-user group (P < 0.01). Logistic regression analysis showed that variables predictive of unfavorable outcomes were: age, initial Glasgow Coma Scale score ≤ 13 and presence of midline shift ≥ 5 mm. The use of warfarin, but not of LDA, might be associated with unfavorable outcomes in elderly with fall-induced TICH. The risk of TICH should be communicated properly to elderly taking warfarin. The information might be important not only to trauma surgeons who take care of injured elderly, but also to geriatric physicians who prescribe warfarin/LDA to them. © 2012 Japan Geriatrics Society.

Modeling and analysis of a large deployable antenna structure

NASA Astrophysics Data System (ADS)

Chu, Zhengrong; Deng, Zongquan; Qi, Xiaozhi; Li, Bing

2014-02-01

One kind of large deployable antenna (LDA) structure is proposed by combining a number of basic deployable units in this paper. In order to avoid vibration caused by fast deployment speed of the mechanism, a braking system is used to control the spring-actuated system. Comparisons between the LDA structure and a similar structure used by the large deployable reflector (LDR) indicate that the former has potential for use in antennas with up to 30 m aperture due to its lighter weight. The LDA structure is designed to form a spherical surface found by the least square fitting method so that it can be symmetrical. In this case, the positions of the terminal points in the structure are determined by two principles. A method to calculate the cable network stretched on the LDA structure is developed, which combines the original force density method and the parabolic surface constraint. Genetic algorithm is applied to ensure that each cable reaches a desired tension, which avoids the non-convergence issue effectively. We find that the pattern for the front and rear cable net must be the same when finding the shape of the rear cable net, otherwise anticlastic surface would generate.

DFT study of CdS-PVA film

NASA Astrophysics Data System (ADS)

Bala, Vaneeta; Tripathi, S. K.; Kumar, Ranjan

2015-02-01

Density functional theory has been applied to study cadmium sulphide-polyvinyl alcohol nanocomposite film. Structural models of two isotactic-polyvinyl alcohol (I-PVA) chains around one cadmium sulphide nanoparticle is considered in which each chain consists three monomer units of [-(CH2CH(OH))-]. All of the hydroxyl groups in I-PVA chains are directed to cadmium sulphide nanoparticle. Electronic and structural properties are investigated using ab-intio density functional code, SIESTA. Structural optimizations are done using local density approximations (LDA). The exchange correlation functional of LDA is parameterized by the Ceperley-Alder (CA) approach. The core electrons are represented by improved Troulier-Martins pseudopotentials. Densities of states clearly show the semiconducting nature of cadmium sulphide polyvinyl alcohol nanocomposite.

Dynamical screening of the van der Waals interaction between graphene layers.

PubMed

Dappe, Y J; Bolcatto, P G; Ortega, J; Flores, F

2012-10-24

The interaction between graphene layers is analyzed combining local orbital DFT and second order perturbation theory. For this purpose we use the linear combination of atomic orbitals-orbital occupancy (LCAO-OO) formalism, that allows us to separate the interaction energy as the sum of a weak chemical interaction between graphene layers plus the van der Waals interaction (Dappe et al 2006 Phys. Rev. B 74 205434). In this work, the weak chemical interaction is calculated by means of corrected-LDA calculations using an atomic-like sp(3)d(5) basis set. The van der Waals interaction is calculated by means of second order perturbation theory using an atom-atom interaction approximation and the atomic-like-orbital occupancies. We also analyze the effect of dynamical screening in the van der Waals interaction using a simple model. We find that this dynamical screening reduces by 40% the van der Waals interaction. Taking this effect into account, we obtain a graphene-graphene interaction energy of 70 ± 5 meV/atom in reasonable agreement with the experimental evidence.

Cd{sub 0.9375}Mn{sub 0.0625}S diluted magnetic semiconductor: A DFT study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rani, Anita; Kaur, Kulwinder; Kumar, Ranjan, E-mail: ranianita64@gmail.com

We studied the spin polarized electronic band structures and magnetic properties of the diluted magnetic semiconductor Cd{sub 1-x}Mn{sub x}S in Zinc Blende phase (B3) with 0.0625 Mn by using ab initio method. The calculations were performed by using Density Functional Theory as implemented in the Spanish Initiative for Electronic Simulations with Thousands of Atoms code using local density approximation (LDA). Calculated electronic band structures and magnetic properties of Cd{sub 1-x}Mn{sub x}S are discussed in terms of contribution of Mn 3d{sup 5} 4s{sup 2}, Cd 4d{sup 10} 5s{sup 2}, S 3s{sup 2} 3p{sup 4} orbitals. The total magnetic moment is foundmore » to be 5.00 µb for Cd{sub 1−x}Mn{sub x}S at x=0.0625. This value indicate that Mn atom adds no hole carrier to the perfect CdS crystal. We found that Mn doped systems are ferromagnetic. Calculated results are in good agreement with previous studies.« less

Analysis and design of fiber-coupled high-power laser diode array

NASA Astrophysics Data System (ADS)

Zhou, Chongxi; Liu, Yinhui; Xie, Weimin; Du, Chunlei

2003-11-01

A conclusion that a single conventional optical system could not realize fiber coupled high-power laser diode array is drawn based on the BPP of laser beam. According to the parameters of coupled fiber, a method to couple LDA beams into a single multi-mode fiber including beams collimating, shaping, focusing and coupling is present. The divergence angles after collimating are calculated and analyzed; the shape equation of the collimating micro-lenses array is deprived. The focusing lens is designed. A fiber coupled LDA result with the core diameter of 800 um and numeric aperture of 0.37 is gotten.

Influence of xc functional on thermal-elastic properties of Ceria: A DFT-based Debye-Grüneisen model approach

NASA Astrophysics Data System (ADS)

Lee, Ji-Hwan; Tak, Youngjoo; Lee, Taehun; Soon, Aloysius

Ceria (CeO2-x) is widely studied as a choice electrolyte material for intermediate-temperature (~ 800 K) solid oxide fuel cells. At this temperature, maintaining its chemical stability and thermal-mechanical integrity of this oxide are of utmost importance. To understand their thermal-elastic properties, we firstly test the influence of various approximations to the density-functional theory (DFT) xc functionals on specific thermal-elastic properties of both CeO2 and Ce2O3. Namely, we consider the local-density approximation (LDA), the generalized gradient approximation (GGA-PBE) with and without additional Hubbard U as applied to the 4 f electron of Ce, as well as the recently popularized hybrid functional due to Heyd-Scuseria-Ernzehof (HSE06). Next, we then couple this to a volume-dependent Debye-Grüneisen model to determine the thermodynamic quantities of ceria at arbitrary temperatures. We find an explicit description of the strong correlation (e.g. via the DFT + U and hybrid functional approach) is necessary to have a good agreement with experimental values, in contrast to the mean-field treatment in standard xc approximations (such as LDA or GGA-PBE). We acknowledge support from Samsung Research Funding Center of Samsung Electronics (SRFC-MA1501-03).

Improving Lightning and Precipitation Prediction of Severe Convection Using Lightning Data Assimilation With NCAR WRF-RTFDDA

NASA Astrophysics Data System (ADS)

Wang, Haoliang; Liu, Yubao; Cheng, William Y. Y.; Zhao, Tianliang; Xu, Mei; Liu, Yuewei; Shen, Si; Calhoun, Kristin M.; Fierro, Alexandre O.

2017-11-01

In this study, a lightning data assimilation (LDA) scheme was developed and implemented in the National Center for Atmospheric Research Weather Research and Forecasting-Real-Time Four-Dimensional Data Assimilation system. In this LDA method, graupel mixing ratio (qg) is retrieved from observed total lightning. To retrieve qg on model grid boxes, column-integrated graupel mass is first calculated using an observation-based linear formula between graupel mass and total lightning rate. Then the graupel mass is distributed vertically according to the empirical qg vertical profiles constructed from model simulations. Finally, a horizontal spread method is utilized to consider the existence of graupel in the adjacent regions of the lightning initiation locations. Based on the retrieved qg fields, latent heat is adjusted to account for the latent heat releases associated with the formation of the retrieved graupel and to promote convection at the observed lightning locations, which is conceptually similar to the method developed by Fierro et al. Three severe convection cases were studied to evaluate the LDA scheme for short-term (0-6 h) lightning and precipitation forecasts. The simulation results demonstrated that the LDA was effective in improving the short-term lightning and precipitation forecasts by improving the model simulation of the qg fields, updrafts, cold pool, and front locations. The improvements were most notable in the first 2 h, indicating a highly desired benefit of the LDA in lightning and convective precipitation nowcasting (0-2 h) applications.

First principles study of hydrogen bond symmetrization in δ-AlOOH

NASA Astrophysics Data System (ADS)

Pillai, Sharad Babu; Jha, Prafulla K.; Padmalal, Akash; Maurya, D. M.; Chamyal, L. S.

2018-03-01

The high pressure behaviour of the hydrous mineral δ-AlOOH has been investigated by many experimental and theoretical studies, but the discrepancy in predicting the value of hydrogen symmetrization pressure was not resolved. Here, we investigated the high pressure behaviour of δ-AlOOH using first principles calculations and found that with proper optimization using pressure routine control, local density approximation (LDA) predicts the hydrogen symmetrization pressure as 15 GPa which is in good agreement with the experimentally predicted value which resolves the existing discrepancy and hence proving the validity of LDA in predicting the hydrogen symmetrization pressure. We further studied the compressibility behaviour of δ-AlOOH at low pressures and confirmed the P21nm to Pnnm transition of δ-AlOOH shown by the experimental work [Kuribayashi et al., Phys. Chem. Miner. 41, 303-312 (2014)]. We have also analysed the dependence of elastic constants, elastic moduli, sound velocities, and Raman spectrum of δ-AlOOH with pressure and found that a subtle change in the position of the hydrogen atom at hydrogen symmetrization pressure results into drastic changes in elastic and vibrational properties. Further, this study has been used to discuss the seismic anomalies observed in the upper mantle beneath the Deccan Volcanic Province in India and the Java subduction zone in the eastern flank of the Indian Ocean.

Exchange potential from the common energy denominator approximation for the Kohn-Sham Green's function: Application to (hyper)polarizabilities of molecular chains

NASA Astrophysics Data System (ADS)

Grüning, M.; Gritsenko, O. V.; Baerends, E. J.

2002-04-01

An approximate Kohn-Sham (KS) exchange potential vxσCEDA is developed, based on the common energy denominator approximation (CEDA) for the static orbital Green's function, which preserves the essential structure of the density response function. vxσCEDA is an explicit functional of the occupied KS orbitals, which has the Slater vSσ and response vrespσCEDA potentials as its components. The latter exhibits the characteristic step structure with "diagonal" contributions from the orbital densities |ψiσ|2, as well as "off-diagonal" ones from the occupied-occupied orbital products ψiσψj(≠1)σ*. Comparison of the results of atomic and molecular ground-state CEDA calculations with those of the Krieger-Li-Iafrate (KLI), exact exchange (EXX), and Hartree-Fock (HF) methods show, that both KLI and CEDA potentials can be considered as very good analytical "closure approximations" to the exact KS exchange potential. The total CEDA and KLI energies nearly coincide with the EXX ones and the corresponding orbital energies ɛiσ are rather close to each other for the light atoms and small molecules considered. The CEDA, KLI, EXX-ɛiσ values provide the qualitatively correct order of ionizations and they give an estimate of VIPs comparable to that of the HF Koopmans' theorem. However, the additional off-diagonal orbital structure of vxσCEDA appears to be essential for the calculated response properties of molecular chains. KLI already considerably improves the calculated (hyper)polarizabilities of the prototype hydrogen chains Hn over local density approximation (LDA) and standard generalized gradient approximations (GGAs), while the CEDA results are definitely an improvement over the KLI ones. The reasons of this success are the specific orbital structures of the CEDA and KLI response potentials, which produce in an external field an ultranonlocal field-counteracting exchange potential.

First principles study on structural, electronic and optical properties of Ga1-xBxP ternary alloys (x = 0, 0.25, 0.5, 0.75 and 1)

NASA Astrophysics Data System (ADS)

Hoat, D. M.; Rivas Silva, J. F.; Méndez Blas, A.

2018-07-01

The structural, electronic and optical properties of GaP, BP binary compounds and their ternary alloys Ga1-xBxP (x = 0.25, 0.5 and 0.75) have been studied by full-potential linearized augmented plane wave (FP-LAPW) method within the framework of density functional theory (DFT) as implemented in WIEN2k package. Local density approximation (LDA) and generalized gradient approximation (GGA) as proposed by Perdew-Burke-Ernzerhof (PBE), Wu-Cohen (WC) and PBE for solid (PBESol) were used for treatment of exchange-correlation effect in calculations. Additionally, the Tran-Blaha modified Becke-Johnson (mBJ) potential was also employed for electronic and optical calculations due to that it gives very accurate band gap of solids. As B concentration increases, the lattice constant reduces and the energy band gap firstly decreases for small composition x and then it shows increasing trend until pure BP. Our results show that the indirect-direct band gap transition can be reached from x = 0.33. The linear optical properties, such as reflectivity, absorption coefficient, refractive index and optical conductivity of binary compounds and ternary alloys were derived from their calculated complex dielectric function in wide energy range up to 30 eV, and the alloying effect on these properties was also analyzed in detail.

Electronic properties of graphene and effect of doping on the same

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nag, Abhinav, E-mail: abhinavn76@gmail.com; Kumar, Jagdish, E-mail: jagdishphysicist@gmail.com; Sastri, O. S. K. S., E-mail: sastri.osks@gmail.com

2015-05-15

The electronic structure of pure and doped two dimensional crystalline material graphene have been computed and analyzed. Density functional theory has been employed to perform calculations. The electronic exchange and correlations are considered using local density approximation (LDA). The doped material is studied within virtual crystal approximation (VCA) upto 0.15e excess as well as deficient charge per unit cell. Full Potential Linear Augmented Plane Wave basis as implemented in ELK code has been used to perform the calculations. To ensures the monolayer of graphene, distance after which energy is almost constant when interlayer seperation is varied, is taken as separatingmore » distance between the layers. The obtained density of states and band structure is analyzed. Results show that there is zero band gap in undoped graphene and conduction and valence band meets at fermi level at symmetry point K. PDOS graph shows that near the fermi level the main contribution is due to 2p{sub z} electrons. By using VCA, calculations for doped graphene are done and the results for doped graphene are compared with undoped graphene. We found that by electron or hole doping, the point where conduction and valence bands meet can shift below or above the fermi level. The shift in bands seems almost as per rigid band model upto doping concentration studied.« less

A two-stage linear discriminant analysis via QR-decomposition.

PubMed

Ye, Jieping; Li, Qi

2005-06-01

Linear Discriminant Analysis (LDA) is a well-known method for feature extraction and dimension reduction. It has been used widely in many applications involving high-dimensional data, such as image and text classification. An intrinsic limitation of classical LDA is the so-called singularity problems; that is, it fails when all scatter matrices are singular. Many LDA extensions were proposed in the past to overcome the singularity problems. Among these extensions, PCA+LDA, a two-stage method, received relatively more attention. In PCA+LDA, the LDA stage is preceded by an intermediate dimension reduction stage using Principal Component Analysis (PCA). Most previous LDA extensions are computationally expensive, and not scalable, due to the use of Singular Value Decomposition or Generalized Singular Value Decomposition. In this paper, we propose a two-stage LDA method, namely LDA/QR, which aims to overcome the singularity problems of classical LDA, while achieving efficiency and scalability simultaneously. The key difference between LDA/QR and PCA+LDA lies in the first stage, where LDA/QR applies QR decomposition to a small matrix involving the class centroids, while PCA+LDA applies PCA to the total scatter matrix involving all training data points. We further justify the proposed algorithm by showing the relationship among LDA/QR and previous LDA methods. Extensive experiments on face images and text documents are presented to show the effectiveness of the proposed algorithm.

Better band gaps with asymptotically corrected local exchange potentials

NASA Astrophysics Data System (ADS)

Singh, Prashant; Harbola, Manoj K.; Hemanadhan, M.; Mookerjee, Abhijit; Johnson, D. D.

2016-02-01

We formulate a spin-polarized van Leeuwen and Baerends (vLB) correction to the local density approximation (LDA) exchange potential [R. van Leeuwen and E. J. Baerends, Phys. Rev. A 49, 2421 (1994), 10.1103/PhysRevA.49.2421] that enforces the ionization potential (IP) theorem following T. Stein et al. [Phys. Rev. Lett. 105, 266802 (2010), 10.1103/PhysRevLett.105.266802]. For electronic-structure problems, the vLB correction replicates the behavior of exact-exchange potentials, with improved scaling and well-behaved asymptotics, but with the computational cost of semilocal functionals. The vLB + IP correction produces a large improvement in the eigenvalues over those from the LDA due to correct asymptotic behavior and atomic shell structures, as shown in rare-gas, alkaline-earth, zinc-based oxides, alkali halides, sulfides, and nitrides. In half-Heusler alloys, this asymptotically corrected LDA reproduces the spin-polarized properties correctly, including magnetism and half-metallicity. We also consider finite-sized systems [e.g., ringed boron nitride (B12N12 ) and graphene (C24)] to emphasize the wide applicability of the method.

Better band gaps with asymptotically corrected local exchange potentials

DOE PAGES

Singh, Prashant; Harbola, Manoj K.; Hemanadhan, M.; ...

2016-02-22

In this study, we formulate a spin-polarized van Leeuwen and Baerends (vLB) correction to the local density approximation (LDA) exchange potential [R. van Leeuwen and E. J. Baerends, Phys. Rev. A 49, 2421 (1994)] that enforces the ionization potential (IP) theorem following T. Stein et al. [Phys. Rev. Lett. 105, 266802 (2010)]. For electronic-structure problems, the vLB correction replicates the behavior of exact-exchange potentials, with improved scaling and well-behaved asymptotics, but with the computational cost of semilocal functionals. The vLB + IP correction produces a large improvement in the eigenvalues over those from the LDA due to correct asymptotic behaviormore » and atomic shell structures, as shown in rare-gas, alkaline-earth, zinc-based oxides, alkali halides, sulfides, and nitrides. In half-Heusler alloys, this asymptotically corrected LDA reproduces the spin-polarized properties correctly, including magnetism and half-metallicity. We also consider finite-sized systems [e.g., ringed boron nitride (B 12N 12) and graphene (C 24)] to emphasize the wide applicability of the method.« less

Dispersion interactions in room-temperature ionic liquids: Results from a non-empirical density functional

NASA Astrophysics Data System (ADS)

Kohanoff, Jorge; Pinilla, Carlos; Youngs, Tristan G. A.; Artacho, Emilio; Soler, José M.

2011-10-01

The role of dispersion or van de Waals (VDW) interactions in imidazolium-based room-temperature ionic liquids is studied within the framework of density functional theory, using a recently developed non-empirical functional [M. Dion, H. Rydberg, E. Schröder, D. C. Langreth, and B. I. Lundqvist, Phys. Rev. Lett. 92, 246401 (2004), 10.1103/PhysRevLett.92.246401], as efficiently implemented in the SIESTA code [G. Román-Pérez and J. M. Soler, Phys. Rev. Lett. 103, 096102 (2009), 10.1103/PhysRevLett.103.096102]. We present results for the equilibrium structure and lattice parameters of several crystalline phases, finding a general improvement with respect to both the local density (LDA) and the generalized gradient approximations (GGA). Similar to other systems characterized by VDW bonding, such as rare gas and benzene dimers as well as solid argon, equilibrium distances and volumes are consistently overestimated by ≈7%, compared to -11% within LDA and 11% within GGA. The intramolecular geometries are retained, while the intermolecular distances and orientations are significantly improved relative to LDA and GGA. The quality is superior to that achieved with tailor-made empirical VDW corrections ad hoc [M. G. Del Pópolo, C. Pinilla, and P. Ballone, J. Chem. Phys. 126, 144705 (2007), 10.1063/1.2715571]. We also analyse the performance of an optimized version of this non-empirical functional, where the screening properties of the exchange have been tuned to reproduce high-level quantum chemical calculations [J. Klimes, D. Bowler, and A. Michaelides, J. Phys.: Condens. Matter 22, 074203 (2010), 10.1088/0953-8984/22/7/074203]. The results for solids are even better with volumes and geometries reproduced within 2% of experimental data. We provide some insight into the issue of polymorphism of [bmim][Cl] crystals, and we present results for the geometry and energetics of [bmim][Tf] and [mmim][Cl] neutral and charged clusters, which validate the use of empirical force fields.

Exchange Energy Density Functionals that reproduce the Linear Response Function of the Free Electron Gas

NASA Astrophysics Data System (ADS)

García-Aldea, David; Alvarellos, J. E.

2009-03-01

We present several nonlocal exchange energy density functionals that reproduce the linear response function of the free electron gas. These nonlocal functionals are constructed following a similar procedure used previously for nonlocal kinetic energy density functionals by Chac'on-Alvarellos-Tarazona, Garc'ia-Gonz'alez et al., Wang-Govind-Carter and Garc'ia-Aldea-Alvarellos. The exchange response function is not known but we have used the approximate response function developed by Utsumi and Ichimaru, even we must remark that the same ansatz can be used to reproduce any other response function with the same scaling properties. We have developed two families of new nonlocal functionals: one is constructed with a mathematical structure based on the LDA approximation -- the Dirac functional for the exchange - and for the second one the structure of the second order gradient expansion approximation is took as a model. The functionals are constructed is such a way that they can be used in localized systems (using real space calculations) and in extended systems (using the momentum space, and achieving a quasilinear scaling with the system size if a constant reference electron density is defined).

Pressure-induced transformations in glassy water: A computer simulation study using the TIP4P/2005 model

NASA Astrophysics Data System (ADS)

Wong, Jessina; Jahn, David A.; Giovambattista, Nicolas

2015-08-01

We study the pressure-induced transformations between low-density amorphous (LDA) and high-density amorphous (HDA) ice by performing out-of-equilibrium molecular dynamics (MD) simulations. We employ the TIP4P/2005 water model and show that this model reproduces qualitatively the LDA-HDA transformations observed experimentally. Specifically, the TIP4P/2005 model reproduces remarkably well the (i) structure (OO, OH, and HH radial distribution functions) and (ii) densities of LDA and HDA at P = 0.1 MPa and T = 80 K, as well as (iii) the qualitative behavior of ρ(P) during compression-induced LDA-to-HDA and decompression-induced HDA-to-LDA transformations. At the rates explored, the HDA-to-LDA transformation is less pronounced than in experiments. By studying the LDA-HDA transformations for a broad range of compression/decompression temperatures, we construct a "P-T phase diagram" for glassy water that is consistent with experiments and remarkably similar to that reported previously for ST2 water. This phase diagram is not inconsistent with the possibility of TIP4P/2005 water exhibiting a liquid-liquid phase transition at low temperatures. A comparison with previous MD simulation studies of SPC/E and ST2 water as well as experiments indicates that, overall, the TIP4P/2005 model performs better than the SPC/E and ST2 models. The effects of cooling and compression rates as well as aging on our MD simulations results are also discussed. The MD results are qualitatively robust under variations of cooling/compression rates (accessible in simulations) and are not affected by aging the hyperquenched glass for at least 1 μs. A byproduct of this work is the calculation of TIP4P/2005 water's diffusion coefficient D(T) at P = 0.1 MPa. It is found that, for T ≥ 210 K, D(T) ≈ (T - TMCT)-γ as predicted by mode coupling theory and in agreement with experiments. For TIP4P/2005 water, TMCT = 209 K and γ = 2.14, very close to the corresponding experimental values TMCT = 221 K and γ = 2.2.

Pressure-induced transformations in glassy water: A computer simulation study using the TIP4P/2005 model.

PubMed

Wong, Jessina; Jahn, David A; Giovambattista, Nicolas

2015-08-21

We study the pressure-induced transformations between low-density amorphous (LDA) and high-density amorphous (HDA) ice by performing out-of-equilibrium molecular dynamics (MD) simulations. We employ the TIP4P/2005 water model and show that this model reproduces qualitatively the LDA-HDA transformations observed experimentally. Specifically, the TIP4P/2005 model reproduces remarkably well the (i) structure (OO, OH, and HH radial distribution functions) and (ii) densities of LDA and HDA at P = 0.1 MPa and T = 80 K, as well as (iii) the qualitative behavior of ρ(P) during compression-induced LDA-to-HDA and decompression-induced HDA-to-LDA transformations. At the rates explored, the HDA-to-LDA transformation is less pronounced than in experiments. By studying the LDA-HDA transformations for a broad range of compression/decompression temperatures, we construct a "P-T phase diagram" for glassy water that is consistent with experiments and remarkably similar to that reported previously for ST2 water. This phase diagram is not inconsistent with the possibility of TIP4P/2005 water exhibiting a liquid-liquid phase transition at low temperatures. A comparison with previous MD simulation studies of SPC/E and ST2 water as well as experiments indicates that, overall, the TIP4P/2005 model performs better than the SPC/E and ST2 models. The effects of cooling and compression rates as well as aging on our MD simulations results are also discussed. The MD results are qualitatively robust under variations of cooling/compression rates (accessible in simulations) and are not affected by aging the hyperquenched glass for at least 1 μs. A byproduct of this work is the calculation of TIP4P/2005 water's diffusion coefficient D(T) at P = 0.1 MPa. It is found that, for T ≥ 210 K, D(T) ≈ (T - T(MCT))(-γ) as predicted by mode coupling theory and in agreement with experiments. For TIP4P/2005 water, T(MCT) = 209 K and γ = 2.14, very close to the corresponding experimental values T(MCT) = 221 K and γ = 2.2.

Ferromagnetic properties of manganese doped iron silicide

NASA Astrophysics Data System (ADS)

Ruiz-Reyes, Angel; Fonseca, Luis F.; Sabirianov, Renat

We report the synthesis of high quality Iron silicide (FeSi) nanowires via Chemical Vapor Deposition (CVD). The materials exhibits excellent magnetic response at room temperature, especially when doped with manganese showing values of 2.0 X 10-04 emu for the FexMnySi nanowires. SEM and TEM characterization indicates that the synthesized nanowires have a diameter of approximately 80nm. MFM measurements present a clear description of the magnetic domains when the nanowires are doped with manganese. Electron Diffraction and XRD measurements confirms that the nanowires are single crystal forming a simple cubic structure with space group P213. First-principle calculations were performed on (111) FeSi surface using the Vienna ab initio simulation package (VASP). The exchange correlations were treated under the Ceperley-Alder (CA) local density approximation (LDA). The Brillouin Zone was sampled with 8x8x1 k-point grid. A total magnetic moment of about 10 μB was obtained for three different surface configuration in which the Iron atom nearest to the surface present the higher magnetization. To study the effect of Mn doping, Fe atom was replaced for a Mn. Stronger magnetization is presented when the Mn atom is close to the surface. The exchange coupling constant have been evaluated calculating the energy difference between the ferromagnetic and anti-ferromagnetic configurations.

Quantum Monte Carlo analysis of a charge ordered insulating antiferromagnet: The Ti 4O 7 Magneli phase

DOE PAGES

Benali, Anouar; Shulenburger, Luke; Krogel, Jaron T.; ...

2016-06-07

The Magneli phase Ti 4O 7 is an important transition metal oxide with a wide range of applications because of its interplay between charge, spin, and lattice degrees of freedom. At low temperatures, it has non-trivial magnetic states very close in energy, driven by electronic exchange and correlation interactions. We have examined three low- lying states, one ferromagnetic and two antiferromagnetic, and calculated their energies as well as Ti spin moment distributions using highly accurate Quantum Monte Carlo methods. We compare our results to those obtained from density functional theory- based methods that include approximate corrections for exchange and correlation.more » Our results confirm the nature of the states and their ordering in energy, as compared with density-functional theory methods. However, the energy differences and spin distributions differ. Here, a detailed analysis suggests that non-local exchange-correlation functionals, in addition to other approximations such as LDA+U to account for correlations, are needed to simultaneously obtain better estimates for spin moments, distributions, energy differences and energy gaps.« less

Heating-induced glass-glass and glass-liquid transformations in computer simulations of water.

PubMed

Chiu, Janet; Starr, Francis W; Giovambattista, Nicolas

2014-03-21

Water exists in at least two families of glassy states, broadly categorized as the low-density (LDA) and high-density amorphous ice (HDA). Remarkably, LDA and HDA can be reversibly interconverted via appropriate thermodynamic paths, such as isothermal compression and isobaric heating, exhibiting first-order-like phase transitions. We perform out-of-equilibrium molecular dynamics simulations of glassy water using the ST2 model to study the evolution of LDA and HDA upon isobaric heating. Depending on pressure, glass-to-glass, glass-to-crystal, glass-to-vapor, as well as glass-to-liquid transformations are found. Specifically, heating LDA results in the following transformations, with increasing heating pressures: (i) LDA-to-vapor (sublimation), (ii) LDA-to-liquid (glass transition), (iii) LDA-to-HDA-to-liquid, (iv) LDA-to-HDA-to-liquid-to-crystal, and (v) LDA-to-HDA-to-crystal. Similarly, heating HDA results in the following transformations, with decreasing heating pressures: (a) HDA-to-crystal, (b) HDA-to-liquid-to-crystal, (c) HDA-to-liquid (glass transition), (d) HDA-to-LDA-to-liquid, and (e) HDA-to-LDA-to-vapor. A more complex sequence may be possible using lower heating rates. For each of these transformations, we determine the corresponding transformation temperature as function of pressure, and provide a P-T "phase diagram" for glassy water based on isobaric heating. Our results for isobaric heating dovetail with the LDA-HDA transformations reported for ST2 glassy water based on isothermal compression/decompression processes [Chiu et al., J. Chem. Phys. 139, 184504 (2013)]. The resulting phase diagram is consistent with the liquid-liquid phase transition hypothesis. At the same time, the glass phase diagram is sensitive to sample preparation, such as heating or compression rates. Interestingly, at least for the rates explored, our results suggest that the LDA-to-liquid (HDA-to-liquid) and LDA-to-HDA (HDA-to-LDA) transformation lines on heating are related, both being associated with the limit of kinetic stability of LDA (HDA).

Heating-induced glass-glass and glass-liquid transformations in computer simulations of water

NASA Astrophysics Data System (ADS)

Chiu, Janet; Starr, Francis W.; Giovambattista, Nicolas

2014-03-01

Water exists in at least two families of glassy states, broadly categorized as the low-density (LDA) and high-density amorphous ice (HDA). Remarkably, LDA and HDA can be reversibly interconverted via appropriate thermodynamic paths, such as isothermal compression and isobaric heating, exhibiting first-order-like phase transitions. We perform out-of-equilibrium molecular dynamics simulations of glassy water using the ST2 model to study the evolution of LDA and HDA upon isobaric heating. Depending on pressure, glass-to-glass, glass-to-crystal, glass-to-vapor, as well as glass-to-liquid transformations are found. Specifically, heating LDA results in the following transformations, with increasing heating pressures: (i) LDA-to-vapor (sublimation), (ii) LDA-to-liquid (glass transition), (iii) LDA-to-HDA-to-liquid, (iv) LDA-to-HDA-to-liquid-to-crystal, and (v) LDA-to-HDA-to-crystal. Similarly, heating HDA results in the following transformations, with decreasing heating pressures: (a) HDA-to-crystal, (b) HDA-to-liquid-to-crystal, (c) HDA-to-liquid (glass transition), (d) HDA-to-LDA-to-liquid, and (e) HDA-to-LDA-to-vapor. A more complex sequence may be possible using lower heating rates. For each of these transformations, we determine the corresponding transformation temperature as function of pressure, and provide a P-T "phase diagram" for glassy water based on isobaric heating. Our results for isobaric heating dovetail with the LDA-HDA transformations reported for ST2 glassy water based on isothermal compression/decompression processes [Chiu et al., J. Chem. Phys. 139, 184504 (2013)]. The resulting phase diagram is consistent with the liquid-liquid phase transition hypothesis. At the same time, the glass phase diagram is sensitive to sample preparation, such as heating or compression rates. Interestingly, at least for the rates explored, our results suggest that the LDA-to-liquid (HDA-to-liquid) and LDA-to-HDA (HDA-to-LDA) transformation lines on heating are related, both being associated with the limit of kinetic stability of LDA (HDA).

Final Technical Report for DE-SC0001878 [Theory and Simulation of Defects in Oxide Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chelikowsky, James R.

2014-04-14

We explored a wide variety of oxide materials and related problems, including materials at the nanoscale and generic problems associated with oxide materials such as the development of more efficient computational tools to examine these materials. We developed and implemented methods to understand the optical and structural properties of oxides. For ground state properties, our work is predominantly based on pseudopotentials and density functional theory (DFT), including new functionals and going beyond the local density approximation (LDA): LDA+U. To study excited state properties (quasiparticle and optical excitations), we use time dependent density functional theory, the GW approach, and GW plusmore » Bethe-Salpeter equation (GW-BSE) methods based on a many-body Green function approaches. Our work focused on the structural, electronic, optical and magnetic properties of defects (such as oxygen vacancies) in hafnium oxide, titanium oxide (both bulk and clusters) and related materials. We calculated the quasiparticle defect states and charge transition levels of oxygen vacancies in monoclinic hafnia. we presented a milestone G0W0 study of two of the crystalline phases of dye-sensitized TiO{sub 2} clusters. We employed hybrid density functional theory to examine the electronic structure of sexithiophene/ZnO interfaces. To identify the possible effect of epitaxial strain on stabilization of the ferromagnetic state of LaCoO{sub 3} (LCO), we compare the total energy of the magnetic and nonmagnetic states of the strained theoretical bulk structure.« less

First principles study of structural, electronic and optical properties of perovskites CaZrO3 and CaHfO3 in cubic phase

NASA Astrophysics Data System (ADS)

Hoat, D. M.; Silva, J. F. Rivas; Blas, A. Méndez

2018-07-01

In this work, we present the first principles calculations for structural, electronic and optical properties of perovskites CaZrO3 and CaHfO3 using the full-potential linearized augmented plane wave method (FP-LAPW) within the framework of density functional theory (DFT) as implemented in WIEN2k package. The exchange-correlation potential is treated with local density approximation (LDA) and generalized gradient approximation (GGA-PBE and PBESol). Additionally, the Tran Blaha modified Becke-Johnson exchange potential (mBJ) also is employed for electronic and optical calculations due to that it gives very accurate band gap of solids. Our obtained structural parameters are in good agreement with experimental datas and other theoretical results. The energy band gap obtained with mBJ is 4.56 eV for CaZrO3 and 5.27 eV for CaHfO3. The hybridization of states of O atom with those of Zr and Hf atoms in CaZrO3 and CaHfO3, respectively, is observed. The spin-orbit coupling effect on electronic properties of considered compounds also is investigated. Finally, the linear optical properties of CaZrO3 and CaHfO3 are derived from their complex dielectric function calculated with mBJ potential for wide energy range up to 45 eV, and all of them analyzed in details.

Stochastic density functional theory at finite temperatures

NASA Astrophysics Data System (ADS)

Cytter, Yael; Rabani, Eran; Neuhauser, Daniel; Baer, Roi

2018-03-01

Simulations in the warm dense matter regime using finite temperature Kohn-Sham density functional theory (FT-KS-DFT), while frequently used, are computationally expensive due to the partial occupation of a very large number of high-energy KS eigenstates which are obtained from subspace diagonalization. We have developed a stochastic method for applying FT-KS-DFT, that overcomes the bottleneck of calculating the occupied KS orbitals by directly obtaining the density from the KS Hamiltonian. The proposed algorithm scales as O (" close=")N3T3)">N T-1 and is compared with the high-temperature limit scaling O Content Coding of Psychotherapy Transcripts Using Labeled Topic Models.

PubMed

Gaut, Garren; Steyvers, Mark; Imel, Zac E; Atkins, David C; Smyth, Padhraic

2017-03-01

Psychotherapy represents a broad class of medical interventions received by millions of patients each year. Unlike most medical treatments, its primary mechanisms are linguistic; i.e., the treatment relies directly on a conversation between a patient and provider. However, the evaluation of patient-provider conversation suffers from critical shortcomings, including intensive labor requirements, coder error, nonstandardized coding systems, and inability to scale up to larger data sets. To overcome these shortcomings, psychotherapy analysis needs a reliable and scalable method for summarizing the content of treatment encounters. We used a publicly available psychotherapy corpus from Alexander Street press comprising a large collection of transcripts of patient-provider conversations to compare coding performance for two machine learning methods. We used the labeled latent Dirichlet allocation (L-LDA) model to learn associations between text and codes, to predict codes in psychotherapy sessions, and to localize specific passages of within-session text representative of a session code. We compared the L-LDA model to a baseline lasso regression model using predictive accuracy and model generalizability (measured by calculating the area under the curve (AUC) from the receiver operating characteristic curve). The L-LDA model outperforms the lasso logistic regression model at predicting session-level codes with average AUC scores of 0.79, and 0.70, respectively. For fine-grained level coding, L-LDA and logistic regression are able to identify specific talk-turns representative of symptom codes. However, model performance for talk-turn identification is not yet as reliable as human coders. We conclude that the L-LDA model has the potential to be an objective, scalable method for accurate automated coding of psychotherapy sessions that perform better than comparable discriminative methods at session-level coding and can also predict fine-grained codes.

Content Coding of Psychotherapy Transcripts Using Labeled Topic Models

PubMed Central

Gaut, Garren; Steyvers, Mark; Imel, Zac E; Atkins, David C; Smyth, Padhraic

2016-01-01

Psychotherapy represents a broad class of medical interventions received by millions of patients each year. Unlike most medical treatments, its primary mechanisms are linguistic; i.e., the treatment relies directly on a conversation between a patient and provider. However, the evaluation of patient-provider conversation suffers from critical shortcomings, including intensive labor requirements, coder error, non-standardized coding systems, and inability to scale up to larger data sets. To overcome these shortcomings, psychotherapy analysis needs a reliable and scalable method for summarizing the content of treatment encounters. We used a publicly-available psychotherapy corpus from Alexander Street press comprising a large collection of transcripts of patient-provider conversations to compare coding performance for two machine learning methods. We used the Labeled Latent Dirichlet Allocation (L-LDA) model to learn associations between text and codes, to predict codes in psychotherapy sessions, and to localize specific passages of within-session text representative of a session code. We compared the L-LDA model to a baseline lasso regression model using predictive accuracy and model generalizability (measured by calculating the area under the curve (AUC) from the receiver operating characteristic (ROC) curve). The L-LDA model outperforms the lasso logistic regression model at predicting session-level codes with average AUC scores of .79, and .70, respectively. For fine-grained level coding, L-LDA and logistic regression are able to identify specific talk-turns representative of symptom codes. However, model performance for talk-turn identification is not yet as reliable as human coders. We conclude that the L-LDA model has the potential to be an objective, scaleable method for accurate automated coding of psychotherapy sessions that performs better than comparable discriminative methods at session-level coding and can also predict fine-grained codes. PMID:26625437

Small-bowel mucosal injuries in low-dose aspirin users with obscure gastrointestinal bleeding

PubMed Central

Iwamoto, Junichi; Mizokami, Yuji; Saito, Yoshifumi; Shimokobe, Koichi; Honda, Akira; Ikegami, Tadashi; Matsuzaki, Yasushi

2014-01-01

AIM: To investigate the clinical differences between small intestinal injuries in low-dose aspirin (LDA) users and in non-steroidal anti-inflammatory drug (NSAID) users who were examined by capsule endoscopy (CE) for obscure gastrointestinal bleeding (OGIB). METHODS: A total of 181 patients who underwent CE for OGIB were included in this study. Based on clinical records, laboratory data such as hemoglobin levels, major symptoms, underlying diseases, the types and duration of LDA and NSAID use, and endoscopic characteristics of CE were reviewed. RESULTS: Out of a total of 45 cases of erosive lesions, 27 cases were taking LDA or NSAIDs (7 were on NSAIDs, 9 were on LDA alone, 9 were on LDA and thienopyridine, and 2 were on LDA and warfarin).The prevalence of ulcers or erosion during chronic use of LDA, LDA and the anti-platelet drug thienopyridine (clopidogrel or ticlopidine), and NSAIDs were 64.3%, 80.0%, and 75.0%, respectively. Erosive lesions were observed predominantly in chronic LDA users, while ulcerative lesions were detected mainly in NSAID users. However, concomitant use of thienopyridine such as clopidogrel with LDA increased the proportion of ulcers. The erosive lesions were located in the whole of the small intestine (jejunum and ileum), whereas ulcerative lesions were mainly observed in the ileum (P < 0.05). CONCLUSION: Our CE findings indicate that chronic LDA users and NSAID users show different types and locations of small-bowel mucosal injuries. The concomitant use of anti-platelet drugs with LDA tends to exacerbate the injuries from LDA-type to NSAID-type injuries. PMID:25278707

Ab-initio Calculation of Optoelectronic and Structural Properties of Cubic Lithium Oxide (Li2O)

NASA Astrophysics Data System (ADS)

Ziegler, Joshua; Polin, Daniel; Malozovsky, Yuriy; Bagayoko, Diola

Using the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF), we performed ab-initio, density functional theory (DFT) calculations of optoelectronic, transport, and bulk properties of Li2S. In so doing, we avoid ``band gap'' and problems plaguing many DET calculations [AIP Advances 4, 127104 (2014)]. We employed a local density approximation (LDA) potential and the linear combination of atomic orbitals (LCAO). With the BZW-EF method, our results possess the full, physical content of DFT and agree with available, corresponding experimental ones. In particular, we found a room temperature indirect band gap of 6.659 eV that compares favorably with experimental values ranging from 5 to 7.99 eV. We also calculated total and partial density of states (DOS and PDOS), effective masses of charge carriers, the equilibrium lattice constant, and the bulk modulus. Acknowledgments: This work was funded in part by the National Science Foundation (NSF) and the Louisiana Board of Regents, through LASiGMA [Award Nos. EPS- 1003897, NSF (2010-15)-RII-SUBR] and NSF HRD-1002541, the US Department of Energy - National, Nuclear Security Administration (NNSA) (Award Nos. DE-NA0001861 and DE- NA0002630), LaSPACE, and LONI-SUBR.

Robust linear discriminant models to solve financial crisis in banking sectors

NASA Astrophysics Data System (ADS)

Lim, Yai-Fung; Yahaya, Sharipah Soaad Syed; Idris, Faoziah; Ali, Hazlina; Omar, Zurni

2014-12-01

Linear discriminant analysis (LDA) is a widely-used technique in patterns classification via an equation which will minimize the probability of misclassifying cases into their respective categories. However, the performance of classical estimators in LDA highly depends on the assumptions of normality and homoscedasticity. Several robust estimators in LDA such as Minimum Covariance Determinant (MCD), S-estimators and Minimum Volume Ellipsoid (MVE) are addressed by many authors to alleviate the problem of non-robustness of the classical estimates. In this paper, we investigate on the financial crisis of the Malaysian banking institutions using robust LDA and classical LDA methods. Our objective is to distinguish the "distress" and "non-distress" banks in Malaysia by using the LDA models. Hit ratio is used to validate the accuracy predictive of LDA models. The performance of LDA is evaluated by estimating the misclassification rate via apparent error rate. The results and comparisons show that the robust estimators provide a better performance than the classical estimators for LDA.

Features of Electron Density Distribution in Delafossite Cualo2

NASA Astrophysics Data System (ADS)

Pogoreltsev, A. I.; Schmidt, S. V.; Gavrilenko, A. N.; Shulgin, D. A.; Korzun, B. V.; Matukhin, V. L.

2015-07-01

We have used pulsed 63,65Cu nuclear quadrupole resonance at room temperature to study the semiconductor compound CuAlO2 with a delafossite crystal structure, and we have determined the quadrupole frequency νQ = 28.12 MHz and the asymmetry parameter η ~ 0, which we used to study the features of the electron density distribution in the vicinity of the quadrupolar nucleus. In order to take into account the influence of correlation effects on the electric field gradient, we carried out ab initio calculations within the density functional theory (DFT) approximation using a set of correlation functionals VWN1RPA, VWN5, PW91LDA, CPW91, and B3LYP1. We mapped the electron density distribution in the vicinity of the quadrupolar copper nucleus for the Cu7Al6o{14/- 1} cluster and we calculated the size of the LUMO-HOMO gap, Δ ~ 3.33 eV. We established the anisotropy of the spatial electron density distribution. Based on analysis of the electron density distribution obtained, we suggest that the bond in CuAlO2 is not purely covalent.

Influence of Van der Waals interaction on the thermodynamics properties of NaCl

NASA Astrophysics Data System (ADS)

Marcondes, M. L.; Wentzcovitch, R. M.; Assali, L. V. C.

2016-12-01

Equations of state (EoS) are extremely important in several scientific domains. However, many applications require EoS parameters at high pressures and temperatures. Experimental determination of these parameters is limited in such conditions and ab initio calculations have become important in computing them. Density Functional Theory (DFT) with its various approximations for exchange and correlation energy is the method of choice, but lack of a good description of the exchange-correlation energy results in large errors in EoS parameters. It is well known that the alkali halides have been problematic from the onset and the quest for DFT functionals appropriate for such ionic and relatively weakly bonded systems has remained an active topic of research. Here we use DFT + van der Waals functionals to calculate the thermal equation of state and thermodynamic properties of the B1 NaCl phase. Our results show a remarkable improvement over the performance of standard the LDA and GGA functionals. This is hardly surprising given that ions in this system have nearly closed shell configurations.

Crystal and electronic structure of copper sulfides

NASA Astrophysics Data System (ADS)

Lukashev, Pavel

Copper sulfides with different copper concentration exist in mineral form ranging from CuS to Cu2S. Among these, chalcosite Cu 2S, and digenite Cu1.8S were the subject of extensive research for decades mainly because of their use as the absorber in photovoltaic cells. Yet; their electronic structure is poorly understood because their crystal structure is complex. Most of the results published so far report the semiconducting nature of these compounds with the energy band gap being in the range of 0.84 to 1.9 eV. The crystal structure consists of a close-packed lattice of S with mobile Cu occupying various types of interstitial sites with a statistical distribution depending on temperature. In this thesis we present the first computational study of their electronic band structure. Initially, we investigated the simpler antifluorite structure. Both local density approximation (LDA) and self-consistent quasiparticle GW calculations with the full-potential linearized muffin-tin orbital method give a semimetallic band structure. Inspection of the nature of the bands shows that the lowest conduction band is mainly Cu-s-like except right near the center of the Brillouin zone where a Cu-s-like state lies about 1 eV below the valence band maximum. Significantly, in GW calculations, this state shifts up by several 0.1 eV but not sufficiently to open a gap. A random distortion of the Cu atoms from the perfect antifluorite positions is found to break the degeneracy of the d state at the Gamma-point and thus opens up a small gap of about 0.1 eV in LDA. As our next step we constructed supercell models for the cubic and hexagonal phases with the Cu positions determined by a weighted random number generator. The low temperature monoclinic phase was also studied. The computed total energies of these structures follow the same order as the reported phases with increasing temperatures. All these models gave similar small band gaps of order 0.1-0.2 eV. However, their conduction band is now mainly s-like and addition of an expected Cu-s level shift opens the gap to about 0.5 eV. Some simpler hexagonal model structures gave slightly larger band gap but were found to be unrealistic. The optical absorption data all show a strong intraband absorption with a minimum in absorption at about 1 eV. Our calculations suggest a significantly lower gap of order 0.5 eV with low absorption cross section, the true nature of which is masked by the free carrier absorption. As part of our study of the related Cu-compounds, we analyzed the quasiparticle effects beyond LDA obtained from a GW calculation on the effective masses and Kohn-Luttinger hamiltonian parameters for CuBr.

Glass Transitions in a Monatomic Liquid with Two Glassy States

NASA Astrophysics Data System (ADS)

Gordon, Andrew; Giovambattista, Nicolas

2014-04-01

We perform out-of-equilibrium molecular dynamics simulations of a monatomic liquid that exhibits liquid and glass polymorphism, with two distinct glasses, low- (LDA) and high-density (HDA) amorphous solids. By performing isobaric heating simulations of LDA and HDA at different pressures, we determine (a) the glass transition temperature of LDA and HDA, TgLDA(P) and TgHDA(P), as well as (b) the corresponding glass-glass transformation temperatures, TLDA-HDA(P) and THDA-LDA(P). It is found that TgLDA(P) is anomalous; i.e., it decreases with increasing pressure, while TgHDA(P) increases with increasing pressure. Interestingly, the TgLDA(P) and TLDA-HDA(P) loci, as well as the TgHDA(P) and THDA-LDA(P) loci, constitute smooth single lines in the P -T plane, suggesting that heating-induced glass-glass and glass transitions are related. We discuss the present results in the context of water experiments and simulations.

Importance of Unit Cells in Accurate Evaluation of the Characteristics of Graphene

NASA Astrophysics Data System (ADS)

Sabzyan, Hassan; Sadeghpour, Narges

2016-04-01

Effects of the size of the unit cell on energy, atomic charges, and phonon frequencies of graphene at the Γ point of the Brillouin zone are studied in the absence and presence of an electric field using density functional theory (DFT) methods (LDA and DFT-PBE functionals with Goedecker-Teter-Hutter (GTH) and Troullier-Martins (TM) norm-conserving pseudopotentials). Two types of unit cells containing nC=4-28 carbon atoms are considered. Results show that stability of graphene increases with increasing size of the unit cell. Energy, atomic charges, and phonon frequencies all converge above nC=24 for all functional-pseudopotentials used. Except for the LDA-GTH calculations, application of an electric field of 0.4 and 0.9 V/nm strengths does not change the trends with the size of the unit cell but instead slightly decreases the binding energy of graphene. Results of this study show that the choice of unit cell size and type is critical for calculation of reliable characteristics of graphene.

Expanded findings from a randomized controlled trial of preconception low-dose aspirin and pregnancy loss

PubMed Central

Mumford, Sunni L.; Silver, Robert M.; Sjaarda, Lindsey A.; Wactawski-Wende, Jean; Townsend, Janet M.; Lynch, Anne M.; Galai, Noya; Lesher, Laurie L.; Faraggi, David; Perkins, Neil J.; Schliep, Karen C.; Zarek, Shvetha M.; Schisterman, Enrique F.

2016-01-01

STUDY QUESTION What is the association between daily preconception-initiated low-dose aspirin (LDA) treatment and very early pregnancy losses or euploid (chromosomally normal) losses among women with one to two prior losses? SUMMARY ANSWER Daily LDA initiated preconception was not associated with the rate or type of pregnancy loss among women with a history of one to two prior pregnancy losses. WHAT IS KNOWN ALREADY LDA is often used to treat recurrent pregnancy loss with reductions in pregnancy loss generally only observed among women with antiphospholipid antibodies, and null associations observed among women without antiphospholipid antibodies. We previously evaluated the association between LDA and pregnancy loss overall among women with one to two prior losses in the Effects of Aspirin in Gestation and Reproduction (EAGeR) trial and found no association, though did not distinguish between potential effects at different stages of pregnancy loss, including implantation failure, or between euploid and aneuploid losses. STUDY DESIGN, SIZE, DURATION The EAGeR trial was a multi-site prospective block-randomized double-blind placebo-controlled trial. In total, 1228 women were randomized to daily LDA (81 mg/day) plus folic acid (400 mcg/day), or placebo plus folic acid. Participants were assigned study drug for less than or equal to six menstrual cycles or if they conceived, throughout pregnancy with study drug discontinued at 36 weeks gestation. This analysis includes additional outcome information obtained from chart abstractions after the completion of the trial, as well as testing of stored urine for measurement of hCG and detection of very early pregnancy losses, and karyotyping of the products of conception for assessment of aneuploidy of the losses. PARTICIPANTS, SETTING, METHODS Women aged 18–40 with a history of one to two prior losses and actively trying to conceive were randomized (n = 615 LDA and n = 613 placebo) at four clinical centers in the USA (2007–2011). Log-binomial regression was used to estimate risk ratios under the intent-to-treat approach. MAIN RESULTS AND THE ROLE OF CHANCE Daily LDA initiated preconception was not associated with clinically recognized pregnancy losses or implantation failures among women with proved fecundity and a history of one to two prior losses. Specifically, 1088 (88.6%) women completed the trial with 797 having an hCG detected pregnancy (64.9%). Overall there were 133 clinical losses (12.7% LDA versus 11.8% placebo, P = 0.71) and 55 implantation failures (5.2% LDA versus 4.9% placebo, P = 0.89). No differences were found in rate of euploid losses (RR 1.11, 95% confidence interval: 0.99, 1.26). LIMITATIONS, REASONS FOR CAUTION Generalizability of these findings is limited to women with a history of one to two prior losses, and may further be limited to women of white race with higher socioeconomic status as given the rigors of the study protocol participants tended to be white and have higher incomes and more education. We were also missing karyotype information on approximately one-third of the clinically recognized pregnancy losses, which may limit our power to detect effects on euploid losses, though detailed sensitivity analysis showed similar results. WIDER IMPLICATIONS OF THE FINDINGS Our data do not support the general use of LDA to decrease pregnancy loss and further demonstrate no increased risk of loss for women on LDA treatment. STUDY FUNDING/COMPETING INTERESTS This research was supported by the Intramural Research Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland (Contract Nos. HHSN267200603423, HHSN267200603424, HHSN267200603426). The authors have no conflicts of interest. TRIAL REGISTRATION NUMBER The trial was registered at ClinicalTrials.gov #NCT00467363. TRIAL REGISTRATION DATE 27 April 2007. DATE OF FIRST PATIENT'S ENROLLMENT 15 June 2007. PMID:26759138

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shephard, Jacob J.; Vickers, Martin; Salzmann, Christoph G., E-mail: c.salzmann@ucl.ac.uk

Low-density amorphous (LDA) ice is involved in critical cosmological processes and has gained prominence as one of the at least two distinct amorphous forms of ice. Despite these accolades, we still have an incomplete understanding of the structural diversity that is encompassed within the LDA state and the dynamic processes that take place upon heating LDA. Heating the high-pressure ice VIII phase at ambient pressure is a remarkable example of temperature-induced amorphisation yielding LDA. We investigate this process in detail using X-ray diffraction and Raman spectroscopy and show that the LDA obtained from ice VIII is structurally different from themore » more “traditional” states of LDA which are approached upon thermal annealing. This new structural relaxation pathway involves an increase of structural order on the intermediate range length scale. In contrast with other LDA materials the local structure is more ordered initially and becomes slightly more disordered upon annealing. We also show that the cascade of phase transitions upon heating ice VIII at ambient pressure includes the formation of ice IX which may be connected with the structural peculiarities of LDA from ice VIII. Overall, this study shows that LDA is a structurally more diverse material than previously appreciated.« less

Deciphering the Routes of invasion of Drosophila suzukii by Means of ABC Random Forest.

PubMed

Fraimout, Antoine; Debat, Vincent; Fellous, Simon; Hufbauer, Ruth A; Foucaud, Julien; Pudlo, Pierre; Marin, Jean-Michel; Price, Donald K; Cattel, Julien; Chen, Xiao; Deprá, Marindia; François Duyck, Pierre; Guedot, Christelle; Kenis, Marc; Kimura, Masahito T; Loeb, Gregory; Loiseau, Anne; Martinez-Sañudo, Isabel; Pascual, Marta; Polihronakis Richmond, Maxi; Shearer, Peter; Singh, Nadia; Tamura, Koichiro; Xuéreb, Anne; Zhang, Jinping; Estoup, Arnaud

2017-04-01

Deciphering invasion routes from molecular data is crucial to understanding biological invasions, including identifying bottlenecks in population size and admixture among distinct populations. Here, we unravel the invasion routes of the invasive pest Drosophila suzukii using a multi-locus microsatellite dataset (25 loci on 23 worldwide sampling locations). To do this, we use approximate Bayesian computation (ABC), which has improved the reconstruction of invasion routes, but can be computationally expensive. We use our study to illustrate the use of a new, more efficient, ABC method, ABC random forest (ABC-RF) and compare it to a standard ABC method (ABC-LDA). We find that Japan emerges as the most probable source of the earliest recorded invasion into Hawaii. Southeast China and Hawaii together are the most probable sources of populations in western North America, which then in turn served as sources for those in eastern North America. European populations are genetically more homogeneous than North American populations, and their most probable source is northeast China, with evidence of limited gene flow from the eastern US as well. All introduced populations passed through bottlenecks, and analyses reveal five distinct admixture events. These findings can inform hypotheses concerning how this species evolved between different and independent source and invasive populations. Methodological comparisons indicate that ABC-RF and ABC-LDA show concordant results if ABC-LDA is based on a large number of simulated datasets but that ABC-RF out-performs ABC-LDA when using a comparable and more manageable number of simulated datasets, especially when analyzing complex introduction scenarios. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Mechanical, electronic and thermodynamic properties of full Heusler compounds Fe2VX(X = Al, Ga)

NASA Astrophysics Data System (ADS)

Khalfa, M.; Khachai, H.; Chiker, F.; Baki, N.; Bougherara, K.; Yakoubi, A.; Murtaza, G.; Harmel, M.; Abu-Jafar, M. S.; Omran, S. Bin; Khenata, R.

2015-11-01

The electronic structure, mechanical and thermodynamic properties of Fe2VX, (with X = Al and Ga), have been studied self consistently by employing state-of-the-art full-potential linearized approach of augmented plane wave plus local orbitals (FP-LAPW + lo) method. The exchange-correlation potential is treated with the local density and generalized gradient approximations (LDA and GGA). Our predicted ground state properties such as lattice constants, bulk modulus and elastic constants appear more accurate when we employed the GGA rather than the LDA, and these results are in very good agreement with the available experimental and theoretical data. Further, thermodynamic properties of Fe2VAl and Fe2VGa are predicted with pressure and temperature in the ranges of 0-40 GPa and 0-1500 K using the quasi-harmonic Debye model. We have obtained successfully the variations of the heat capacities, primitive cell volume and volume expansion coefficient.

Formation of orbital-selective electron states in LaTiO3/SrTiO3 superlattices

NASA Astrophysics Data System (ADS)

Lechermann, Frank; Boehnke, Lewin; Grieger, Daniel

2013-06-01

The interface electronic structure of correlated LaTiO3/SrTiO3 superlattices is investigated by means of the charge self-consistent combination of the local density approximation (LDA) to density functional theory with dynamical mean-field theory. Utilizing a pseudopotential technique together with a continuous-time quantum Monte Carlo approach, the resulting complex multiorbital electronic states are addressed in a coherent fashion beyond static mean field. General structural relaxations are taken into account on the LDA level and cooperate with the driving forces from strong electronic correlations. This alliance leads to a Ti(3dxy) dominated low-energy quasiparticle peak and a lower Hubbard band in line with photoemission studies. Furthermore correlation effects close to the band-insulating bulk SrTiO3 limit as well as the Mott-insulating bulk LaTiO3 limit are studied via realistic single-layer embeddings.

Density functional theory investigation of the LiIn 1-xGa xSe 2 solid solution

DOE PAGES

Wiggins, Brenden; Batista, Enrique; Burger, Arnold; ...

2016-06-07

Here, the electronic structure and optical properties of the LiIn 1-xGa xSe 2 (x=0, 0.25, 0.5, 0.75, 1) solid solution were studied by density functional theory (DFT) with pure functionals. The exchange-correlation is treated within the local density approximation (LDA) and generalized-gradient approximation (GGA). The electronic structures for each respective compound are discussed in detail. Calculations reveal that gallium incorporation can be used to tune the optical-electrical properties of the solid solution and correlates with the lattice parameter. The band gap trend of the LiIn 1-xGa xSe 2 system follows a nonlinear behavior between the LiInSe 2 and LiGaSe 2more » ternary boundaries. The bowing parameter is estimated to be on the order of 0.1- 0.3 eV at the point. Low-temperature optical absorption revealed a 30% change in the temperature dependence of the band gap for the intermediate compound LiIn 0.6Ga 0.4Se 2 compared to ternary boundaries and suggests the heat capacity to be another control element through strain.« less

Comparative Study of Exchange-Correlation Functional and Potential for Evaluating Thermoelectric Transport Properties in d0 Perovskite Oxides

NASA Astrophysics Data System (ADS)

Ohkubo, Isao; Mori, Takao

2017-07-01

The influence of two different types of exchange-correlation functional/potential, namely, the generalized gradient approximation Perdew-Burke-Ernzerhof (GGA-PBE) functional and the modified Becke-Johnson (mBJ) potential, on the thermoelectric transport properties of d0 perovskite oxides (SrTiO3 and KTaO3) was investigated. The reduction of band dispersion induced by the mBJ scheme allows the improved prediction of band gap values by thelocal density approximation (LDA) and GGA, which increases the resolution of the increases in the density of states (DOS), carrier concentration, and effective mass near the conduction band edge. A comparison of the experimental effective mass values of d0 perovskite oxides shows that the effective mass values provided by the mBJ potential are similar to those provided by the GGA-PBE functional. Comparative analysis of the data obtained from Boltzmann theory calculations using the electronic structures determined with the GGA-PBE functional and the mBJ potential shows a difference in the transport coefficients owing to the increases in the DOS, carrier concentration, and effective mass induced by the mBJ scheme.

Score-moment combined linear discrimination analysis (SMC-LDA) as an improved discrimination method.

PubMed

Han, Jintae; Chung, Hoeil; Han, Sung-Hwan; Yoon, Moon-Young

2007-01-01

A new discrimination method called the score-moment combined linear discrimination analysis (SMC-LDA) has been developed and its performance has been evaluated using three practical spectroscopic datasets. The key concept of SMC-LDA was to use not only the score from principal component analysis (PCA), but also the moment of the spectrum, as inputs for LDA to improve discrimination. Along with conventional score, moment is used in spectroscopic fields as an effective alternative for spectral feature representation. Three different approaches were considered. Initially, the score generated from PCA was projected onto a two-dimensional feature space by maximizing Fisher's criterion function (conventional PCA-LDA). Next, the same procedure was performed using only moment. Finally, both score and moment were utilized simultaneously for LDA. To evaluate discrimination performances, three different spectroscopic datasets were employed: (1) infrared (IR) spectra of normal and malignant stomach tissue, (2) near-infrared (NIR) spectra of diesel and light gas oil (LGO) and (3) Raman spectra of Chinese and Korean ginseng. For each case, the best discrimination results were achieved when both score and moment were used for LDA (SMC-LDA). Since the spectral representation character of moment was different from that of score, inclusion of both score and moment for LDA provided more diversified and descriptive information.

Tofacitinib in Rheumatoid Arthritis: Lack of Early Change in Disease Activity Predicts a Low Probability of Achieving Low Disease Activity at Month 6.

PubMed

Van Vollenhoven, Ronald F; Lee, Eun Bong; Fallon, Lara; Zwillich, Samuel H; Wilkinson, Bethanie; Chapman, Douglass; Demasi, Ryan; Keystone, Edward

2018-04-26

Optimal targeted treatment in rheumatoid arthritis requires early identification of failure to respond. This post-hoc analysis explored the relationship between early disease activity changes and achievement of low disease activity (LDA) and remission targets with tofacitinib. Data were from two randomized, double-blind, Phase 3 studies. In ORAL Start (NCT01039688), methotrexate (MTX)-naïve patients received tofacitinib 5 or 10 mg BID, or MTX, for 24 months. In placebo-controlled ORAL Standard (NCT00853385), MTX-inadequate responder (MTX-IR) patients received tofacitinib 5 or 10 mg BID or adalimumab 40 mg Q2W, with MTX, for 12 months. Probabilities of achieving LDA (CDAI ≤10; DAS28-4[ESR] ≤3.2) at months 6 and 12 were calculated, given failure to achieve threshold improvement from baseline (change in CDAI ≥6; DAS28-4[ESR] ≥1.2) at month 1 or 3. In ORAL Start, 7.2% and 5.4% of patients receiving tofacitinib 5 and 10 mg BID, respectively, failed to improve CDAI ≥6 at month 3; of those who failed, 3.8% and 28.6%, respectively, achieved month 6 CDAI-defined LDA. In ORAL Standard, 18.8% and 17.5% of patients receiving tofacitinib 5 and 10 mg BID, respectively, failed to improve CDAI ≥6 at month 3; of those who failed, 0% and 2.9%, respectively, achieved month 6 CDAI-defined LDA. Findings were similar when considering month 1 improvements or DAS28-4(ESR) thresholds. In MTX-IR patients, lack of response to tofacitinib after 1 or 3 months predicted low probability of achieving LDA at month 6. Lack of early response may be considered when deciding whether to continue treatment with tofacitinib. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

A randomized, double-blind, placebo-controlled study of rebamipide for gastric mucosal injury taking aspirin with or without clopidogrel.

PubMed

Tozawa, Katsuyuki; Oshima, Tadayuki; Okugawa, Takuya; Ogawa, Tomohiro; Ohda, Yoshio; Tomita, Toshihiko; Hida, Nobuyuki; Fukui, Hirokazu; Hori, Kazutoshi; Watari, Jiro; Nakamura, Shiro; Miwa, Hiroto

2014-08-01

Antithrombotic drugs, such as low-dose aspirin (LDA) and clopidogrel, can cause upper gastrointestinal complications. The goal of the present study was to investigate whether a mucosal-protective agent, rebamipide, could prevent gastric mucosal injuries induced by LDA with or without clopidogrel in healthy subjects. A randomized, double-blind, placebo-controlled trial was performed with 32 healthy male volunteers. Subjects were randomly assigned to a 14-day course of one of the following regimens: group A, placebo (tid) + LDA; group B, rebamipide (100 mg tid) + LDA (100 mg once-daily); group C, placebo + LDA + clopidogrel (75 mg once-daily); or group D, rebamipide + LDA + clopidogrel. The grade of gastric mucosal injuries was evaluated by esophagogastroduodenoscopy before and after dosing (on day 0 and day 14), and the grade of gastric mucosal injury was assessed according to the modified Lanza score. Subjective symptoms were assessed using the Gastrointestinal Symptom Rating Scale (GSRS). A rapid urease test was performed on day 0, and blood tests were performed on day 0 and day 14. Rebamipide significantly inhibited gastric mucosal injury induced by LDA alone or by LDA plus clopidogrel when compared with placebo in healthy subjects. GSRS score and hemoglobin level were not significantly different among the four groups. Rebamipide is useful for the primary prevention of gastric mucosal injury induced by LDA alone or by LDA plus clopidogrel in healthy subjects.

DFT Predictions of Electronic, Transport, and Bulk Properties of Cubic Antifluorite A2B Compounds (A = Li, Na, B = O,S,Se)

NASA Astrophysics Data System (ADS)

Malozovsky, Yuriy; Franklin, Lashounda; Bagayoko, Diola

We present results from ab-initio,self-consistent calculations of electronic, transport, and bulk properties of cubic antifluorite (anti-CaF2) compounds A2B (A = Li, Na, B = O, S, Se). Our computations employed the local density approximation (LDA) potential of Ceperley and Alder and the linear combination of atomic orbital (LCAO) formalism. The implementation of the LCAO formalism followed the Bagayoko, Zhao, and Williams method, as enhanced by Ekuma and Franklin (BZW-EF). Consequently, our calculations search for and attained the ground states of the systems under study, as required by DFT; our results therefore possess the full, physical content of DFT. We discuss band structures, band gaps, and related properties of these materials, including calculated, total and partial densities of states (DOS and PDOS), effective masses of charge carriers, equilibrium lattice constants, and the bulk moduli of cubic antifluorite compounds A2B (A = Li, Na, B = O, S, Se). Our results are predictions in some cases, due to the lack of experimental data. Work funded in part by the US Department of Energy (DOE), National Nuclear Security Administration (NNSA) (Award No.DE-NA0002630), the National Science Foundation (NSF) (Award No, 1503226), LaSPACE, and LONI-SUBR.

Theoretical and experimental investigations of optical, structural and electronic properties of the lower-dimensional hybrid [NH3-(CH2)10-NH3]ZnCl4

NASA Astrophysics Data System (ADS)

El Mrabet, R.; Kassou, S.; Tahiri, O.; Belaaraj, A.; Guionneau, P.

2016-10-01

In the current study, a combination between theoretical and experimental studies has been made for the hybrid perovskite [NH3-(CH2)10-NH3]ZnCl4. The density functional theory (DFT) was performed to investigate structural and electronic properties of the tilted compound. A local approximation (LDA) and semi-local approach (GGA) were employed. The results are obtained using, respectively, the local exchange correlation functional of Perdew-Wang 92 (PW92) and semi local functional of Perdew-Burke-Ernzerhof (PBE). The optimized cell parameters are in good agreement with the experimental results. Electronic properties have been studied through the calculation of band structures and density of state (DOS), while structural properties are investigated by geometry optimization of the cell. Fritz-Haber-Institute (FHI) pseudopotentials were employed to perform all calculations. The optical diffuse reflectance spectra was mesured and applied to deduce the refractive index ( n), the extinction coefficient ( k), the absorption coefficient (α), the real and imaginary dielectric permittivity parts (ɛr,ɛi)) and the optical band gap energy Eg. The optical band gap energy value shows good consistent with that obtained from DFT calculations and reveals the insulating behavior of the material.

Ab initio DFT+U study of He atom incorporation into UO(2) crystals.

PubMed

Gryaznov, Denis; Heifets, Eugene; Kotomin, Eugene

2009-09-07

We present and discuss results of the density functional theory (DFT) for perfect UO(2) crystals with He atoms in octahedral interstitial positions therein. We have calculated basic bulk crystal properties and He incorporation energies into the low temperature anti-ferromagnetic UO(2) phase using several exchange-correlation functionals within the spin-polarized local density (LDA) and generalized gradient (GGA) approximations. In all DFT calculations we included the on-site correlation corrections using the Hubbard model (DFT+U approach). We analysed a potential crystalline symmetry reduction from tetragonal down to orthorhombic structure and confirmed the presence of the Jahn-Teller effect in a perfect UO(2). We discuss also the problem of a conducting electronic state arising when He is placed into a tetragonal antiferromagnetic phase of UO(2) commonly used in defect modelling. Consequently, we found a specific monoclinic lattice distortion which allowed us to restore the semiconducting state and properly estimate He incorporation energies. Unlike the bulk properties, the He incorporation energy strongly depends on several factors, including the supercell size, the use of spin polarization, the exchange-correlation functionals and on-site correlation corrections. We compare our results for the He incorporation with the previous shell model and ab initio DFT calculations.

Quasiparticle self-consistent GW study of cuprates: electronic structure, model parameters, and the two-band theory for Tc

PubMed Central

Jang, Seung Woo; Kotani, Takao; Kino, Hiori; Kuroki, Kazuhiko; Han, Myung Joon

2015-01-01

Despite decades of progress, an understanding of unconventional superconductivity still remains elusive. An important open question is about the material dependence of the superconducting properties. Using the quasiparticle self-consistent GW method, we re-examine the electronic structure of copper oxide high-Tc materials. We show that QSGW captures several important features, distinctive from the conventional LDA results. The energy level splitting between and is significantly enlarged and the van Hove singularity point is lowered. The calculated results compare better than LDA with recent experimental results from resonant inelastic xray scattering and angle resolved photoemission experiments. This agreement with the experiments supports the previously suggested two-band theory for the material dependence of the superconducting transition temperature, Tc. PMID:26206417

Fast Solution in Sparse LDA for Binary Classification

NASA Technical Reports Server (NTRS)

Moghaddam, Baback

2010-01-01

An algorithm that performs sparse linear discriminant analysis (Sparse-LDA) finds near-optimal solutions in far less time than the prior art when specialized to binary classification (of 2 classes). Sparse-LDA is a type of feature- or variable- selection problem with numerous applications in statistics, machine learning, computer vision, computational finance, operations research, and bio-informatics. Because of its combinatorial nature, feature- or variable-selection problems are NP-hard or computationally intractable in cases involving more than 30 variables or features. Therefore, one typically seeks approximate solutions by means of greedy search algorithms. The prior Sparse-LDA algorithm was a greedy algorithm that considered the best variable or feature to add/ delete to/ from its subsets in order to maximally discriminate between multiple classes of data. The present algorithm is designed for the special but prevalent case of 2-class or binary classification (e.g. 1 vs. 0, functioning vs. malfunctioning, or change versus no change). The present algorithm provides near-optimal solutions on large real-world datasets having hundreds or even thousands of variables or features (e.g. selecting the fewest wavelength bands in a hyperspectral sensor to do terrain classification) and does so in typical computation times of minutes as compared to days or weeks as taken by the prior art. Sparse LDA requires solving generalized eigenvalue problems for a large number of variable subsets (represented by the submatrices of the input within-class and between-class covariance matrices). In the general (fullrank) case, the amount of computation scales at least cubically with the number of variables and thus the size of the problems that can be solved is limited accordingly. However, in binary classification, the principal eigenvalues can be found using a special analytic formula, without resorting to costly iterative techniques. The present algorithm exploits this analytic form along with the inherent sequential nature of greedy search itself. Together this enables the use of highly-efficient partitioned-matrix-inverse techniques that result in large speedups of computation in both the forward-selection and backward-elimination stages of greedy algorithms in general.

A comparison of machine learning methods for classification using simulation with multiple real data examples from mental health studies.

PubMed

Khondoker, Mizanur; Dobson, Richard; Skirrow, Caroline; Simmons, Andrew; Stahl, Daniel

2016-10-01

Recent literature on the comparison of machine learning methods has raised questions about the neutrality, unbiasedness and utility of many comparative studies. Reporting of results on favourable datasets and sampling error in the estimated performance measures based on single samples are thought to be the major sources of bias in such comparisons. Better performance in one or a few instances does not necessarily imply so on an average or on a population level and simulation studies may be a better alternative for objectively comparing the performances of machine learning algorithms. We compare the classification performance of a number of important and widely used machine learning algorithms, namely the Random Forests (RF), Support Vector Machines (SVM), Linear Discriminant Analysis (LDA) and k-Nearest Neighbour (kNN). Using massively parallel processing on high-performance supercomputers, we compare the generalisation errors at various combinations of levels of several factors: number of features, training sample size, biological variation, experimental variation, effect size, replication and correlation between features. For smaller number of correlated features, number of features not exceeding approximately half the sample size, LDA was found to be the method of choice in terms of average generalisation errors as well as stability (precision) of error estimates. SVM (with RBF kernel) outperforms LDA as well as RF and kNN by a clear margin as the feature set gets larger provided the sample size is not too small (at least 20). The performance of kNN also improves as the number of features grows and outplays that of LDA and RF unless the data variability is too high and/or effect sizes are too small. RF was found to outperform only kNN in some instances where the data are more variable and have smaller effect sizes, in which cases it also provide more stable error estimates than kNN and LDA. Applications to a number of real datasets supported the findings from the simulation study. © The Author(s) 2013.

Glass polymorphism in glycerol–water mixtures: I. A computer simulation study

PubMed Central

Jahn, David A.; Wong, Jessina; Bachler, Johannes; Loerting, Thomas

2016-01-01

We perform out-of-equilibrium molecular dynamics (MD) simulations of water–glycerol mixtures in the glass state. Specifically, we study the transformations between low-density (LDA) and high-density amorphous (HDA) forms of these mixtures induced by compression/decompression at constant temperature. Our MD simulations reproduce qualitatively the density changes observed in experiments. Specifically, the LDA–HDA transformation becomes (i) smoother and (ii) the hysteresis in a compression/decompression cycle decreases as T and/or glycerol content increase. This is surprising given the fast compression/decompression rates (relative to experiments) accessible in MD simulations. We study mixtures with glycerol molar concentration χ g = 0–13% and find that, for the present mixture models and rates, the LDA–HDA transformation is detectable up to χ g ≈ 5%. As the concentration increases, the density of the starting glass (i.e., LDA at approximately χ g ≤ 5%) rapidly increases while, instead, the density of HDA remains practically constant. Accordingly, the LDA state and hence glass polymorphism become inaccessible for glassy mixtures with approximately χ g > 5%. We present an analysis of the molecular-level changes underlying the LDA–HDA transformation. As observed in pure glassy water, during the LDA-to-HDA transformation, water molecules within the mixture approach each other, moving from the second to the first hydration shell and filling the first interstitial shell of water molecules. Interestingly, similar changes also occur around glycerol OH groups. It follows that glycerol OH groups contribute to the density increase during the LDA–HDA transformation. An analysis of the hydrogen bond (HB)-network of the mixtures shows that the LDA–HDA transformation is accompanied by minor changes in the number of HBs of water and glycerol. Instead, large changes in glycerol and water coordination numbers occur. We also perform a detailed analysis of the effects that the glycerol force field (FF) has on our results. By comparing MD simulations using two different glycerol models, we find that glycerol conformations indeed depend on the FF employed. Yet, the thermodynamic and microscopic mechanisms accompanying the LDA–HDA transformation and hence, our main results, do not. This work is accompanied by an experimental report where we study the glass polymorphism in glycerol–water mixtures prepared by isobaric cooling at 1 bar. PMID:27063705

Evaluation of four supervised learning methods for groundwater spring potential mapping in Khalkhal region (Iran) using GIS-based features

NASA Astrophysics Data System (ADS)

Naghibi, Seyed Amir; Moradi Dashtpagerdi, Mostafa

2017-01-01

One important tool for water resources management in arid and semi-arid areas is groundwater potential mapping. In this study, four data-mining models including K-nearest neighbor (KNN), linear discriminant analysis (LDA), multivariate adaptive regression splines (MARS), and quadric discriminant analysis (QDA) were used for groundwater potential mapping to get better and more accurate groundwater potential maps (GPMs). For this purpose, 14 groundwater influence factors were considered, such as altitude, slope angle, slope aspect, plan curvature, profile curvature, slope length, topographic wetness index (TWI), stream power index, distance from rivers, river density, distance from faults, fault density, land use, and lithology. From 842 springs in the study area, in the Khalkhal region of Iran, 70 % (589 springs) were considered for training and 30 % (253 springs) were used as a validation dataset. Then, KNN, LDA, MARS, and QDA models were applied in the R statistical software and the results were mapped as GPMs. Finally, the receiver operating characteristics (ROC) curve was implemented to evaluate the performance of the models. According to the results, the area under the curve of ROCs were calculated as 81.4, 80.5, 79.6, and 79.2 % for MARS, QDA, KNN, and LDA, respectively. So, it can be concluded that the performances of KNN and LDA were acceptable and the performances of MARS and QDA were excellent. Also, the results depicted high contribution of altitude, TWI, slope angle, and fault density, while plan curvature and land use were seen to be the least important factors.

Changes of hematological and biochemical parameters and levels of pepsinogen, histamine and prostaglandins in dairy cows affected with left displacement of the abomasum.

PubMed

Al-Rawashdeh, O; Ismail, Z Bani; Talafha, A; Al-Momani, A

2017-03-28

The aims of this study were to determine the serum levels of pepsinogen, histamine, and prostaglandins F2α and E2 in lactating dairy cows affected with left displacement of the abomasum (LDA). In addition, the hematological and serum biochemical parameters were also determined in cows affected with LDA. A total of 52 adult lactating Holstein-Friesian cows affected with LDA and 30 normal cows (control) were used. In LDA cows, the average age, BCS and body weight were 4.9 ± 1.2 years, 2.5 ± 0.75, and 525 ± 150kg respectively. The average days-in-milk (DIM) in affected cows was 14 ± 6 with a range between 7 to 45 days. There were no significant differences in values of rectal temperature, heart rate and respiration rate between LDA cows and control. Rumen motility was significantly (p≤0.05) decreased in LDA cows. Cows affected with LDA had significantly (p≤0.05) increased glucose levels, and decreased levels of calcium and magnesium. There were significantly (p≤0.05) increased serum levels of pepsinogen and histamine in LDA cows while levels of prostaglandin E2 were significantly decreased in comparison to those in control cows. There were no significant changes in serum levels of prostaglandin F2α. In the hematology analyses, there were no significant changes in cows with LDA when compared to those in control cows. This study provides evidence of a possible role for pepsinogen, histamine and prostaglandin E2 in the etiopathophysiology of LDA in dairy cows.

Protein S deficiency complicated pregnancy in women with recurrent pregnancy loss.

PubMed

Shinozaki, Nanae; Ebina, Yasuhiko; Deguchi, Masashi; Tanimura, Kenji; Morizane, Mayumi; Yamada, Hideto

2016-08-01

This prospective study aimed to evaluate pregnancy outcome and complications in women with recurrent pregnancy loss (RPL) and protein S (PS) deficiency, who received low dose aspirin (LDA) or LDA plus heparin (LDA/H) therapies. Clinical characteristics, pregnancy outcome and complications of 38 women with two or more RPL and <60% of plasma free PS antigen were compared among three groups: antiphospholipid antibody (aPL)-negative women who received LDA (group A), aPL-negative women who received LDA/H (group B) and aPL-positive women who received LDA/H (group C). Gestational weeks (GW) at delivery in group C (median 32 GW) were earlier than 40 GW in group A and 38.5 GW in group B (p < 0.05). The birth weight in group C (median 1794 g) was less than 2855 g in group B (p < 0.05). The incidences of fetal growth restriction (37.5%), pregnancy-induced hypertension (37.5%), and preterm delivery (62.5%) in group C were higher than those (4.5%, 0%, and 4.5%, respectively) in group B (p<0.05). Women with RPL, PS deficiency, and positive aPL had high risks for adverse pregnancy outcome and complications, even when they received LDA/H therapy. Among women with RPL, PS, and negative aPL, there was no difference in these risks between LDA alone and LDA/H therapies.

Application of Linear Discriminant Analysis in Dimensionality Reduction for Hand Motion Classification

NASA Astrophysics Data System (ADS)

Phinyomark, A.; Hu, H.; Phukpattaranont, P.; Limsakul, C.

2012-01-01

The classification of upper-limb movements based on surface electromyography (EMG) signals is an important issue in the control of assistive devices and rehabilitation systems. Increasing the number of EMG channels and features in order to increase the number of control commands can yield a high dimensional feature vector. To cope with the accuracy and computation problems associated with high dimensionality, it is commonplace to apply a processing step that transforms the data to a space of significantly lower dimensions with only a limited loss of useful information. Linear discriminant analysis (LDA) has been successfully applied as an EMG feature projection method. Recently, a number of extended LDA-based algorithms have been proposed, which are more competitive in terms of both classification accuracy and computational costs/times with classical LDA. This paper presents the findings of a comparative study of classical LDA and five extended LDA methods. From a quantitative comparison based on seven multi-feature sets, three extended LDA-based algorithms, consisting of uncorrelated LDA, orthogonal LDA and orthogonal fuzzy neighborhood discriminant analysis, produce better class separability when compared with a baseline system (without feature projection), principle component analysis (PCA), and classical LDA. Based on a 7-dimension time domain and time-scale feature vectors, these methods achieved respectively 95.2% and 93.2% classification accuracy by using a linear discriminant classifier.

Evaluation of burst-mode LDA spectra with implications

NASA Astrophysics Data System (ADS)

Velte, Clara; George, William

2009-11-01

Burst-mode LDA spectra, as described in [1], are compared to spectra obtained from corresponding HWA measurements using the FFT in a round jet and cylinder wake experiment. The phrase ``burst-mode LDA'' refers to an LDA which operates with at most one particle present in the measuring volume at a time. Due to the random sampling and velocity bias of the LDA signal, the Direct Fourier Transform with accompanying weighting by the measured residence times was applied to obtain a correct interpretation of the spectral estimate. Further, the self-noise was removed as described in [2]. In addition, resulting spectra from common interpolation and uniform resampling techniques are compared to the above mentioned estimates. The burst-mode LDA spectra are seen to concur well with the HWA spectra up to the emergence of the noise floor, caused mainly by the intermittency of the LDA signal. The interpolated and resampled counterparts yield unphysical spectra, which are buried in frequency dependent noise and step noise, except at very high LDA data rates where they perform well up to a limited frequency.[4pt] [1] Buchhave, P. PhD Thesis, SUNY/Buffalo, 1979.[0pt] [2] Velte, C.M. PhD Thesis, DTU/Copenhagen, 2009.

Comparison of Fecal Microbiota between German Holstein Dairy Cows with and without Left-Sided Displacement of the Abomasum

PubMed Central

Song, Eun-Sik; Jung, Sang Il; Park, Hyung-Jin; Seo, Kyoung-Won; Son, Jeong-Hoon; Hong, Sanghyun; Shim, Minkyung

2016-01-01

One of the most common diseases in high-performance German Holstein dairy cows is left-sided displacement of the abomasum (LDA). Hypomotility of the abomasum is detrimental during the pathogenesis of LDA. It is known that improper interactions between the gut microbiota and the enteric nervous system contribute to dysfunctions of gastrointestinal motility. Therefore, we hypothesized that the gut microbial composition will be different between German Holstein dairy cows with and without LDA. We used 16S rRNA gene analysis to evaluate whether there are any differences in bacterial composition between German Holstein dairy cows with and without LDA. Even though our data are limited to being used to correlate compositional changes with corresponding functional aspects in the pathogenesis of LDA, results from this study show that the fecal microbial compositions of German Holstein dairy cows with LDA shifted and were less diverse than those in normal cows. In particular, Spirochaetes were absent in cows with LDA. PMID:26842700

Shock-Compressed Hydrogen

NASA Astrophysics Data System (ADS)

Bickham, S. R.; Collins, L. A.; Kress, J. D.; Lenosky, T. J.

1999-06-01

To investigate recent gas-gun and laser experiments on hydrogen at elevated temperatures and high densities, we have performed quantum molecular dynamics simulations using a variety of sophisticated models, ranging from tight-binding(TB) to density functional(DF)(T.J. Lenosky, J.D. Kress, L.A. Collins, and I. Kwon Phys. Rev. B 55), R11907(1997) and references therein.. The TB models have been especially tailored to reproduce experimental findings, such as Diamond-Anvil Cell data, and ab initio calculations, such as H_2, H_3, and H4 potential energy surfaces. The DF calculations have employed the local-density approximation(LDA) as well as generalized gradient corrections(GGA) with large numbers of plane-waves ( ~10^5) that represent a very broad range of excited and continuum electronic states. Good agreement obtains among all these models. The simulations exhibit a rapidly rising electrical conductivity at low temperatures and high pressures in good agreement with the gas-gun results. This conduction property stems from a mobility of the electrons provided principally by the dissociated monomers. The Hugoniot for the conditions of the laser experiment, generated from the TB Equation-of-State, shows a maximum compression of around four instead of the observed six. We also report optical properties of the hydrogen media.

The Dynamical Structure Factor of NiO and CoO*

NASA Astrophysics Data System (ADS)

Larson, B. C.; Zschack, P.; Finkelstein, K. D.; Ku, Wei; Restrepo, O.; Equiluz, A. G.

2005-03-01

Non-resonant inelastic x-ray scattering (IXS) and ab initio dynamical electronic response calculations have been used to investigate highly correlated transition metal monoxides NiO and CoO. Absolute IXS measurements were made as a function of the magnitude and orientation of momentum transfers, q, at the APS and CHESS using energy resolution ranging from 0.3 -- 1.1 eV. In addition to ˜4 eV energy gaps observed for all q, sharp excitonic peaks were observed below the gap of both NiO and CoO for momentum transfers higher than ˜2 A-1. Comparisons of S(q,w) measurements with dynamical response calculations performed within LDA+U (including crystal field effects) show that the gap energy and the electronic response above the gap are described by U ˜8 eV within RPA for low q-values. However, the excitonic peaks are not described by LDA+U calculations, nor are the calculated S(q,w) spectra in agreement with the measured response for large q. The results will be compared with resonant x-ray emission and resonant electron energy loss spectra in the literature. *Work at the APS supported by the DOE Office of Science, DMS under contract with ORNL, managed by UT-Battelle, LLC; UNI-CAT is supported by UIUC, ORNL, NIST and UOP Res., Inc. The APS is supported by the DOE and CHESS is supported by the NSF.

Moments and Root-Mean-Square Error of the Bayesian MMSE Estimator of Classification Error in the Gaussian Model.

PubMed

Zollanvari, Amin; Dougherty, Edward R

2014-06-01

The most important aspect of any classifier is its error rate, because this quantifies its predictive capacity. Thus, the accuracy of error estimation is critical. Error estimation is problematic in small-sample classifier design because the error must be estimated using the same data from which the classifier has been designed. Use of prior knowledge, in the form of a prior distribution on an uncertainty class of feature-label distributions to which the true, but unknown, feature-distribution belongs, can facilitate accurate error estimation (in the mean-square sense) in circumstances where accurate completely model-free error estimation is impossible. This paper provides analytic asymptotically exact finite-sample approximations for various performance metrics of the resulting Bayesian Minimum Mean-Square-Error (MMSE) error estimator in the case of linear discriminant analysis (LDA) in the multivariate Gaussian model. These performance metrics include the first, second, and cross moments of the Bayesian MMSE error estimator with the true error of LDA, and therefore, the Root-Mean-Square (RMS) error of the estimator. We lay down the theoretical groundwork for Kolmogorov double-asymptotics in a Bayesian setting, which enables us to derive asymptotic expressions of the desired performance metrics. From these we produce analytic finite-sample approximations and demonstrate their accuracy via numerical examples. Various examples illustrate the behavior of these approximations and their use in determining the necessary sample size to achieve a desired RMS. The Supplementary Material contains derivations for some equations and added figures.

Detection of attenuated plaque in stable angina with 64-multidetector computed tomography: a comparison with intravascular ultrasound.

PubMed

Jinzaki, Masahiro; Okabe, Teruo; Endo, Ayaka; Kawamura, Akio; Koga, Seiko; Yamada, Minoru; Fukuda, Keiichi; Kuribayashi, Sachio

2012-01-01

To clarify multidetector computed tomography (MDCT) findings of attenuated plaque detected by intravascular ultrasound (IVUS). One hundred and fifty-four patients with stable angina underwent MDCT before IVUS. The attenuated plaque was identified in the targeted artery with IVUS, and the same artery was analyzed with MDCT for the presence of a high density area (HDA) >130 Hounsfield units (HU), and a low density area (LDA) <30 HU. A HDA in attenuated plaque was compared with that in calcified plaque. Ten attenuated plaques and 15 calcified plaques were identified in 9 of 154 patients (males=9, 66.2 ± 9.5 years). Eight of the 10 attenuated plaques and all 15 calcified plaques were accompanied with a HDA on MDCT. The HDA ranged from 174 to 667 HU (mean 389.0 ± 148.3 HU) in the 8 attenuated plaques, and from 545 to 1,205 HU (mean 920.9 ± 215.9 HU) in 15 calcified plaques. There was a significant difference in CT density of the HDA between the attenuated and calcified plaque (P<0.001). All attenuated plaques contained LDA <30 HU in the portions without HDA. MDCT has the ability to demonstrate attenuated plaque as the combination of HDA (approximately 400 HU on average) and LDA <30 HU. The HDA can be differentiated from calcified plaque by its lower CT density value.

Simultaneous measurement of acoustic and streaming velocities in a standing wave using laser Doppler anemometry.

PubMed

Thompson, Michael W; Atchley, Anthony A

2005-04-01

Laser Doppler anemometry (LDA) with burst spectrum analysis (BSA) is used to study the acoustic streaming generated in a cylindrical standing-wave resonator filled with air. The air column is driven sinusoidally at a frequency of approximately 310 Hz and the resultant acoustic-velocity amplitudes are less than 1.3 m/s at the velocity antinodes. The axial component of fluid velocity is measured along the resonator axis, across the diameter, and as a function of acoustic amplitude. The velocity signals are postprocessed using the Fourier averaging method [Sonnenberger et al., Exp. Fluids 28, 217-224 (2000)]. Equations are derived for determining the uncertainties in the resultant Fourier coefficients. The time-averaged velocity-signal components are seen to be contaminated by significant errors due to the LDA/BSA system. In order to avoid these errors, the Lagrangian streaming velocities are determined using the time-harmonic signal components and the arrival times of the velocity samples. The observed Lagrangian streaming velocities are consistent with Rott's theory [N. Rott, Z. Angew. Math. Phys. 25, 417-421 (1974)], indicating that the dependence of viscosity on temperature is important. The onset of streaming is observed to occur within approximately 5 s after switching on the acoustic field.

Pressure effect on the energy structure and superexchange interaction in undoped orthorhombic La2CuO4

NASA Astrophysics Data System (ADS)

Gavrichkov, Vladimir A.; Pchelkina, Zlata V.; Nekrasov, Igor A.; Ovchinnikov, Sergey G.

2016-09-01

We studied the pressure dependences of the electronic structure and superexchange interaction J(P) = JA - JB (where JA and JB are antiferromagnetic (AFM) and ferromagnetic (FM) contributions) in antiferromagnetic La214 under hydrostatic, uniaxial (along c-axial) 3% compressions and 1% in-plane compressions by the local density approximation with generalized tight-binding method (LDA + GTB cell approach). The changes in J(P) correlated with the experimentally known TC(P) dependence are in accordance with the relation dTC/dP = (∂TC/∂J)(∂J/∂P), where ∂TC/∂J ˜ 0.1. The in-plane pressure more effectively stabilizes the ground singlet two-hole state A1 than the simple hydrostatic pressure, its effect on J and TC is the largest. Within the same cell approach together with the superexchange interaction J(P), the valence band structure was calculated. Its changes with pressure clearly reproduce the k-distribution of the singlet and triplet quasi-particles over the Brillouin zone (BZ).

Quasiparticle self-consistent GW study of cuprates: electronic structure, model parameters, and the two-band theory for Tc.

PubMed

Jang, Seung Woo; Kotani, Takao; Kino, Hiori; Kuroki, Kazuhiko; Han, Myung Joon

2015-07-24

Despite decades of progress, an understanding of unconventional superconductivity still remains elusive. An important open question is about the material dependence of the superconducting properties. Using the quasiparticle self-consistent GW method, we re-examine the electronic structure of copper oxide high-Tc materials. We show that QSGW captures several important features, distinctive from the conventional LDA results. The energy level splitting between d(x(2)-y(2)) and d(3z(2)-r(2)) is significantly enlarged and the van Hove singularity point is lowered. The calculated results compare better than LDA with recent experimental results from resonant inelastic xray scattering and angle resolved photoemission experiments. This agreement with the experiments supports the previously suggested two-band theory for the material dependence of the superconducting transition temperature, Tc.

A DFT study on the enthalpies of thermite reactions and enthalpies of formation of metal composite oxide

NASA Astrophysics Data System (ADS)

Zhang, Yu-ying; Wang, Meng-jie; Chang, Chun-ran; Xu, Kang-zhen; Ma, Hai-xia; Zhao, Feng-qi

2018-05-01

The standard thermite reaction enthalpies (ΔrHmθ) for seven metal oxides were theoretically analyzed using density functional theory (DFT) under five different functional levels, and the results were compared with experimental values. Through the comparison of the linear fitting constants, mean error and root mean square error, the Perdew-Wang functional within the framework of local density approximation (LDA-PWC) and Perdew-Burke-Ernzerhof exchange-correlation functional within the framework of generalized gradient approximation (GGA-PBE) were selected to further calculate the thermite reaction enthalpies for metal composite oxides (MCOs). According to the Kirchhoff formula, the standard molar reaction enthalpies for these MCOs were obtained and their standard molar enthalpies of formation (ΔfHmθ) were finally calculated. The results indicated that GGA-PBE is the most suitable one out of the total five methods to calculate these oxides. Tungstate crystals present the maximum deviation of the enthalpies of thermite reactions for MCOs and these of their physical metal oxide mixtures, but ferrite crystals are the minimum. The correlation coefficients are all above 0.95, meaning linear fitting results are very precise. And the molar enthalpies of formation for NiMoO4, CuMoO4, PbZrO3 (Pm/3m), PbZrO3 (PBA2), PbZrO3 (PBam), MgZrO3, CdZrO3, MnZrO3, CuWO4 and Fe2WO6 were first obtained as -1078.75, -1058.45, -1343.87, -1266.54, -1342.29, -1333.03, -1210.43, -1388.05, -1131.07 and - 1860.11 kJ·mol-1, respectively.

Predicting critical temperatures of iron(II) spin crossover materials: Density functional theory plus U approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yachao, E-mail: yczhang@nano.gznc.edu.cn

2014-12-07

A first-principles study of critical temperatures (T{sub c}) of spin crossover (SCO) materials requires accurate description of the strongly correlated 3d electrons as well as much computational effort. This task is still a challenge for the widely used local density or generalized gradient approximations (LDA/GGA) and hybrid functionals. One remedy, termed density functional theory plus U (DFT+U) approach, introduces a Hubbard U term to deal with the localized electrons at marginal computational cost, while treats the delocalized electrons with LDA/GGA. Here, we employ the DFT+U approach to investigate the T{sub c} of a pair of iron(II) SCO molecular crystals (αmore » and β phase), where identical constituent molecules are packed in different ways. We first calculate the adiabatic high spin-low spin energy splitting ΔE{sub HL} and molecular vibrational frequencies in both spin states, then obtain the temperature dependent enthalpy and entropy changes (ΔH and ΔS), and finally extract T{sub c} by exploiting the ΔH/T − T and ΔS − T relationships. The results are in agreement with experiment. Analysis of geometries and electronic structures shows that the local ligand field in the α phase is slightly weakened by the H-bondings involving the ligand atoms and the specific crystal packing style. We find that this effect is largely responsible for the difference in T{sub c} of the two phases. This study shows the applicability of the DFT+U approach for predicting T{sub c} of SCO materials, and provides a clear insight into the subtle influence of the crystal packing effects on SCO behavior.« less

Letter to Russia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tobin, J G

Below is the referee report. It is not as bad as it seems at first. The manuscript has not been rejected. Instead, the referee is 'not recommending publication.' On the APS website, the status is 'with authors,' instead of 'not under consideration.' Thus, this manuscript is still alive, but we will need to work on it. Please take a look at what the referee says below and let me know how you would respond. I will do the same. Hopefully, we will be able to respond well and find a way for this manuscript to get into PRB. According tomore » the introduction of their manuscript, the authors intend to study the electronic structure of clusters of Pu atoms and, among other things, to illustrate how the properties of the cluster's central region approach those of the bulk Pu metal as the cluster size increases. It is then somewhat surprising to find out that all the 'cluster' calculations discussed in the paper are in fact set up in such a way that they model the bulk properties - the clusters are embedded in a kind of mean field that is designed to approximate the rest of an infinite lattice (the authors call it the extended cluster scheme). Consequently, all the observed finite-size effects are essentially artificial since they represent the inaccuracies of the embedding procedure. The results for the finite clusters themselves do not carry a direct physical meaning (which contradicts authors statements from the introduction), only the extrapolation to the infinite cluster would, if done properly. The authors propose that the number of 5f electrons n{_}5f is a linear function of the cubic root of N, where N is the number of atoms in the cluster. This function fits the calculated data well (Fig. 8), but, as the authors indeed note, it cannot hold for very large N where n{_}5f must saturate at a finite value. The calculated data show no sign of such saturation (Fig. 8), which indicates that the considered clusters are too small to draw conclusions about the bulk properties. I find it puzzling that the authors nonetheless claim in their conclusions that 'An evaluation of state occupations supports the proposal that the occupation of the 5f levels in bulk Pu must be near 5'. Apart from the aforementioned conceptual inconsistencies, there are a number of more technical aspects that are not discussed in sufficient detail. Among these are: (1) The authors use LDA to approximate the electron correlations. A lively debate takes place in the literature whether this approximation can adequately describe the electronic structure of Pu metal or not, yet the authors do not discuss the choice of the approximation at all, which they should, in my opinion. They should also specify if their solutions are spin polarized or whether they use spin-restricted LDA. (2) The quality of the employed basis set is not clear. Are the results converged with respect to the basis size? What is the estimated magnitude of the residual errors? (3) There are statements in the manuscript indicating that the cluster calculations depend somehow on the calculations of the diatomic molecule. Namely: 'Underpinning these calculations, there is a geometry optimization of diatomic molecules...' and 'Underlying the Pu cluster simulations is the calculation of the electronic structure of a Pu2 dimer with the bond length 3.28 {angstrom} corresponding to the inter-atomic distances in delta-Pu.' What does this underpinning/underlying mean in more technical terms? What role does the geometry optimization play when the cluster calculations seem to be performed at a fixed geometry corresponding to the delta-Pu? Lastly, the manuscript contains a lot of material that was previously (and often multiple times) published elsewhere, including the Physical Review journals. For instance, the experimental part of Fig. 2 was shown already in Refs. 26, 27 and 28 in essentially the same graphical form; the top part of Fig. 9 appeared in Refs. 19, 4 and in PRL 90, 196404 (2003). I think that reprinting these results is not necessary and just referencing the earlier papers would be sufficient.« less

Novel 3D bio-macromolecular bilinear descriptors for protein science: Predicting protein structural classes.

PubMed

Marrero-Ponce, Yovani; Contreras-Torres, Ernesto; García-Jacas, César R; Barigye, Stephen J; Cubillán, Néstor; Alvarado, Ysaías J

2015-06-07

In the present study, we introduce novel 3D protein descriptors based on the bilinear algebraic form in the ℝ(n) space on the coulombic matrix. For the calculation of these descriptors, macromolecular vectors belonging to ℝ(n) space, whose components represent certain amino acid side-chain properties, were used as weighting schemes. Generalization approaches for the calculation of inter-amino acidic residue spatial distances based on Minkowski metrics are proposed. The simple- and double-stochastic schemes were defined as approaches to normalize the coulombic matrix. The local-fragment indices for both amino acid-types and amino acid-groups are presented in order to permit characterizing fragments of interest in proteins. On the other hand, with the objective of taking into account specific interactions among amino acids in global or local indices, geometric and topological cut-offs are defined. To assess the utility of global and local indices a classification model for the prediction of the major four protein structural classes, was built with the Linear Discriminant Analysis (LDA) technique. The developed LDA-model correctly classifies the 92.6% and 92.7% of the proteins on the training and test sets, respectively. The obtained model showed high values of the generalized square correlation coefficient (GC(2)) on both the training and test series. The statistical parameters derived from the internal and external validation procedures demonstrate the robustness, stability and the high predictive power of the proposed model. The performance of the LDA-model demonstrates the capability of the proposed indices not only to codify relevant biochemical information related to the structural classes of proteins, but also to yield suitable interpretability. It is anticipated that the current method will benefit the prediction of other protein attributes or functions. Copyright © 2015 Elsevier Ltd. All rights reserved.

Proton pump inhibitors in prevention of low-dose aspirin-associated upper gastrointestinal injuries.

PubMed

Mo, Chen; Sun, Gang; Lu, Ming-Liang; Zhang, Li; Wang, Yan-Zhi; Sun, Xi; Yang, Yun-Sheng

2015-05-07

To determine the preventive effect and safety of proton pump inhibitors (PPIs) in low-dose aspirin (LDA)-associated gastrointestinal (GI) ulcers and bleeding. We searched MEDLINE, EMBASE and the Cochrane Controlled Trials Register from inception to December 2013, and checked conference abstracts of randomized controlled trials (RCTs) on the effect of PPIs in reducing adverse GI events (hemorrhage, ulcer, perforation, or obstruction) in patients taking LDA. The preventive effects of PPIs were compared with the control group [taking placebo, a cytoprotective agent, or an H2 receptor antagonist (H2RA)] in LDA-associated upper GI injuries. The meta-analysis was performed using RevMan 5.1 software. We evaluated 8780 participants in 10 RCTs. The meta-analysis showed that PPIs decreased the risk of LDA-associated upper GI ulcers (OR = 0.16; 95%CI: 0.12-0.23) and bleeding (OR = 0.27; 95%CI: 0.16-0.43) compared with control. For patients treated with dual anti-platelet therapy of LDA and clopidogrel, PPIs were able to prevent the LDA-associated GI bleeding (OR = 0.36; 95%CI: 0.15-0.87) without increasing the risk of major adverse cardiovascular events (MACE) (OR = 1.00; 95%CI: 0.76-1.31). PPIs were superior to H2RA in prevention of LDA-associated GI ulcers (OR = 0.12; 95%CI: 0.02-0.65) and bleeding (OR = 0.32; 95%CI: 0.13-0.79). PPIs are effective in preventing LDA-associated upper GI ulcers and bleeding. Concomitant use of PPI, LDA and clopidogrel did not increase the risk of MACE.

Redundancy-Aware Topic Modeling for Patient Record Notes

PubMed Central

Cohen, Raphael; Aviram, Iddo; Elhadad, Michael; Elhadad, Noémie

2014-01-01

The clinical notes in a given patient record contain much redundancy, in large part due to clinicians’ documentation habit of copying from previous notes in the record and pasting into a new note. Previous work has shown that this redundancy has a negative impact on the quality of text mining and topic modeling in particular. In this paper we describe a novel variant of Latent Dirichlet Allocation (LDA) topic modeling, Red-LDA, which takes into account the inherent redundancy of patient records when modeling content of clinical notes. To assess the value of Red-LDA, we experiment with three baselines and our novel redundancy-aware topic modeling method: given a large collection of patient records, (i) apply vanilla LDA to all documents in all input records; (ii) identify and remove all redundancy by chosing a single representative document for each record as input to LDA; (iii) identify and remove all redundant paragraphs in each record, leaving partial, non-redundant documents as input to LDA; and (iv) apply Red-LDA to all documents in all input records. Both quantitative evaluation carried out through log-likelihood on held-out data and topic coherence of produced topics and qualitative assessement of topics carried out by physicians show that Red-LDA produces superior models to all three baseline strategies. This research contributes to the emerging field of understanding the characteristics of the electronic health record and how to account for them in the framework of data mining. The code for the two redundancy-elimination baselines and Red-LDA is made publicly available to the community. PMID:24551060

Redundancy-aware topic modeling for patient record notes.

PubMed

Cohen, Raphael; Aviram, Iddo; Elhadad, Michael; Elhadad, Noémie

2014-01-01

The clinical notes in a given patient record contain much redundancy, in large part due to clinicians' documentation habit of copying from previous notes in the record and pasting into a new note. Previous work has shown that this redundancy has a negative impact on the quality of text mining and topic modeling in particular. In this paper we describe a novel variant of Latent Dirichlet Allocation (LDA) topic modeling, Red-LDA, which takes into account the inherent redundancy of patient records when modeling content of clinical notes. To assess the value of Red-LDA, we experiment with three baselines and our novel redundancy-aware topic modeling method: given a large collection of patient records, (i) apply vanilla LDA to all documents in all input records; (ii) identify and remove all redundancy by chosing a single representative document for each record as input to LDA; (iii) identify and remove all redundant paragraphs in each record, leaving partial, non-redundant documents as input to LDA; and (iv) apply Red-LDA to all documents in all input records. Both quantitative evaluation carried out through log-likelihood on held-out data and topic coherence of produced topics and qualitative assessment of topics carried out by physicians show that Red-LDA produces superior models to all three baseline strategies. This research contributes to the emerging field of understanding the characteristics of the electronic health record and how to account for them in the framework of data mining. The code for the two redundancy-elimination baselines and Red-LDA is made publicly available to the community.

Tunable optical properties of ZnCdTe2-xSex(x =0.625) chalcopyrite for photovoltaics; a mBJLDA approach

NASA Astrophysics Data System (ADS)

Kashyap, Manish K.; Paudyal, D.; Harmon, B. N.

In the present study, we have performed ab-initio simulations of sp-element defect in ZnCdTe2-xSex (x =0.625) chalcopyrite to check the tuning of band gap as compared to the pristine case. The exchange and correlation (XC) effects are taken into account by an orbital independent modified Becke-Johnson (mBJ) potential as coupled with Local Density Approximation (LDA) for these calculations. The calculated energy band structures show a direct band gap at the point in the brillouin zone for the pristine as well as the defected case and the band gap decreases with inclusion of sp-disorder. The imaginary dielectric function predicts the optical band gap of pristine ZnCdTe2 very close to the experimental value and the results are in reasonable agreement without applying any scissor operator. With inclusion of sp-element defect, the optical spectra is tuned to optimal region, suitable for photovoltaics. It is apparent that mBJ functional is well suited for calculating electronic structure of pristine as well as defected ZnCdTe2chalcopyrite. MKK acknowledges financial support from UGC, India in the form of RAMAN Post-doctoral fellowship. This work at Ames Laboratory was supported by the DOE, Office of Basic Energy Sciences, Materials Sciences Division under contract No. DE-AC02-07CH11358.

Band gap characterization of ternary BBi1-xNx (0≤x≤1) alloys using modified Becke-Johnson (mBJ) potential

NASA Astrophysics Data System (ADS)

Yalcin, Battal G.

2015-04-01

The semi-local Becke-Johnson (BJ) exchange-correlation potential and its modified form proposed by Tran and Blaha have attracted a lot of interest recently because of the surprisingly accurate band gaps they can deliver for many semiconductors and insulators (e.g., sp semiconductors, noble-gas solids, and transition-metal oxides). The structural and electronic properties of ternary alloys BBi1-xNx (0≤x≤1) in zinc-blende phase have been reported in this study. The results of the studied binary compounds (BN and BBi) and ternary alloys BBi1-xNx structures are presented by means of density functional theory. The exchange and correlation effects are taken into account by using the generalized gradient approximation (GGA) functional of Wu and Cohen (WC) which is an improved form of the most popular Perdew-Burke-Ernzerhof (PBE). For electronic properties the modified Becke-Johnson (mBJ) potential, which is more accurate than standard semi-local LDA and PBE calculations, has been chosen. Geometric optimization has been implemented before the volume optimization calculations for all the studied alloys structure. The obtained equilibrium lattice constants of the studied binary compounds are in coincidence with experimental works. And, the variation of the lattice parameter of ternary alloys BBi1-xNx almost perfectly matches with Vegard's law. The spin-orbit interaction (SOI) has been also considered for structural and electronic calculations and the results are compared to those of non-SOI calculations.

Preconception Low-Dose Aspirin Restores Diminished Pregnancy and Live Birth Rates in Women With Low-Grade Inflammation: A Secondary Analysis of a Randomized Trial.

PubMed

Sjaarda, Lindsey A; Radin, Rose G; Silver, Robert M; Mitchell, Emily; Mumford, Sunni L; Wilcox, Brian; Galai, Noya; Perkins, Neil J; Wactawski-Wende, Jean; Stanford, Joseph B; Schisterman, Enrique F

2017-05-01

Inflammation is linked to causes of infertility. Low-dose aspirin (LDA) may improve reproductive success in women with chronic, low-grade inflammation. To investigate the effect of preconception-initiated LDA on pregnancy rate, pregnancy loss, live birth rate, and inflammation during pregnancy. Stratified secondary analysis of a multicenter, block-randomized, double-blind, placebo-controlled trial. Four US academic medical centers, 2007 to 2012. Healthy women aged 18 to 40 years (N = 1228) with one to two prior pregnancy losses actively attempting to conceive. Preconception-initiated, daily LDA (81 mg) or matching placebo taken up to six menstrual cycles attempting pregnancy and through 36 weeks' gestation in women who conceived. Confirmed pregnancy, live birth, and pregnancy loss were compared between LDA and placebo, stratified by tertile of preconception, preintervention serum high-sensitivity C-reactive protein (hsCRP) (low, <0.70 mg/L; middle, 0.70 to <1.95 mg/L; high, ≥1.95 mg/L). Live birth occurred in 55% of women overall. The lowest pregnancy and live birth rates occurred among the highest hsCRP tertile receiving placebo (44% live birth). LDA increased live birth among high-hsCRP women to 59% (relative risk, 1.35; 95% confidence interval, 1.08 to 1.67), similar to rates in the lower and mid-CRP tertiles. LDA did not affect clinical pregnancy or live birth in the low (live birth: 59% LDA, 54% placebo) or midlevel hsCRP tertiles (live birth: 59% LDA, 59% placebo). In women attempting conception with elevated hsCRP and prior pregnancy loss, LDA may increase clinical pregnancy and live birth rates compared with women without inflammation and reduce hsCRP elevation during pregnancy. Copyright © 2017 by the Endocrine Society

Proton pump inhibitors in prevention of low-dose aspirin-associated upper gastrointestinal injuries

PubMed Central

Mo, Chen; Sun, Gang; Lu, Ming-Liang; Zhang, Li; Wang, Yan-Zhi; Sun, Xi; Yang, Yun-Sheng

2015-01-01

AIM: To determine the preventive effect and safety of proton pump inhibitors (PPIs) in low-dose aspirin (LDA)-associated gastrointestinal (GI) ulcers and bleeding. METHODS: We searched MEDLINE, EMBASE and the Cochrane Controlled Trials Register from inception to December 2013, and checked conference abstracts of randomized controlled trials (RCTs) on the effect of PPIs in reducing adverse GI events (hemorrhage, ulcer, perforation, or obstruction) in patients taking LDA. The preventive effects of PPIs were compared with the control group [taking placebo, a cytoprotective agent, or an H2 receptor antagonist (H2RA)] in LDA-associated upper GI injuries. The meta-analysis was performed using RevMan 5.1 software. RESULTS: We evaluated 8780 participants in 10 RCTs. The meta-analysis showed that PPIs decreased the risk of LDA-associated upper GI ulcers (OR = 0.16; 95%CI: 0.12-0.23) and bleeding (OR = 0.27; 95%CI: 0.16-0.43) compared with control. For patients treated with dual anti-platelet therapy of LDA and clopidogrel, PPIs were able to prevent the LDA-associated GI bleeding (OR = 0.36; 95%CI: 0.15-0.87) without increasing the risk of major adverse cardiovascular events (MACE) (OR = 1.00; 95%CI: 0.76-1.31). PPIs were superior to H2RA in prevention of LDA-associated GI ulcers (OR = 0.12; 95%CI: 0.02-0.65) and bleeding (OR = 0.32; 95%CI: 0.13-0.79). CONCLUSION: PPIs are effective in preventing LDA-associated upper GI ulcers and bleeding. Concomitant use of PPI, LDA and clopidogrel did not increase the risk of MACE. PMID:25954113

Many-Body Perturbation Theory (MBPT) and Time-Dependent Density-Functional Theory (TD-DFT): MBPT Insights About What Is Missing In, and Corrections To, the TD-DFT Adiabatic Approximation.

PubMed

Casida, Mark E; Huix-Rotllant, Miquel

2016-01-01

In their famous paper, Kohn and Sham formulated a formally exact density-functional theory (DFT) for the ground-state energy and density of a system of N interacting electrons, albeit limited at the time by certain troubling representability questions. As no practical exact form of the exchange-correlation (xc) energy functional was known, the xc-functional had to be approximated, ideally by a local or semilocal functional. Nowadays, however, the realization that Nature is not always so nearsighted has driven us up Perdew's Jacob's ladder to find increasingly nonlocal density/wavefunction hybrid functionals. Time-dependent (TD-) DFT is a younger development which allows DFT concepts to be used to describe the temporal evolution of the density in the presence of a perturbing field. Linear response (LR) theory then allows spectra and other information about excited states to be extracted from TD-DFT. Once again the exact TD-DFT xc-functional must be approximated in practical calculations and this has historically been done using the TD-DFT adiabatic approximation (AA) which is to TD-DFT very similar to what the local density approximation (LDA) is to conventional ground-state DFT. Although some of the recent advances in TD-DFT focus on what can be done within the AA, others explore ways around the AA. After giving an overview of DFT, TD-DFT, and LR-TD-DFT, this chapter focuses on many-body corrections to LR-TD-DFT as one way to build hybrid density-functional/wavefunction methodology for incorporating aspects of nonlocality in time not present in the AA.

Age and Stratigraphic Relationships in Massif-Debris-Apron Terrain in Western Phlegra Montes, Mars

NASA Astrophysics Data System (ADS)

Kress, A.; Head, J. W.; Safaeinili, A.; Holt, J.; Plaut, J.; Posiolova, L.; Phillips, R.; Seu, R.; Sharad Team

2010-03-01

SHARAD returns from lobate debris aprons (LDA) near Phlegra Montes may show similarly high ice contents to other LDA on Mars; geomorphology and surface ages of the deposits confirm this detection and support a debris-covered-glacier origin for LDA.

Electronic properties and structural phase transition in A4 [M4O4] (A=Li, Na, K and Rb; M=Ag and Cu): A first principles study

NASA Astrophysics Data System (ADS)

Umamaheswari, R.; Yogeswari, M.; Kalpana, G.

2013-02-01

Self-consistent scalar relativistic band structure calculations for AMO (A=Li, Na, K and Rb; M=Ag and Cu) compounds have been performed using the tight-binding linear muffin-tin orbital (TB-LMTO) method within the local density approximation (LDA). At ambient conditions, these compounds are found to crystallize in tetragonal KAgO-type structure with two different space group I-4m2 and I4/mmm. Nowadays, hypothetical structures are being considered to look for new functional materials. AMO compounds have stoichiometry similar to eight-electron half-Heusler materials of type I-I-VI which crystallizes in cubic (C1b) MgAgAs-type structure with space group F-43m. For all these compounds, by interchanging the positions of atoms in the hypothetical cubic structure, three phases (α, β and γ) are formed. The energy-volume relation for these compounds in tetragonal KAgO-type structure and cubic α, β and γ phases of related structure have been obtained. Under ambient conditions these compounds are more stable in tetragonal KAgO-type (I4/mmm) structure. The total energies calculated within the atomic sphere approximation (ASA) were used to determine the ground state properties such as equilibrium lattice parameters, c/a ratio, bulk modulus, cohesive energy and are compared with the available experimental results. The results of the electronic band structure calculations at ambient condition show that LiCuO and NaMO are indirect band gap semiconductors whereas KMO and RbMO are direct band gap semiconductors. At high pressure the band gap decreases and the phenomenon of band overlap metallization occur. Also these compounds undergo structural phase transition from tetragonal I-4m2 phase to cubic α-phase and transition pressures were calculated.

Assessment of the GLLB-SC potential for solid-state properties and attempts for improvement

NASA Astrophysics Data System (ADS)

Tran, Fabien; Ehsan, Sohaib; Blaha, Peter

2018-02-01

Based on the work of Gritsenko et al. (GLLB) [Phys. Rev. A 51, 1944 (1995), 10.1103/PhysRevA.51.1944], the method of Kuisma et al. [Phys. Rev. B 82, 115106 (2010), 10.1103/PhysRevB.82.115106] to calculate the band gap in solids was shown to be much more accurate than the common local density approximation (LDA) and generalized gradient approximation (GGA). The main feature of the GLLB-SC potential (SC stands for solid and correlation) is to lead to a nonzero derivative discontinuity that can be conveniently calculated and then added to the Kohn-Sham band gap for a comparison with the experimental band gap. In this work, a thorough comparison of GLLB-SC with other methods, e.g., the modified Becke-Johnson (mBJ) potential [Tran and Blaha, Phys. Rev. Lett. 102, 226401 (2009), 10.1103/PhysRevLett.102.226401], for electronic, magnetic, and density-related properties is presented. It is shown that for the band gap, GLLB-SC does not perform as well as mBJ for systems with a small band gap and strongly correlated systems, but is on average of similar accuracy as hybrid functionals. The results on itinerant metals indicate that GLLB-SC overestimates significantly the magnetic moment (much more than mBJ does), but leads to excellent results for the electric field gradient, for which mBJ is in general not recommended. In the aim of improving the results, variants of the GLLB-SC potential are also tested.

Interaction between benzenedithiolate and gold: classical force field for chemical bonding.

PubMed

Leng, Yongsheng; Krstić, Predrag S; Wells, Jack C; Cummings, Peter T; Dean, David J

2005-06-22

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Cobalt spin states and hyperfine interactions in LaCoO3 investigated by LDA+U calculations

NASA Astrophysics Data System (ADS)

Leighton, C.; Hsu, H.; Blaha, P.; Wentzcovitch, R. M.

2010-12-01

The spin states of cobalt ions in the bulk and epitaxial-thin-film lanthanum cobaltite (LaCoO3) have been controversial for years. The controversial point is mainly the presence of intermediate-spin (IS) Co in the temperature range of 0-85 K. In this region, bulk LaCoO3 experiences a crossover from a diamagnetic to a paramagnetic phase, and the thin-film LaCoO3 is ferromagnetic and insulator. An approach to probe the Co spin state is thus of interest. With a series of LDA+U calculations, we have demonstrated that the electric field gradient (EFG) at the Co nucleus can be used as a fingerprint to identify the spin state of the Co ion in each case. Therefore, in principle, the spin state of the Co ion can be unambiguously determined from nuclear magnetic resonance (NMR) spectra. Our calculations also suggest that the presence of IS Co in this temperature range is unlikely, based not only on its relatively higher energy, but also on its associated conducting band structure incompatible with the measured insulating conductivity. This work was primarily supported by the MRSEC Program of NSF under Awards Number DMR-0212302 and DMR-0819885, and partially supported by NSF under ATM-0428774 (V-Lab), EAR-1019853, and EAR-0810272. The computations were performed mainly at the Minnesota Supercomputing Institute (MSI).

Constraints on Lobate Debris Apron Evolution and Rheology from Numerical Modeling of Ice Flow

NASA Astrophysics Data System (ADS)

Parsons, R.; Nimmo, F.

2010-12-01

Recent radar observations of mid-latitude lobate debris aprons (LDAs) have confirmed the presence of ice within these deposits. Radar observations in Deuteronilus Mensae have constrained the concentration of dust found within the ice deposits to <30% by volume based on the strength of the returned signal. In addition to constraining the dust fraction, these radar observations can measure the ice thickness - providing an opportunity to more accurately estimate the flow behavior of ice responsible for the formation of LDAs. In order to further constrain the age and rheology of LDA ice, we developed a numerical model simulating ice flow under Martian conditions using results from ice deformation experiments, theory of ice grain growth based on terrestrial ice cores, and observational constraints from radar profiles and laser altimetry. This finite difference model calculates the LDA profile shape as it flows over time assuming no basal slip. In our model, the ice rheology is determined by the concentration of dust which influences the ice grain size by pinning the ice grain boundaries and halting ice grain growth. By varying the dust fraction (and therefore the ice grain size), the ice temperature, the subsurface slope, and the initial ice volume we are able to determine the combination of parameters that best reproduce the observed LDA lengths and thicknesses over a period of time comparable to crater age dates of LDA surfaces (90 - 300 My, see figure). Based on simulations using different combinations of ice temperature, ice grain size, and basal slope, we find that an ice temperature of 205 K, a dust volume fraction of 0.5% (resulting in an ice grain size of 5 mm), and a flat subsurface slope give reasonable model LDA ages for many LDAs in the northern mid-latitudes of Mars. However, we find that there is no single combination of dust fraction, temperature, and subsurface slope which can give realistic ages for all LDAs suggesting that all or some of these variables are spatially heterogeneous. We conclude that there are important regional differences in either the amount of dust mixed in with the ice, or in the presence of a basal slope below the LDA ice. Alternatively, the ice temperature and/or timing of ice deposition may vary significantly between different mid-latitude regions. a) Topographic profiles plotted every 200 My (thin, solid lines) from a 1 Gy simulation of ice flow for an initial ice deposit (thick, solid line) 5 km long and 1 km thick using an ice temperature of 205 K and a dust fraction, φ, of 0.047%. A MOLA profile of an LDA at 38.6oN, 24.3oE (dashed line) is shown for comparison. b) Final profiles for simulations lasting 100 My using temperatures of 195, 205 and 215 K illustrate the effect of both temperature and increasing the dust volume fraction to 1.2% (resulting in an ice grain size of 1 mm).

p53-Based Strategy for Protection of Bone Marrow From Y-90 Ibritumomab Tiuxetan

DOE Office of Scientific and Technical Information (OSTI.GOV)

Su, Hang, E-mail: suh3@uthscsa.edu; Ganapathy, Suthakar; Li, Xiaolei

Purpose: The main drawbacks of radioimmunotherapy have been severe hematological toxicity and potential development of myelodysplastic syndrome and secondary leukemia. Activation of p53 follows a major pathway by which normal tissues respond to DNA-damaging agents, such as chemotherapy and radiation therapy, that result in injuries and pathological consequences. This pathway is separate from the tumor suppressor pathway of p53. We have previously reported that use of low-dose arsenic (LDA) temporarily and reversibly suppresses p53 activation, thereby ameliorating normal tissue toxicity from exposure to 5-fluorouracil and X rays. We have also demonstrated that LDA-mediated protection requires functional p53 and thus ismore » selective to normal tissues, as essentially every cancer cell has dysfunctional p53. Here we tested the protective efficacy of LDA for bone marrow tissue against radioimmunotherapy through animal experiments. Methods and Materials: Mice were subjected to LDA pretreatment for 3 days, followed by treatment with Y-90 ibritumomab tiuxetan. Both dose course (10, 25, 50, 100, and 200 μCi) and time course (6, 24, and 72 hours and 1 and 2 weeks) experiments were performed. The response of bone marrow cells to LDA was determined by examining the expression of NFκB, Glut1, and Glut3. Staining with hematoxylin and eosin, γ-H2AX, and terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) was used to examine morphology, DNA damage response, and apoptotic cell populations. Results: Elevated levels of NFκB, Glut1, and Glut3 were observed in bone marrow cells after LDA treatment. Bone marrow damage levels induced by Y-90 ibritumomab tiuxetan were greatly reduced by LDA pretreatment. Consistent with this observation, significantly less DNA damage and fewer apoptotic cells were accumulated after Y-90 ibritumomab tiuxetan treatment in LDA-pretreated mice. Furthermore, in the mouse xenograft model implanted with human Karpas-422 lymphoma cells, LDA pretreatment did not have any detectable effect on either tumor growth or Y-90 ibritumomab tiuxetan (200 μCi)-induced tumor suppression. Conclusions: LDA pretreatment protected bone marrow without compromising tumor control caused by Y-90 ibritumomab tiuxetan.« less

Glass and liquid phase diagram of a polyamorphic monatomic system.

PubMed

Reisman, Shaina; Giovambattista, Nicolas

2013-02-14

We perform out-of-equilibrium molecular dynamics (MD) simulations of a monatomic system with Fermi-Jagla (FJ) pair potential interactions. This model system exhibits polyamorphism both in the liquid and glass state. The two liquids, low-density (LDL) and high-density liquid (HDL), are accessible in equilibrium MD simulations and can form two glasses, low-density (LDA) and high-density amorphous (HDA) solid, upon isobaric cooling. The FJ model exhibits many of the anomalous properties observed in water and other polyamorphic liquids and thus, it is an excellent model system to explore qualitatively the thermodynamic properties of such substances. The liquid phase behavior of the FJ model system has been previously characterized. In this work, we focus on the glass behavior of the FJ system. Specifically, we perform systematic isothermal compression and decompression simulations of LDA and HDA at different temperatures and determine "phase diagrams" for the glass state; these phase diagrams varying with the compression/decompression rate used. We obtain the LDA-to-HDA and HDA-to-LDA transition pressure loci, P(LDA-HDA)(T) and P(HDA-LDA)(T), respectively. In addition, the compression-induced amorphization line, at which the low-pressure crystal (LPC) transforms to HDA, P(LPC-HDA)(T), is determined. As originally proposed by Poole et al. [Phys. Rev. E 48, 4605 (1993)] simulations suggest that the P(LDA-HDA)(T) and P(HDA-LDA)(T) loci are extensions of the LDL-to-HDL and HDL-to-LDL spinodal lines into the glass domain. Interestingly, our simulations indicate that the P(LPC-HDA)(T) locus is an extension, into the glass domain, of the LPC metastability limit relative to the liquid. We discuss the effects of compression/decompression rates on the behavior of the P(LDA-HDA)(T), P(HDA-LDA)(T), P(LPC-HDA)(T) loci. The competition between glass polyamorphism and crystallization is also addressed. At our "fast rate," crystallization can be partially suppressed and the glass phase diagram can be related directly with the liquid phase diagram. However, at our "slow rate," crystallization cannot be prevented at intermediate temperatures, within the glass region. In these cases, multiple crystal-crystal transformations are found upon compression/decompression (polymorphism).

Effect of substitutions and defects in half-Heusler FeVSb studied by electron transport measurements and KKR-CPA electronic structure calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jodin, L.; Tobola, J.; Pecheur, P.

2004-11-01

The structural and electron transport properties of the pure and Co-, Ti-, and Zr-substituted FeVSb half-Heusler phases have been investigated using x-ray diffraction, Moessbauer spectroscopy, and Electron Probe Microscopy Analysis as well as resistivity, thermopower, and Hall effect measurements in the 80-900 K temperature range. In a parallel study, the electronic structures of FeVSb and the aforementioned alloys were calculated using the Korringa-Kohn-Rostoker method with the coherent potential approximation (KKR-CPA) in the LDA framework. The electronic densities of states and dispersion curves were obtained. The crystal structure stability and site preference analysis were addressed using total energy computations. Most ofmore » these experimental results correspond to electronic structure computations only if they take into account extra crystal defects such as antisite defects or vacancies present to various extents in the samples. Indeed a remarkable variation of KKR-CPA density of states occurring both in FeVSb and FeV{sub 1-x}Zr{sub x}Sb including defects may explain why FeVSb is not fully semiconducting as well as why there is a change of the thermopower sign in the FeV{sub 1-x}Zr{sub x}Sb versus x content.« less

Ab-initio Density Functional Theory (DFT) Studies of Electronic, Transport, and Bulk Properties of Sodium Oxide (Na2O)

NASA Astrophysics Data System (ADS)

Polin, Daniel; Ziegler, Joshua; Malozovsky, Yuriy; Bagayoko, Diola

We present the findings of ab-initio calculations of electronic, transport, and structural properties of cubic sodium oxide (Na2O). These results were obtained using density functional theory (DFT), specifically a local density approximation (LDA) potential, and the linear combination of Gaussian orbitals (LCGO). Our implementation of LCGO followed the Bagayoko, Zhao, and Williams method as enhanced by the work of Ekuma and Franklin (BZW-EF). We describe the electronic band structure of Na2O with a direct band gap of 2.22 eV. Our results include predicted values for the electronic band structure and associated energy eigenvalues, the total and partial density of states (DOS and pDOS), the equilibrium lattice constant of Na2O, and the bulk modulus. We have also calculated the electron and holes effective masses in the Γ to L, Γ to X, and Γ to K directions. Acknowledgments: This work was funded in part by the National Science Foundation (NSF) and the Louisiana Board of Regents, through LASiGMA [Award Nos. EPS- 1003897, NSF (2010-15)-RII-SUBR] and NSF HRD-1002541, the US Department of Energy - National, Nuclear Security Administration (NNSA) (Award No. DE- NA0002630), LaSPACE, and LONI-SUBR.

Spin crossover in (Mg,Fe3+)(Si,Fe3+)O3 bridgmanite: effects of disorder, iron concentration, and temperature

NASA Astrophysics Data System (ADS)

Shukla, Gaurav; Wentzcovitch, Renata

The spin crossover of iron in Fe3+-bearing bridgmanite, the most abundant mineral of the Earth's lower mantle, is by now a well-established phenomenon, though several aspects of this crossover remain unclear. Here we investigate effects of disorder, iron concentration, and temperature on this crossover using ab initio LDA + USC calculations. Disorder and concentration effects are addressed using complete statistical samplings of coupled substituted configurations up to 80 atoms supercells, while the vibrational effects using the quasiharmonic approximation. Our calculated compression curves for iron-free and iron-bearing bridgmanite compare well with the latest experimental measurements. The comparison also suggests that in a closed system, Fe2+ present in the sample may transform into Fe3+ by introduction of Mg and O vacancies with increasing pressure. As in the spin crossover in ferropericlase, this crossover in bridgmanite is accompanied by a clear volume reduction and an anomalous softening of the bulk modulus throughout the crossover pressure range. Though the concentration of [Fe3+]Si in bridgmanite may be small, related elastic anomalies may impact the interpretation of radial and lateral velocity structures of the Earth's lower mantle. This research was supported primarily by NSF Grant EAR 1348066. Computations are performed at the Minnesota Supercomputing Institute (MSI).

LDA merging and splitting with applications to multiagent cooperative learning and system alteration.

PubMed

Pang, Shaoning; Ban, Tao; Kadobayashi, Youki; Kasabov, Nikola K

2012-04-01

To adapt linear discriminant analysis (LDA) to real-world applications, there is a pressing need to equip it with an incremental learning ability to integrate knowledge presented by one-pass data streams, a functionality to join multiple LDA models to make the knowledge sharing between independent learning agents more efficient, and a forgetting functionality to avoid reconstruction of the overall discriminant eigenspace caused by some irregular changes. To this end, we introduce two adaptive LDA learning methods: LDA merging and LDA splitting. These provide the benefits of ability of online learning with one-pass data streams, retained class separability identical to the batch learning method, high efficiency for knowledge sharing due to condensed knowledge representation by the eigenspace model, and more preferable time and storage costs than traditional approaches under common application conditions. These properties are validated by experiments on a benchmark face image data set. By a case study on the application of the proposed method to multiagent cooperative learning and system alternation of a face recognition system, we further clarified the adaptability of the proposed methods to complex dynamic learning tasks.

Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry.

PubMed

Wandy, Joe; Zhu, Yunfeng; van der Hooft, Justin J J; Daly, Rónán; Barrett, Michael P; Rogers, Simon

2017-09-14

We recently published MS2LDA, a method for the decomposition of sets of molecular fragment data derived from large metabolomics experiments. To make the method more widely available to the community, here we present ms2lda.org, a web application that allows users to upload their data, run MS2LDA analyses and explore the results through interactive visualisations. Ms2lda.org takes tandem mass spectrometry data in many standard formats and allows the user to infer the sets of fragment and neutral loss features that co-occur together (Mass2Motifs). As an alternative workflow, the user can also decompose a dataset onto predefined Mass2Motifs. This is accomplished through the web interface or programmatically from our web service. The website can be found at http://ms2lda.org , while the source code is available at https://github.com/sdrogers/ms2ldaviz under the MIT license. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Potential energy landscape of the apparent first-order phase transition between low-density and high-density amorphous ice.

PubMed

Giovambattista, Nicolas; Sciortino, Francesco; Starr, Francis W; Poole, Peter H

2016-12-14

The potential energy landscape (PEL) formalism is a valuable approach within statistical mechanics to describe supercooled liquids and glasses. Here we use the PEL formalism and computer simulations to study the pressure-induced transformations between low-density amorphous ice (LDA) and high-density amorphous ice (HDA) at different temperatures. We employ the ST2 water model for which the LDA-HDA transformations are remarkably sharp, similar to what is observed in experiments, and reminiscent of a first-order phase transition. Our results are consistent with the view that LDA and HDA configurations are associated with two distinct regions (megabasins) of the PEL that are separated by a potential energy barrier. At higher temperature, we find that low-density liquid (LDL) configurations are located in the same megabasin as LDA, and that high-density liquid (HDL) configurations are located in the same megabasin as HDA. We show that the pressure-induced LDL-HDL and LDA-HDA transformations occur along paths that interconnect these two megabasins, but that the path followed by the liquid is different from the path followed by the amorphous solid. At higher pressure, we also study the liquid-to-ice-VII first-order phase transition, and find that the behavior of the PEL properties across this transition is qualitatively similar to the changes found during the LDA-HDA transformation. This similarity supports the interpretation that the LDA-HDA transformation is a first-order phase transition between out-of-equilibrium states. Finally, we compare the PEL properties explored during the LDA-HDA transformations in ST2 water with those reported previously for SPC/E water, for which the LDA-HDA transformations are rather smooth. This comparison illuminates the previous work showing that, at accessible computer times scales, a liquid-liquid phase transition occurs in the case of ST2 water, but not for SPC/E water.

Potential energy landscape of the apparent first-order phase transition between low-density and high-density amorphous ice

NASA Astrophysics Data System (ADS)

Giovambattista, Nicolas; Sciortino, Francesco; Starr, Francis W.; Poole, Peter H.

2016-12-01

The potential energy landscape (PEL) formalism is a valuable approach within statistical mechanics to describe supercooled liquids and glasses. Here we use the PEL formalism and computer simulations to study the pressure-induced transformations between low-density amorphous ice (LDA) and high-density amorphous ice (HDA) at different temperatures. We employ the ST2 water model for which the LDA-HDA transformations are remarkably sharp, similar to what is observed in experiments, and reminiscent of a first-order phase transition. Our results are consistent with the view that LDA and HDA configurations are associated with two distinct regions (megabasins) of the PEL that are separated by a potential energy barrier. At higher temperature, we find that low-density liquid (LDL) configurations are located in the same megabasin as LDA, and that high-density liquid (HDL) configurations are located in the same megabasin as HDA. We show that the pressure-induced LDL-HDL and LDA-HDA transformations occur along paths that interconnect these two megabasins, but that the path followed by the liquid is different from the path followed by the amorphous solid. At higher pressure, we also study the liquid-to-ice-VII first-order phase transition, and find that the behavior of the PEL properties across this transition is qualitatively similar to the changes found during the LDA-HDA transformation. This similarity supports the interpretation that the LDA-HDA transformation is a first-order phase transition between out-of-equilibrium states. Finally, we compare the PEL properties explored during the LDA-HDA transformations in ST2 water with those reported previously for SPC/E water, for which the LDA-HDA transformations are rather smooth. This comparison illuminates the previous work showing that, at accessible computer times scales, a liquid-liquid phase transition occurs in the case of ST2 water, but not for SPC/E water.

Relationships between metabolite and IGF1 concentrations with fertility and production outcomes following left abomasal displacement.

PubMed

Lyons, N A; Cooke, J S; Wilson, S; van Winden, S C; Gordon, P J; Wathes, D C

2014-06-28

Left displacement of the abomasum (LDA) is an important periparturient disorder of dairy cows. This study evaluated differences in metabolic parameters between case-control pairs of cows (n=67) from 24 farms, and related these to outcomes in fertility and production. Cows with an assisted delivery were ×3 more likely to develop LDA, and affected cows tended to have had a longer dry period. At recruitment, cows with LDA tended to be in lower body condition accompanied by significantly higher circulating concentrations of β-hydroxybutyrate (BHB), non-esterified fatty acid (NEFA) and glucose and lower IGF1. Overall culling rate for all cows in the subsequent lactation was 22.5 per cent. Cows with LDA were not at increased odds of being culled but they produced, on average, 2272 l less milk and tended to have longer intervals to conception. Considering all cows irrespective of LDA status, the mean IGF1 level at recruitment was the only measured parameter associated with subsequent risk of culling (culled 11.7 ng/ml, not culled 23.5 ng/ml; P=0.005). Our findings support previous work indicating that poor insulin sensitivity through an uncoupling of the somatotrophic axis may be an important factor associated with LDA. Improved nutritional management of dry cows should reduce the incidence of both LDA and culling. British Veterinary Association.

Potential Energy Landscape of the Liquid-Liquid Phase Transition in Water and the transformation between Low-Density and High-Density Amorphous Ice

NASA Astrophysics Data System (ADS)

Giovambattista, N.; Sciortino, F.; Starr, F. W.; Poole, P. H.

The potential energy landscape (PEL) formalism is a valuable approach within statistical mechanics for describing supercooled liquids and glasses. We use the PEL formalism and computer simulations to study the transformation between low-density (LDL) and high-density liquid (HDL) water, and between low-density (LDA) and high-density amorphous ice (HDA). We employ the ST2 water model that exhibits a LDL-HDL first-order phase transition and a sharp LDA-HDA transformation, as observed in experiments. Our results are consistent with the view that LDA and HDA configurations are associated with two distinct regions (megabasins) of the PEL that are separated by a potential energy barrier. At higher temperature, we find that LDL configurations are located in the same megabasin as LDA, and that HDL configurations are located in the same megabasin as HDA. We show that the pressure-induced LDL-HDL and LDA-HDA transformations occur along paths that interconnect these two megabasins, but that the path followed by the liquid and the amorphous ice differ. We also study the liquid-to-ice-VII first-order phase transition. The PEL properties across this transition are qualitatively similar to the changes found during the LDA-HDA transformation, supporting the interpretation that the LDA-HDA transformation is a first-order-like phase transition between out-of-equilibrium states.

Transcription Factor Binding Site Polymorphism in the Motilin Gene Associated with Left-Sided Displacement of the Abomasum in German Holstein Cattle

PubMed Central

Mömke, Stefanie; Sickinger, Marlene; Rehage, Jürgen; Doll, Klaus; Distl, Ottmar

2012-01-01

Left-sided displacement of the abomasum (LDA) is a common disease in many dairy cattle breeds. A genome-wide screen for QTL for LDA in German Holstein (GH) cows indicated motilin (MLN) as a candidate gene on bovine chromosome 23. Genomic DNA sequence analysis of MLN revealed a total of 32 polymorphisms. All informative polymorphisms used for association analyses in a random sample of 1,136 GH cows confirmed MLN as a candidate for LDA. A single nucleotide polymorphism (FN298674:g.90T>C) located within the first non-coding exon of bovine MLN affects a NKX2-5 transcription factor binding site and showed significant associations (ORallele = 0.64; −log10Pallele = 6.8, −log10Pgenotype = 7.0) with LDA. An expression study gave evidence of a significantly decreased MLN expression in cows carrying the mutant allele (C). In individuals heterozygous or homozygous for the mutation, MLN expression was decreased by 89% relative to the wildtype. FN298674:g.90T>C may therefore play a role in bovine LDA via the motility of the abomasum. This MLN SNP appears useful to reduce the incidence of LDA in German Holstein cattle and provides a first step towards a deeper understanding of the genetics of LDA. PMID:22536407

Time-trends in the prescribing of gastroprotective agents to primary care patients initiating low-dose aspirin or non-steroidal anti-inflammatory drugs: a population-based cohort study

PubMed Central

Warlé-van Herwaarden, Margaretha F; Koffeman, Aafke R; Valkhoff, Vera E; ’t Jong, Geert W; Kramers, Cornelis; Sturkenboom, Miriam C; De Smet, Peter A G M

2015-01-01

Aims Low-dose aspirin (LDA) and non-steroidal-anti-inflammatory drugs (NSAIDs) both increase the risk of upper gastrointestinal events (UGIEs). In the Netherlands, recommendations regarding the prescription of gastroprotective agents (GPAs) in LDA users were first issued in 2009 in the HARM-Wrestling consensus. National guidelines on gastroprotective strategies (GPSs) in NSAID users were issued in the first part of the preceding. The aim of the present study was to examine time-trends in GPSs in patients initiating LDA and those initiating NSAIDs between 2000 and 2012. Methods Within a large electronic primary healthcare database, two cohorts were selected: (i) patients newly prescribed LDA and (ii) patients newly prescribed NSAIDs between 2000 and 2012. Patients who had been prescribed a GPA in the previous six months were excluded. For both cohorts, patients’ risk of a UGIE was classified as low, moderate or high, based on the HARM-Wrestling consensus, and the presence of an adequate GPSwas determined. Results A total of 37 578 patients were included in the LDA cohort and 352 025 patients in the NSAID cohort. In both cohorts, an increase in GPSs was observed over time, but prescription of GPAs was lower in the LDA cohort. By 2012, an adequate GPS was present in 31.8% of high-risk LDA initiators, vs. 48.0% of high-risk NSAID initiators. Conclusions Despite a comparable risk of UGIEs, GPSs are prescribed less in high-risk LDA initiators than in high-risk NSAID initiators. For both groups of patients, there is still room for improvement in guideline adherence. PMID:25777983

Time-trends in the prescribing of gastroprotective agents to primary care patients initiating low-dose aspirin or non-steroidal anti-inflammatory drugs: a population-based cohort study.

PubMed

Warlé-van Herwaarden, Margaretha F; Koffeman, Aafke R; Valkhoff, Vera E; 't Jong, Geert W; Kramers, Cornelis; Sturkenboom, Miriam C; De Smet, Peter A G M

2015-09-01

Low-dose aspirin (LDA) and non-steroidal-anti-inflammatory drugs (NSAIDs) both increase the risk of upper gastrointestinal events (UGIEs). In the Netherlands, recommendations regarding the prescription of gastroprotective agents (GPAs) in LDA users were first issued in 2009 in the HARM-Wrestling consensus. National guidelines on gastroprotective strategies (GPSs) in NSAID users were issued in the first part of the preceding. The aim of the present study was to examine time-trends in GPSs in patients initiating LDA and those initiating NSAIDs between 2000 and 2012. Within a large electronic primary healthcare database, two cohorts were selected: (i) patients newly prescribed LDA and (ii) patients newly prescribed NSAIDs between 2000 and 2012. Patients who had been prescribed a GPA in the previous six months were excluded. For both cohorts, patients' risk of a UGIE was classified as low, moderate or high, based on the HARM-Wrestling consensus, and the presence of an adequate GPSwas determined. A total of 37 578 patients were included in the LDA cohort and 352 025 patients in the NSAID cohort. In both cohorts, an increase in GPSs was observed over time, but prescription of GPAs was lower in the LDA cohort. By 2012, an adequate GPS was present in 31.8% of high-risk LDA initiators, vs. 48.0% of high-risk NSAID initiators. Despite a comparable risk of UGIEs, GPSs are prescribed less in high-risk LDA initiators than in high-risk NSAID initiators. For both groups of patients, there is still room for improvement in guideline adherence. © 2015 The British Pharmacological Society.

Pharmacokinetic Drug-Drug Interactions Between Vonoprazan and Low-Dose Aspirin or Nonsteroidal Anti-inflammatory Drugs: A Phase 2, Open-Label, Study in Healthy Japanese Men.

PubMed

Sakurai, Yuuichi; Shiino, Madoka; Horii, Sayako; Okamoto, Hiroyuki; Nakamura, Koki; Nishimura, Akira; Sakata, Yukikuni

2017-01-01

Gastroprotective agents are recommended for patients receiving low-dose aspirin (LDA) or nonsteroidal anti-inflammatory drugs (NSAIDs). Vonoprazan is a potassium-competitive acid blocker recently approved for the prevention of peptic ulcer recurrence in patients receiving LDA or NSAIDs. This phase 2, open-label, single-center study in healthy Japanese males evaluated drug-drug interactions between vonoprazan 40 mg and LDA (100 mg) or NSAIDs [loxoprofen sodium (60 mg), diclofenac sodium (25 mg), or meloxicam (10 mg)] and vice versa. Subjects were allocated to one of eight cohorts and received their orally administered treatment regimen (to assess the effect of vonoprazan vs. NSAID or LDA, or vice versa) once daily. Endpoints were the pharmacokinetics of plasma concentrations of the study drugs alone and in combination (primary), safety (secondary), and vonoprazan effects on aspirin-mediated inhibition of platelet-aggregation. Of 109 subjects screened, 64 were assigned to one of eight cohorts (n = 8 per cohort) and received treatment, one subject discontinued due to a treatment-emergent adverse event (TEAE), and 63 completed the study. There were few differences in the pharmacokinetics of vonoprazan when administered with LDA or NSAIDs, and few differences in the pharmacokinetics of LDA or NSAIDs when administered with vonoprazan. The differences were small and not clinically meaningful. Inhibition of arachidonic-induced platelet aggregation by LDA was not influenced by vonoprazan. Six patients experienced a TEAE, all were mild and were deemed unrelated to study drugs. One subject withdrew due to infection (tonsillitis). No clinically meaningful drug-drug interactions were observed and vonoprazan was well tolerated when administered with LDA or NSAIDs. JapicCTI-153100.

An open-label randomized-controlled trial of low dose aspirin with an early screening test for pre-eclampsia and growth restriction (TEST): Trial protocol.

PubMed

Mone, Fionnuala; Mulcahy, Cecilia; McParland, Peter; Stanton, Alice; Culliton, Marie; Downey, Paul; McCormack, Dorothy; Tully, Elizabeth; Dicker, Patrick; Breathnach, Fionnuala; Malone, Fergal D; McAuliffe, Fionnuala M

2016-07-01

Pre-eclampsia remains a worldwide cause of maternal and perinatal morbidity and mortality. Low dose aspirin (LDA) can reduce the occurrence of pre-eclampsia in women with identifiable risk factors. Emerging screening tests can determine the maternal risk of developing placental disease, such as pre-eclampsia from the first trimester of pregnancy. The aim of this study is to determine if it is more beneficial in terms of efficacy and acceptability to routinely prescribe LDA to nulliparous low-risk women compared to test indicated LDA on the basis of a positive screening test for placental disease. We propose a three armed multi-center open-labeled randomized control trial of; (i) routine LDA, (ii) no aspirin, and (iii) LDA on the basis of a positive first trimester pre-eclampsia screening test. LDA (75mg once daily) shall be given from the first trimester until 36-week gestation. The primary outcome measures include; (i) the proportion of eligible women that agree to participate (acceptability), (ii) compliance with study protocol (acceptability and feasibility), (iii) the proportion of women in whom it is possible to obtain first trimester trans-abdominal uterine artery Doppler examination (feasibility) and (iv) the proportion of women with a completed screening test that are issued the screening result within one week of having the test performed (feasibility). This will be the first clinical trial to determine the efficacy and acceptability in low-risk women of taking routine LDA versus no aspirin versus LDA based on a positive first trimester screening test for the prevention of placental disease. Copyright © 2016 Elsevier Inc. All rights reserved.

High-density amorphous ice: nucleation of nanosized low-density amorphous ice

NASA Astrophysics Data System (ADS)

Tonauer, Christina M.; Seidl-Nigsch, Markus; Loerting, Thomas

2018-01-01

The pressure dependence of the crystallization temperature of different forms of expanded high-density amorphous ice (eHDA) was scrutinized. Crystallization at pressures 0.05-0.30 GPa was followed using volumetry and powder x-ray diffraction. eHDA samples were prepared via isothermal decompression of very high-density amorphous ice at 140 K to different end pressures between 0.07-0.30 GPa (eHDA0.07-0.3). At 0.05-0.17 GPa the crystallization line T x (p) of all eHDA variants is the same. At pressures  >0.17 GPa, all eHDA samples decompressed to pressures  <0.20 GPa exhibit significantly lower T x values than eHDA0.2 and eHDA0.3. We rationalize our findings with the presence of nanoscaled low-density amorphous ice (LDA) seeds that nucleate in eHDA when it is decompressed to pressures  <0.20 GPa at 140 K. Below ~0.17 GPa, these nanosized LDA domains are latent within the HDA matrix, exhibiting no effect on T x of eHDA<0.2. Upon heating at pressures  ⩾0.17 GPa, these nanosized LDA nuclei transform to ice IX nuclei. They are favored sites for crystallization and, hence, lower T x . By comparing crystallization experiments of bulk LDA with the ones involving nanosized LDA we are able to estimate the Laplace pressure and radius of ~0.3-0.8 nm for the nanodomains of LDA. The nucleation of LDA in eHDA revealed here is evidence for the first-order-like nature of the HDA  →  LDA transition, supporting water’s liquid-liquid transition scenarios.

Describing three-class task performance: three-class linear discriminant analysis and three-class ROC analysis

NASA Astrophysics Data System (ADS)

He, Xin; Frey, Eric C.

2007-03-01

Binary ROC analysis has solid decision-theoretic foundations and a close relationship to linear discriminant analysis (LDA). In particular, for the case of Gaussian equal covariance input data, the area under the ROC curve (AUC) value has a direct relationship to the Hotelling trace. Many attempts have been made to extend binary classification methods to multi-class. For example, Fukunaga extended binary LDA to obtain multi-class LDA, which uses the multi-class Hotelling trace as a figure-of-merit, and we have previously developed a three-class ROC analysis method. This work explores the relationship between conventional multi-class LDA and three-class ROC analysis. First, we developed a linear observer, the three-class Hotelling observer (3-HO). For Gaussian equal covariance data, the 3- HO provides equivalent performance to the three-class ideal observer and, under less strict conditions, maximizes the signal to noise ratio for classification of all pairs of the three classes simultaneously. The 3-HO templates are not the eigenvectors obtained from multi-class LDA. Second, we show that the three-class Hotelling trace, which is the figureof- merit in the conventional three-class extension of LDA, has significant limitations. Third, we demonstrate that, under certain conditions, there is a linear relationship between the eigenvectors obtained from multi-class LDA and 3-HO templates. We conclude that the 3-HO based on decision theory has advantages both in its decision theoretic background and in the usefulness of its figure-of-merit. Additionally, there exists the possibility of interpreting the two linear features extracted by the conventional extension of LDA from a decision theoretic point of view.

Comparison of diluents for holding cock semen six hours at 41 C.

PubMed

Howarth, B

1983-06-01

Beltsville Poultry Semen Extender (BPSE) and Lake's Diluent A (LDA) were compared with minimum essential medium (MEM) for their ability to maintain the fertilizing capacity of cock semen held 6 hr at 41 C. Motility significantly declined from the beginning to the end of the holding period for semen in BPSE and LDA. Only in LDA, however, were the number of live spermatozoa significantly reduced. Although there were no differences in oxygen (O2) consumption measured at 1 and 6 hr for semen in BPSE and MEM, a significant reduction in O2 consumption was observed between these time periods for semen in LDA. Fertility of semen held in MEM (90.3%) was significantly higher than the unstored control semen (82.9%) and semen held in either BPSE (3.5%) or LDA (1.9%). No differences in hatchability of fertile eggs were observed between the semen groups.

Flow patterns of lobate debris aprons and lineated valley fill north of Ismeniae Fossae, Mars: Evidence for extensive mid-latitude glaciation in the Late Amazonian

NASA Astrophysics Data System (ADS)

Baker, David M. H.; Head, James W.; Marchant, David R.

2010-05-01

A variety of Late Amazonian landforms on Mars have been attributed to the dynamics of ice-related processes. Evidence for large-scale, mid-latitude glacial episodes existing within the last 100 million to 1 billion years on Mars has been presented from analyses of lobate debris aprons (LDA) and lineated valley fill (LVF) in the northern and southern mid-latitudes. We test the glacial hypothesis for LDA and LVF along the dichotomy boundary in the northern mid-latitudes by examining the morphological characteristics of LDA and LVF surrounding two large plateaus, proximal massifs, and the dichotomy boundary escarpment north of Ismeniae Fossae (centered at 45.3°N and 39.2°E). Lineations and flow directions within LDA and LVF were mapped using images from the Context (CTX) camera, the Thermal Emission Imaging Spectrometer (THEMIS), and the High Resolution Stereo Camera (HRSC). Flow directions were then compared to topographic contours derived from the Mars Orbiter Laser Altimeter (MOLA) to determine the down-gradient components of LDA and LVF flow. Observations indicate that flow patterns emerge from numerous alcoves within the plateau walls, are integrated over distances of up to tens of kilometers, and have down-gradient flow directions. Smaller lobes confined within alcoves and superposed on the main LDA and LVF represent a later, less extensive glacial phase. Crater size-frequency distributions of LDA and LVF suggest a minimum (youngest) age of 100 Ma. The presence of ring-mold crater morphologies is suggestive that LDA and LVF are formed of near-surface ice-rich bodies. From these observations, we interpret LDA and LVF within our study region to result from formerly active debris-covered glacial flow, consistent with similar observations in the northern mid-latitudes of Mars. Glacial flow was likely initiated from the accumulation and compaction of snow and ice on plateaus and in alcoves within the plateau walls as volatiles were mobilized to the mid-latitudes during higher obliquity excursions. Together with similar analyses elsewhere along the dichotomy boundary, these observations suggest that multiple glacial episodes occurred in the Late Amazonian and that LDA and LVF represent significant reservoirs of non-polar ice sequestered below a surface lag for hundreds of millions of years.

Theoretical study on the electronic and optical properties of bulk and surface (001) InxGa1-xAs

NASA Astrophysics Data System (ADS)

Liu, XueFei; Ding, Zhao; Luo, ZiJiang; Zhou, Xun; Wei, JieMin; Wang, Yi; Guo, Xiang; Lang, QiZhi

2018-05-01

The optical properties of surface and bulk InxGa1-xAs materials are compared systematically first time in this paper. The band structures, density of states and optical properties including dielectric function, reflectivity, absorption coefficient, loss function and refractive index of bulk and surface InxGa1-xAs materials are investigated by first-principles based on plane-wave pseudo-potentials method within the LDA approximation. The results agree well with the available theoretical and experimental studies and indicate that the electronic and optical properties of bulk and surface InxGa1-xAs materials are much different, and the results show that the considered optical properties of the both materials vary with increasing indium composition in an opposite way. The calculations show that the optical properties of surface In0.75Ga0.25As material are unexpected to be far from the other two indium compositions of surface InxGa1-xAs materials while the optical properties of bulk InxGa1-xAs materials vary with increasing indium composition in an expected regular way.

Ab-initio Electronic, Transport and Related Properties of Zinc Blende Boron Arsenide (zb-BAs)

NASA Astrophysics Data System (ADS)

Nwigboji, Ifeanyi H.; Malozovsky, Yuriy; Bagayoko, Diola

We present results from ab-initio, self-consistent density functional theory (DFT) calculations of electronic, transport, and bulk properties of zinc blende boron arsenide (zb-BAs). We utilized a local density approximation (LDA) potential and the linear combination of atomic orbital (LCAO) formalism. Our computational technique follows the Bagayoko, Zhao, and Williams method, as enhanced by Ekuma and Franklin. Our results include electronic energy bands, densities of states, and effective masses. We explain the agreement between these findings, including the indirect band gap, and available, corresponding, experimental ones. This work confirms the capability of DFT to describe accurately properties of materials, provided the computations adhere to the conditions of validity of DFT [AIP Advances, 4, 127104 (2014)]. Acknowledgments: This work was funded in part by the National Science Foundation (NSF) and the Louisiana Board of Regents, through LASiGMA [Award Nos. EPS- 1003897, NSF (2010-15)-RII-SUBR] and NSF HRD-1002541, the US Department of Energy - National, Nuclear Security Administration (NNSA) (Award No. DE- NA0002630), LaSPACE, and LONI-SUBR.

Curie temperature study of {Y(Fe_{1-\\it x} {Co_{\\it x})_2}} and {Zr(Fe_{1-\\it x} {Co_{\\it x})_2}} systems using mean field theory and Monte Carlo method

NASA Astrophysics Data System (ADS)

Wasilewski, Bartosz; Marciniak, Wojciech; Werwiński, Mirosław

2018-05-01

Cubic Laves phases including , , , and are considered as promising candidates for application in hydrogen storage and magnetic refrigeration. While and are ferromagnets, alloying with Co decreases magnetic moments and Curie temperatures (T C) of pseudobinary and systems, leading to the paramagnetic states of and . The following study focuses on the investigation of Curie temperature of the and system from first principles. To do it, Monte Carlo (MC) simulations and the mean field theory (MFT) based on the disordered local moments (DLM) calculations are used. The DLM-MFT results agree qualitatively with the experimental data from the literature and preserve the characteristic features of dependencies for both and . However, we have encountered complications in the Co-rich regions due to failure of the local density approximation (LDA) in describing the Co magnetic moment in the DLM state. The analysis of Fe–Fe exchange couplings for and phases indicates that the nearest-neighbor interactions play the main role in the formation of .

A polarized neutron study of the magnetization distribution in Co₂FeSi.

PubMed

Brown, P J; Kainuma, R; Kanomata, T; Neumann, K-U; Okubo, A; Umetsu, R Y; Ziebeck, K R A

2013-05-22

The magnetization distribution in Co2FeSi which has the largest moment per formula unit ∼6 μB of all Heusler alloys, has been determined using polarized neutron diffraction. The experimentally determined magnetization has been integrated over spheres centred on the three sites of the L12 structure giving μ Fe = 3.10(3) μB and μ Co = 1.43(2) μB, results which are slightly lower than the moments in atomic spheres of similar radii obtained in recent LDA + U band structure calculations (Li et al 2010 Chin. Phys. B 19 097102). Approximately 50% of the magnetic carriers at the Fe sites were found to be in orbitals with eg symmetry. This was higher, ≃65%, at the Co sites. Both Fe and Co were found to have orbital moments that are larger than those predicted. Comparison with similar results obtained for related alloys suggests that there must be a finite density of states in both spin bands at the Fermi energy indicating that Co2FeSi is not a perfect half-metallic ferromagnet.

First-principles study on the structural, elastic and electronic properties of Ti4N3 and Ti6N5 under high pressure

NASA Astrophysics Data System (ADS)

Yang, Ruike; Chai, Bao; Zhu, Chuanshuai; Wei, Qun; Du, Zheng

2017-12-01

The structural, elastic and electronic properties of Ti4N3 and Ti6N5 have been systematically studied by first-principles calculations based on density functional theory (DFT) with generalized gradient approximation (GGA) and local density approximation (LDA). Basic physical properties for Ti4N3 and Ti6N5, such as the lattice constants, the bulk modulus, shear modulus, and elastic constants are calculated. The results show that Ti4N3 and Ti6N5 are mechanically stable under ambient pressure. The phonon dispersion spectra are researched throughout the Brillouin zone via the linear response approach as implemented in the CASTEP code, which indicate the optimized structures are stable dynamically. The Young’s modulus E and Poisson’s ratios ν are also determined within the framework of the Voigt-Reuss-Hill approximation. The analyses show that Ti4N3 is more ductile than Ti6N5 at the same pressure and ductility increases as the pressure increases. Moreover, the anisotropies of the Ti4N3 and Ti6N5 are discussed by the Young’s modulus at different directions, and the results indicate that the anisotropy of the two Ti-N compounds is obvious. The total density of states (TDOS) and partial density of states (PDOS) show that the TDOS of TiN, Ti4N3 and Ti6N5 originate mainly from Ti “d” and N “p” states. The results show that Ti4N3 and Ti6N5 present semimetal character. Pressure makes the level range of DOS significantly extended, for TiN, Ti4N3 and Ti6N5. The TDOS decreases with the pressure rise, at Fermi level.

An Initiative Toward Reliable Long-Duration Operation of Diode Lasers in Space

NASA Technical Reports Server (NTRS)

Tratt, David M.; Amzajerdian, Farzin; Stephen, Mark A.; Shapiro, Andrew A.

2006-01-01

This viewgraph presentation reviews the workings of the Laser Diode Arrays (LDA) working group. The group facilitates focused interaction between the LDA user and provider communities and it will author standards document for the specification and qualification of LDA's for operation in the space environment. It also reviews the NASA test and evaluation facilities that are available to the community.

Topological Phase Transitions in Zinc-Blende Semimetals Driven Exclusively by Electronic Temperature

NASA Astrophysics Data System (ADS)

Trushin, Egor; Görling, Andreas

2018-04-01

We show that electronic phase transitions in zinc-blende semimetals with quadratic band touching (QBT) at the center of the Brillouin zone, like GaBi, InBi, or HgTe, can occur exclusively due to a change of the electronic temperature without the need to involve structural transformations or electron-phonon coupling. The commonly used Kohn-Sham density-functional methods based on local and semilocal density functionals employing the local density approximation (LDA) or generalized gradient approximations (GGAs), however, are not capable of describing such phenomena because they lack an intrinsic temperature dependence and account for temperature only via the occupation of bands, which essentially leads only to a shift of the Fermi level without changing the shape or topology of bands. Kohn-Sham methods using the exact temperature-dependent exchange potential, not to be confused with the Hartree-Fock exchange potential, on the other hand, describe such phase transitions. A simple modeling of correlation effects can be achieved by screening of the exchange. In the considered zinc-blende compounds the QBT is unstable at low temperatures and a transition to electronic states without QBT takes place. In the case of HgTe and GaBi Weyl points of type I and type II, respectively, emerge during the transitions. This demonstrates that Kohn-Sham methods can describe such topological phase transitions provided they are based on functionals more accurate than those within the LDA or GGA. Moreover, the electronic temperature is identified as a handle to tune topological materials.

Launch Deployment Assembly Extravehicular Activity Neutral Buoyancy Development Test Report

NASA Technical Reports Server (NTRS)

Loughead, T.

1996-01-01

This test evaluated the Launch Deployment Assembly (LDA) design for Extravehicular Activity (EVA) work sites (setup, igress, egress), reach and visual access, and translation required for cargo item removal. As part of the LDA design, this document describes the method and results of the LDA EVA Neutral Buoyancy Development Test to ensure that the LDA hardware support the deployment of the cargo items from the pallet. This document includes the test objectives, flight and mockup hardware description, descriptions of procedures and data collection used in the testing, and the results of the development test at the National Aeronautics and Space Administrations (NASA) Marshall Space Flight Center (MSFC) Neutral Buoyancy Simulator (NBS).

Quantification of Coffea arabica and Coffea canephora var. robusta concentration in blends by means of synchronous fluorescence and UV-Vis spectroscopies.

PubMed

Dankowska, A; Domagała, A; Kowalewski, W

2017-09-01

The potential of fluorescence, UV-Vis spectroscopies as well as the low- and mid-level data fusion of both spectroscopies for the quantification of concentrations of roasted Coffea arabica and Coffea canephora var. robusta in coffee blends was investigated. Principal component analysis was used to reduce data multidimensionality. To calculate the level of undeclared addition, multiple linear regression (PCA-MLR) models were used with lowest root mean square error of calibration (RMSEC) of 3.6% and root mean square error of cross-validation (RMSECV) of 7.9%. LDA analysis was applied to fluorescence intensities and UV spectra of Coffea arabica, canephora samples, and their mixtures in order to examine classification ability. The best performance of PCA-LDA analysis was observed for data fusion of UV and fluorescence intensity measurements at wavelength interval of 60nm. LDA showed that data fusion can achieve over 96% of correct classifications (sensitivity) in the test set and 100% of correct classifications in the training set, with low-level data fusion. The corresponding results for individual spectroscopies ranged from 90% (UV-Vis spectroscopy) to 77% (synchronous fluorescence) in the test set, and from 93% to 97% in the training set. The results demonstrate that fluorescence, UV, and visible spectroscopies complement each other, giving a complementary effect for the quantification of roasted Coffea arabica and Coffea canephora var. robusta concentration in blends. Copyright © 2017 Elsevier B.V. All rights reserved.

Fast mental states decoding in mixed reality.

PubMed

De Massari, Daniele; Pacheco, Daniel; Malekshahi, Rahim; Betella, Alberto; Verschure, Paul F M J; Birbaumer, Niels; Caria, Andrea

2014-01-01

The combination of Brain-Computer Interface (BCI) technology, allowing online monitoring and decoding of brain activity, with virtual and mixed reality (MR) systems may help to shape and guide implicit and explicit learning using ecological scenarios. Real-time information of ongoing brain states acquired through BCI might be exploited for controlling data presentation in virtual environments. Brain states discrimination during mixed reality experience is thus critical for adapting specific data features to contingent brain activity. In this study we recorded electroencephalographic (EEG) data while participants experienced MR scenarios implemented through the eXperience Induction Machine (XIM). The XIM is a novel framework modeling the integration of a sensing system that evaluates and measures physiological and psychological states with a number of actuators and effectors that coherently reacts to the user's actions. We then assessed continuous EEG-based discrimination of spatial navigation, reading and calculation performed in MR, using linear discriminant analysis (LDA) and support vector machine (SVM) classifiers. Dynamic single trial classification showed high accuracy of LDA and SVM classifiers in detecting multiple brain states as well as in differentiating between high and low mental workload, using a 5 s time-window shifting every 200 ms. Our results indicate overall better performance of LDA with respect to SVM and suggest applicability of our approach in a BCI-controlled MR scenario. Ultimately, successful prediction of brain states might be used to drive adaptation of data representation in order to boost information processing in MR.

Fast mental states decoding in mixed reality

PubMed Central

De Massari, Daniele; Pacheco, Daniel; Malekshahi, Rahim; Betella, Alberto; Verschure, Paul F. M. J.; Birbaumer, Niels; Caria, Andrea

2014-01-01

The combination of Brain-Computer Interface (BCI) technology, allowing online monitoring and decoding of brain activity, with virtual and mixed reality (MR) systems may help to shape and guide implicit and explicit learning using ecological scenarios. Real-time information of ongoing brain states acquired through BCI might be exploited for controlling data presentation in virtual environments. Brain states discrimination during mixed reality experience is thus critical for adapting specific data features to contingent brain activity. In this study we recorded electroencephalographic (EEG) data while participants experienced MR scenarios implemented through the eXperience Induction Machine (XIM). The XIM is a novel framework modeling the integration of a sensing system that evaluates and measures physiological and psychological states with a number of actuators and effectors that coherently reacts to the user's actions. We then assessed continuous EEG-based discrimination of spatial navigation, reading and calculation performed in MR, using linear discriminant analysis (LDA) and support vector machine (SVM) classifiers. Dynamic single trial classification showed high accuracy of LDA and SVM classifiers in detecting multiple brain states as well as in differentiating between high and low mental workload, using a 5 s time-window shifting every 200 ms. Our results indicate overall better performance of LDA with respect to SVM and suggest applicability of our approach in a BCI-controlled MR scenario. Ultimately, successful prediction of brain states might be used to drive adaptation of data representation in order to boost information processing in MR. PMID:25505878

Real-Space Multiple-Scattering Theory and Its Applications at Exascale

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eisenbach, Markus; Wang, Yang

In recent decades, the ab initio methods based on density functional theory (DFT) (Hohenberg and Kohn 1964, Kohn and Sham 1965) have become a widely used tool in computational materials science, which allows theoretical prediction of physical properties of materials from the first principles and theoretical interpretation of new physical phenomena found in experiments. In the framework of DFT, the original problem that requires solving a quantum mechanical equation for a many-electron system is reduced to a one-electron problem that involves an electron moving in an effective field, while the effective field potential is made up of an electrostatic potential,more » also known as Hartree potential, arising from the electronic and ion charge distribution in space and an exchange–correlation potential, which is a function of the electron density and encapsulates the exchange and correlation effects of the many-electron system. Even though the exact functional form of the exchange-correlation potential is formally unknown, a local density approximation (LDA) or a generalized gradient approximation (GGA) is usually applied so that the calculation of the exchange–correlation potential, as well as the exchange–correlation energy, becomes tractable while a required accuracy is retained. Based on DFT, ab initio electronic structure calculations for a material generally involve a self-consistent process that iterates between two computational tasks: (1) solving an one-electron Schrödinger equation, also known as Kohn–Sham equation, to obtain the electron density and, if needed, the magnetic moment density, and (2) solving the Poisson equation to obtain the electrostatic potential corresponding to the electron density and constructing the effective potential by adding the exchange–correlation potential to the electrostatic potential. This self-consistent process proceeds until a convergence criteria is reached.« less

Impact of strain on electronic and transport properties of 6 nm hydrogenated germanane nano-ribbon channel double gate field effect transistor

NASA Astrophysics Data System (ADS)

Meher Abhinav, E.; Sundararaj, Anuraj; Gopalakrishnan, Chandrasekaran; Kasmir Raja, S. V.; Chokhra, Saurabh

2017-11-01

In this work, chair like fully hydrogenated germanane (CGeH) nano-ribbon 6 nm short channel double gate field effect transistor (DG-FET) has been modeled and the impact of strain on the I-V characteristics of CGeH channel has been examined. The bond lengths, binding and formation energies of various hydrogenated geometries of buckled germanane channel were calculated using local density approximation (LDA) with Perdew-Zunger (PZ) and generalized gradient approximation (GGA) with Perdew Burke Ernzerhof (PBE) parameterization. From four various geometries, chair like structure is found to be more stable compared to boat like obtuse, stiruup structure and table like structure. The bandgap versus width, bandgap versus strain characteristics and I-V characteristics had been analyzed at room temperature using density functional theory (DFT). Using self consistent calculation it was observed that the electronic properties of nano-ribbon is independent of length and band structure, but dependent on edge type, strain [Uni-axial (ɛ xx ), bi-axial (ɛ xx   =  ɛ yy )] and width of the ribbon. The strain engineered hydrogenated germanane (GeH) showed wide direct bandgap (2.3 eV) which could help to build low noise electronic devices that operates at high frequencies. The observed bi-axial compression has high impact on the device transport characteristics with peak to valley ratio (PVR) of 2.14 and 380% increase in peak current compared to pristine CGeH device. The observed strain in CGeH DG-FET could facilitate in designing novel multiple-logic memory devices due to multiple negative differential resistance (NDR) regions.

Partial Membership Latent Dirichlet Allocation for Soft Image Segmentation.

PubMed

Chen, Chao; Zare, Alina; Trinh, Huy N; Omotara, Gbenga O; Cobb, James Tory; Lagaunne, Timotius A

2017-12-01

Topic models [e.g., probabilistic latent semantic analysis, latent Dirichlet allocation (LDA), and supervised LDA] have been widely used for segmenting imagery. However, these models are confined to crisp segmentation, forcing a visual word (i.e., an image patch) to belong to one and only one topic. Yet, there are many images in which some regions cannot be assigned a crisp categorical label (e.g., transition regions between a foggy sky and the ground or between sand and water at a beach). In these cases, a visual word is best represented with partial memberships across multiple topics. To address this, we present a partial membership LDA (PM-LDA) model and an associated parameter estimation algorithm. This model can be useful for imagery, where a visual word may be a mixture of multiple topics. Experimental results on visual and sonar imagery show that PM-LDA can produce both crisp and soft semantic image segmentations; a capability previous topic modeling methods do not have.

Orthogonal sparse linear discriminant analysis

NASA Astrophysics Data System (ADS)

Liu, Zhonghua; Liu, Gang; Pu, Jiexin; Wang, Xiaohong; Wang, Haijun

2018-03-01

Linear discriminant analysis (LDA) is a linear feature extraction approach, and it has received much attention. On the basis of LDA, researchers have done a lot of research work on it, and many variant versions of LDA were proposed. However, the inherent problem of LDA cannot be solved very well by the variant methods. The major disadvantages of the classical LDA are as follows. First, it is sensitive to outliers and noises. Second, only the global discriminant structure is preserved, while the local discriminant information is ignored. In this paper, we present a new orthogonal sparse linear discriminant analysis (OSLDA) algorithm. The k nearest neighbour graph is first constructed to preserve the locality discriminant information of sample points. Then, L2,1-norm constraint on the projection matrix is used to act as loss function, which can make the proposed method robust to outliers in data points. Extensive experiments have been performed on several standard public image databases, and the experiment results demonstrate the performance of the proposed OSLDA algorithm.

Glass-to-cryogenic-liquid transitions in aqueous solutions suggested by crack healing

PubMed Central

Kim, Chae Un; Tate, Mark W.; Gruner, Sol M.

2015-01-01

Observation of theorized glass-to-liquid transitions between low-density amorphous (LDA) and high-density amorphous (HDA) water states had been stymied by rapid crystallization below the homogeneous water nucleation temperature (∼235 K at 0.1 MPa). We report optical and X-ray observations suggestive of glass-to-liquid transitions in these states. Crack healing, indicative of liquid, occurs when LDA ice transforms to cubic ice at 160 K, and when HDA ice transforms to the LDA state at temperatures as low as 120 K. X-ray diffraction study of the HDA to LDA transition clearly shows the characteristics of a first-order transition. Study of the glass-to-liquid transitions in nanoconfined aqueous solutions shows them to be independent of the solute concentrations, suggesting that they represent an intrinsic property of water. These findings support theories that LDA and HDA ice are thermodynamically distinct and that they are continuously connected to two different liquid states of water. PMID:26351671

A general soft label based linear discriminant analysis for semi-supervised dimensionality reduction.

PubMed

Zhao, Mingbo; Zhang, Zhao; Chow, Tommy W S; Li, Bing

2014-07-01

Dealing with high-dimensional data has always been a major problem in research of pattern recognition and machine learning, and Linear Discriminant Analysis (LDA) is one of the most popular methods for dimension reduction. However, it only uses labeled samples while neglecting unlabeled samples, which are abundant and can be easily obtained in the real world. In this paper, we propose a new dimension reduction method, called "SL-LDA", by using unlabeled samples to enhance the performance of LDA. The new method first propagates label information from the labeled set to the unlabeled set via a label propagation process, where the predicted labels of unlabeled samples, called "soft labels", can be obtained. It then incorporates the soft labels into the construction of scatter matrixes to find a transformed matrix for dimension reduction. In this way, the proposed method can preserve more discriminative information, which is preferable when solving the classification problem. We further propose an efficient approach for solving SL-LDA under a least squares framework, and a flexible method of SL-LDA (FSL-LDA) to better cope with datasets sampled from a nonlinear manifold. Extensive simulations are carried out on several datasets, and the results show the effectiveness of the proposed method. Copyright © 2014 Elsevier Ltd. All rights reserved.

Rapid Analysis of Deoxynivalenol in Durum Wheat by FT-NIR Spectroscopy

PubMed Central

De Girolamo, Annalisa; Cervellieri, Salvatore; Visconti, Angelo; Pascale, Michelangelo

2014-01-01

Fourier-transform-near infrared (FT-NIR) spectroscopy has been used to develop quantitative and classification models for the prediction of deoxynivalenol (DON) levels in durum wheat samples. Partial least-squares (PLS) regression analysis was used to determine DON in wheat samples in the range of <50–16,000 µg/kg DON. The model displayed a large root mean square error of prediction value (1,977 µg/kg) as compared to the EU maximum limit for DON in unprocessed durum wheat (i.e., 1,750 µg/kg), thus making the PLS approach unsuitable for quantitative prediction of DON in durum wheat. Linear discriminant analysis (LDA) was successfully used to differentiate wheat samples based on their DON content. A first approach used LDA to group wheat samples into three classes: A (DON ≤ 1,000 µg/kg), B (1,000 < DON ≤ 2,500 µg/kg), and C (DON > 2,500 µg/kg) (LDA I). A second approach was used to discriminate highly contaminated wheat samples based on three different cut-off limits, namely 1,000 (LDA II), 1,200 (LDA III) and 1,400 µg/kg DON (LDA IV). The overall classification and false compliant rates for the three models were 75%–90% and 3%–7%, respectively, with model LDA IV using a cut-off of 1,400 µg/kg fulfilling the requirement of the European official guidelines for screening methods. These findings confirmed the suitability of FT-NIR to screen a large number of wheat samples for DON contamination and to verify the compliance with EU regulation. PMID:25384107

Rapid analysis of deoxynivalenol in durum wheat by FT-NIR spectroscopy.

PubMed

De Girolamo, Annalisa; Cervellieri, Salvatore; Visconti, Angelo; Pascale, Michelangelo

2014-11-06

Fourier-transform-near infrared (FT-NIR) spectroscopy has been used to develop quantitative and classification models for the prediction of deoxynivalenol (DON) levels in durum wheat samples. Partial least-squares (PLS) regression analysis was used to determine DON in wheat samples in the range of <50-16,000 µg/kg DON. The model displayed a large root mean square error of prediction value (1,977 µg/kg) as compared to the EU maximum limit for DON in unprocessed durum wheat (i.e., 1,750 µg/kg), thus making the PLS approach unsuitable for quantitative prediction of DON in durum wheat. Linear discriminant analysis (LDA) was successfully used to differentiate wheat samples based on their DON content. A first approach used LDA to group wheat samples into three classes: A (DON ≤ 1,000 µg/kg), B (1,000 < DON ≤ 2,500 µg/kg), and C (DON > 2,500 µg/kg) (LDA I). A second approach was used to discriminate highly contaminated wheat samples based on three different cut-off limits, namely 1,000 (LDA II), 1,200 (LDA III) and 1,400 µg/kg DON (LDA IV). The overall classification and false compliant rates for the three models were 75%-90% and 3%-7%, respectively, with model LDA IV using a cut-off of 1,400 µg/kg fulfilling the requirement of the European official guidelines for screening methods. These findings confirmed the suitability of FT-NIR to screen a large number of wheat samples for DON contamination and to verify the compliance with EU regulation.

Heating- and pressure-induced transformations in amorphous and hexagonal ice: A computer simulation study using the TIP4P/2005 model

NASA Astrophysics Data System (ADS)

Engstler, Justin; Giovambattista, Nicolas

2017-08-01

We characterize the phase behavior of glassy water by performing extensive out-of-equilibrium molecular dynamics simulations using the TIP4P/2005 water model. Specifically, we study (i) the pressure-induced transformations between low-density (LDA) and high-density amorphous ice (HDA), (ii) the pressure-induced amorphization (PIA) of hexagonal ice (Ih), (iii) the heating-induced LDA-to-HDA transformation at high pressures, (iv) the heating-induced HDA-to-LDA transformation at low and negative pressures, (v) the glass transition temperatures of LDA and HDA as a function of pressure, and (vi) the limit of stability of LDA upon isobaric heating and isothermal decompression (at negative pressures). These transformations are studied systematically, over a wide range of temperatures and pressures, allowing us to construct a P-T phase diagram for glassy TIP4P/2005 water. Our results are in qualitative agreement with experimental observations and with the P-T phase diagram obtained for glassy ST2 water that exhibits a liquid-liquid phase transition and critical point. We also discuss the mechanism for PIA of ice Ih and show that this is a two-step process where first, the hydrogen-bond network (HBN) is distorted and then the HBN abruptly collapses. Remarkably, the collapse of the HB in ice Ih occurs when the average molecular orientations order, a measure of the tetrahedrality of the HBN, is of the same order as in LDA, suggesting a common mechanism for the LDA-to-HDA and Ih-to-HDA transformations.

Heating- and pressure-induced transformations in amorphous and hexagonal ice: A computer simulation study using the TIP4P/2005 model.

PubMed

Engstler, Justin; Giovambattista, Nicolas

2017-08-21

We characterize the phase behavior of glassy water by performing extensive out-of-equilibrium molecular dynamics simulations using the TIP4P/2005 water model. Specifically, we study (i) the pressure-induced transformations between low-density (LDA) and high-density amorphous ice (HDA), (ii) the pressure-induced amorphization (PIA) of hexagonal ice (I h ), (iii) the heating-induced LDA-to-HDA transformation at high pressures, (iv) the heating-induced HDA-to-LDA transformation at low and negative pressures, (v) the glass transition temperatures of LDA and HDA as a function of pressure, and (vi) the limit of stability of LDA upon isobaric heating and isothermal decompression (at negative pressures). These transformations are studied systematically, over a wide range of temperatures and pressures, allowing us to construct a P-T phase diagram for glassy TIP4P/2005 water. Our results are in qualitative agreement with experimental observations and with the P-T phase diagram obtained for glassy ST2 water that exhibits a liquid-liquid phase transition and critical point. We also discuss the mechanism for PIA of ice I h and show that this is a two-step process where first, the hydrogen-bond network (HBN) is distorted and then the HBN abruptly collapses. Remarkably, the collapse of the HB in ice I h occurs when the average molecular orientations order, a measure of the tetrahedrality of the HBN, is of the same order as in LDA, suggesting a common mechanism for the LDA-to-HDA and I h -to-HDA transformations.

Excitation energies from range-separated time-dependent density and density matrix functional theory.

PubMed

Pernal, Katarzyna

2012-05-14

Time-dependent density functional theory (TD-DFT) in the adiabatic formulation exhibits known failures when applied to predicting excitation energies. One of them is the lack of the doubly excited configurations. On the other hand, the time-dependent theory based on a one-electron reduced density matrix functional (time-dependent density matrix functional theory, TD-DMFT) has proven accurate in determining single and double excitations of H(2) molecule if the exact functional is employed in the adiabatic approximation. We propose a new approach for computing excited state energies that relies on functionals of electron density and one-electron reduced density matrix, where the latter is applied in the long-range region of electron-electron interactions. A similar approach has been recently successfully employed in predicting ground state potential energy curves of diatomic molecules even in the dissociation limit, where static correlation effects are dominating. In the paper, a time-dependent functional theory based on the range-separation of electronic interaction operator is rigorously formulated. To turn the approach into a practical scheme the adiabatic approximation is proposed for the short- and long-range components of the coupling matrix present in the linear response equations. In the end, the problem of finding excitation energies is turned into an eigenproblem for a symmetric matrix. Assignment of obtained excitations is discussed and it is shown how to identify double excitations from the analysis of approximate transition density matrix elements. The proposed method used with the short-range local density approximation (srLDA) and the long-range Buijse-Baerends density matrix functional (lrBB) is applied to H(2) molecule (at equilibrium geometry and in the dissociation limit) and to Be atom. The method accounts for double excitations in the investigated systems but, unfortunately, the accuracy of some of them is poor. The quality of the other excitations is in general much better than that offered by TD-DFT-LDA or TD-DMFT-BB approximations if the range-separation parameter is properly chosen. The latter remains an open problem.

Anion-Driven Self-Assembly Processes Based on Halogen-Bonding

DTIC Science & Technology

2007-07-10

23993041 Fax: +39-02-23993180 E-mail: pierangelo.metrangolo@polimi.it Sede Leonardo : Piazza L.Da Vinci , 32 – 20133 Milano Tel. ++39-02...02-23993180 E-mail: pierangelo.metrangolo@polimi.it Sede Leonardo : Piazza L.Da Vinci , 32 – 20133 Milano Tel. ++39-02 2399.3200 Fax ++39-02...Pierangelo Metrangolo Ph. +39-02-23993041 Fax: +39-02-23993180 E-mail: pierangelo.metrangolo@polimi.it Sede Leonardo : Piazza L.Da Vinci , 32

Lithium Diisopropylamide-Mediated Reactions of Imines, Unsaturated Esters, Epoxides, and Aryl Carbamates: Influence of Hexamethylphosphoramide and Ethereal Cosolvents on Reaction Mechanisms

PubMed Central

Ma, Yun

2010-01-01

Several reactions mediated by lithium diisopropylamide (LDA) with added hex-amethylphosphoramide (HMPA) are described. The N-isopropylimine of cyclohex-anone lithiates via an ensemble of monomer-based pathways. Conjugate addition of LDA/HMPA to an unsaturated ester proceeds via di- and tetra-HMPA-solvated dimers. Deprotonation of norbornene epoxide by LDA/HMPA proceeds via an intermediate metalated epoxide as a mixed dimer with LDA. Ortholithiation of an aryl carbamate proceeds via a mono-HMPA-solvated monomer-based pathway. Dependencies on THF and other ethereal cosolvents suggest that secondary-shell solvation effects are important in some instances. The origins of the inordinate mechanistic complexity are discussed. PMID:17985891

Application of the weighted-density approximation to the accurate description of electron-positron correlation effects in materials

NASA Astrophysics Data System (ADS)

Callewaert, Vincent; Saniz, Rolando; Barbiellini, Bernardo; Bansil, Arun; Partoens, Bart

2017-08-01

We discuss positron-annihilation lifetimes for a set of illustrative bulk materials within the framework of the weighted-density approximation (WDA). The WDA can correctly describe electron-positron correlations in strongly inhomogeneous systems, such as surfaces, where the applicability of (semi-)local approximations is limited. We analyze the WDA in detail and show that the electrons which cannot screen external charges efficiently, such as the core electrons, cannot be treated accurately via the pair correlation of the homogeneous electron gas. We discuss how this problem can be addressed by reducing the screening in the homogeneous electron gas by adding terms depending on the gradient of the electron density. Further improvements are obtained when core electrons are treated within the LDA and the valence electron using the WDA. Finally, we discuss a semiempirical WDA-based approach in which a sum rule is imposed to reproduce the experimental lifetimes.

High-dose aspirin for Kawasaki disease: outdated myth or effective aid?

PubMed

Amarilyo, Gil; Koren, Yael; Brik Simon, Dafna; Bar-Meir, Maskit; Bahat, Hilla; Helou, Mona Hanna; Mendelson, Amir; Hezkelo, Nofar; Chodick, Gabriel; Berkun, Yackov; Eisenstein, Eli; Butbul Aviel, Yonatan; Barkai, Galia; Bolkier, Yoav; Padeh, Shai; Brik, Riva; Hashkes, Phillip J; Harel, Liora; Uziel, Yosef

2017-01-01

To compare the efficacy and safety of intravenous immunoglobulin (IVIG) plus high-dose aspirin (HDA) vs. IVIG plus low-dose aspirin (LDA) for the treatment of Kawasaki disease, with an emphasis on coronary artery outcomes. This study was a retrospective, medical record review of paediatric patients with Kawasaki disease comparing 6 centres that routinely used HAD for initial treatment and 2 that used LDA in 2004-2013. Treatment response and adverse events were compared. The primary outcome measure was the occurrence of coronary aneurysm at the subacute or convalescent stage. The cohort included 358 patients, of whom 315 were initially treated with adjunctive HDA and 43 with LDA. There were no demographic differences between the groups. Coronary aneurysms occurred in 10% (20/196) of the HDA group and 4% (1/24) of the LDA group (p=0.34). Equivalence tests indicate it is unlikely that the risk of coronary aneurysm in LDA exceeds HDA by more than 3.5%. There were no significant between-group differences in the need for glucocorticoid pulse therapy or disease recurrence. Coronary ectasia rate and hospitalisation time were significantly greater in the HDA group. Adverse events were similar in the two groups. We found no significant clinical benefit in using IVIG+HDA in Kawasaki disease compared to IVIG+LDA. The use of adjunctive HDA in this setting should be reconsidered.

Role of non-local exchange in the electronic structure of correlated oxides

NASA Astrophysics Data System (ADS)

Iori, Federico; Gatti, Matteo; Rubio Secades, Angel

Transition-metal oxides (TMO) with partially filled d or f shells are a prototype of correlated materials. They exhibit very interesting properties, like metal-insulator phase transitions (MIT). In this work we consider several TMO insulators in which Kohn-Sham LDA band structures are metallic: VO2, V2O3, Ti2O3, LaTiO3 and YTiO3. In the past, this failure of LDA has been explained in terms of its inadequacy to capture the strong interactions taking place between correlated electrons. In the spirit of the Hubbard model, possible corrections to improve onsite correlation are the LDA +U and LDA +DMFT approaches. Here we make use of the HSE06 hybrid functional. We show that, without invoking strong-correlation effects, the contribution of the non-local Fock exchange is essential to correct the LDA results, by curing its delocalization error. In fact, HSE06 provides insulating band structures and correctly describes the MIT in all the considered compounds. We further discuss the advantages and the limitations of the HSE06 hybrid functional in correlated TMO

Complexity-reduced implementations of complete and null-space-based linear discriminant analysis.

PubMed

Lu, Gui-Fu; Zheng, Wenming

2013-10-01

Dimensionality reduction has become an important data preprocessing step in a lot of applications. Linear discriminant analysis (LDA) is one of the most well-known dimensionality reduction methods. However, the classical LDA cannot be used directly in the small sample size (SSS) problem where the within-class scatter matrix is singular. In the past, many generalized LDA methods has been reported to address the SSS problem. Among these methods, complete linear discriminant analysis (CLDA) and null-space-based LDA (NLDA) provide good performances. The existing implementations of CLDA are computationally expensive. In this paper, we propose a new and fast implementation of CLDA. Our proposed implementation of CLDA, which is the most efficient one, is equivalent to the existing implementations of CLDA in theory. Since CLDA is an extension of null-space-based LDA (NLDA), our implementation of CLDA also provides a fast implementation of NLDA. Experiments on some real-world data sets demonstrate the effectiveness of our proposed new CLDA and NLDA algorithms. Copyright © 2013 Elsevier Ltd. All rights reserved.

Robust linear discriminant analysis with distance based estimators

NASA Astrophysics Data System (ADS)

Lim, Yai-Fung; Yahaya, Sharipah Soaad Syed; Ali, Hazlina

2017-11-01

Linear discriminant analysis (LDA) is one of the supervised classification techniques concerning relationship between a categorical variable and a set of continuous variables. The main objective of LDA is to create a function to distinguish between populations and allocating future observations to previously defined populations. Under the assumptions of normality and homoscedasticity, the LDA yields optimal linear discriminant rule (LDR) between two or more groups. However, the optimality of LDA highly relies on the sample mean and pooled sample covariance matrix which are known to be sensitive to outliers. To alleviate these conflicts, a new robust LDA using distance based estimators known as minimum variance vector (MVV) has been proposed in this study. The MVV estimators were used to substitute the classical sample mean and classical sample covariance to form a robust linear discriminant rule (RLDR). Simulation and real data study were conducted to examine on the performance of the proposed RLDR measured in terms of misclassification error rates. The computational result showed that the proposed RLDR is better than the classical LDR and was comparable with the existing robust LDR.

Influence of sample preparation on the transformation of low-density to high-density amorphous ice: An explanation based on the potential energy landscape

NASA Astrophysics Data System (ADS)

Giovambattista, Nicolas; Starr, Francis W.; Poole, Peter H.

2017-07-01

Experiments and computer simulations of the transformations of amorphous ices display different behaviors depending on sample preparation methods and on the rates of change of temperature and pressure to which samples are subjected. In addition to these factors, simulation results also depend strongly on the chosen water model. Using computer simulations of the ST2 water model, we study how the sharpness of the compression-induced transition from low-density amorphous ice (LDA) to high-density amorphous ice (HDA) is influenced by the preparation of LDA. By studying LDA samples prepared using widely different procedures, we find that the sharpness of the LDA-to-HDA transformation is correlated with the depth of the initial LDA sample in the potential energy landscape (PEL), as characterized by the inherent structure energy. Our results show that the complex phenomenology of the amorphous ices reported in experiments and computer simulations can be understood and predicted in a unified way from knowledge of the PEL of the system.

Linear discriminant analysis based on L1-norm maximization.

PubMed

Zhong, Fujin; Zhang, Jiashu

2013-08-01

Linear discriminant analysis (LDA) is a well-known dimensionality reduction technique, which is widely used for many purposes. However, conventional LDA is sensitive to outliers because its objective function is based on the distance criterion using L2-norm. This paper proposes a simple but effective robust LDA version based on L1-norm maximization, which learns a set of local optimal projection vectors by maximizing the ratio of the L1-norm-based between-class dispersion and the L1-norm-based within-class dispersion. The proposed method is theoretically proved to be feasible and robust to outliers while overcoming the singular problem of the within-class scatter matrix for conventional LDA. Experiments on artificial datasets, standard classification datasets and three popular image databases demonstrate the efficacy of the proposed method.

Smoke detection

DOEpatents

Warmack, Robert J. Bruce; Wolf, Dennis A.; Frank, Steven Shane

2016-09-06

Various apparatus and methods for smoke detection are disclosed. In one embodiment, a method of training a classifier for a smoke detector comprises inputting sensor data from a plurality of tests into a processor. The sensor data is processed to generate derived signal data corresponding to the test data for respective tests. The derived signal data is assigned into categories comprising at least one fire group and at least one non-fire group. Linear discriminant analysis (LDA) training is performed by the processor. The derived signal data and the assigned categories for the derived signal data are inputs to the LDA training. The output of the LDA training is stored in a computer readable medium, such as in a smoke detector that uses LDA to determine, based on the training, whether present conditions indicate the existence of a fire.

Smoke detection

DOEpatents

Warmack, Robert J. Bruce; Wolf, Dennis A.; Frank, Steven Shane

2015-10-27

Various apparatus and methods for smoke detection are disclosed. In one embodiment, a method of training a classifier for a smoke detector comprises inputting sensor data from a plurality of tests into a processor. The sensor data is processed to generate derived signal data corresponding to the test data for respective tests. The derived signal data is assigned into categories comprising at least one fire group and at least one non-fire group. Linear discriminant analysis (LDA) training is performed by the processor. The derived signal data and the assigned categories for the derived signal data are inputs to the LDA training. The output of the LDA training is stored in a computer readable medium, such as in a smoke detector that uses LDA to determine, based on the training, whether present conditions indicate the existence of a fire.

Abs-initio, Predictive Calculations for Optoelectronic and Advanced Materials Research

NASA Astrophysics Data System (ADS)

Bagayoko, Diola

2010-10-01

Most density functional theory (DFT) calculations find band gaps that are 30-50 percent smaller than the experimental ones. Some explanations of this serious underestimation by theory include self-interaction and the derivative discontinuity of the exchange correlation energy. Several approaches have been developed in the search for a solution to this problem. Most of them entail some modification of DFT potentials. The Green function and screened Coulomb approximation (GWA) is a non-DFT formalism that has led to some improvements. Despite these efforts, the underestimation problem has mostly persisted in the literature. Using the Rayleigh theorem, we describe a basis set and variational effect inherently associated with calculations that employ a linear combination of atomic orbitals (LCAO) in a variational approach of the Rayleigh-Ritz type. This description concomitantly shows a source of large underestimation errors in calculated band gaps, i.e., an often dramatic lowering of some unoccupied energies on account of the Rayleigh theorem as opposed to a physical interaction. We present the Bagayoko, Zhao, and Williams (BZW) method [Phys. Rev. B 60, 1563 (1999); PRB 74, 245214 (2006); and J. Appl. Phys. 103, 096101 (2008)] that systematically avoids this effect and leads (a) to DFT and LDA calculated band gaps of semiconductors in agreement with experiment and (b) theoretical predictions of band gaps that are confirmed by experiment. Unlike most calculations, BZW computations solve, self-consistently, a system of two coupled equations. DFT-BZW calculated effective masses and optical properties (dielectric functions) also agree with measurements. We illustrate ten years of success of the BZW method with its results for GaN, C, Si, 3C-SIC, 4H-SiC, ZnO, AlAs, Ge, ZnSe, w-InN, c-InN, InAs, CdS, AlN and nanostructures. We conclude with potential applications of the BZW method in optoelectronic and advanced materials research.

Electronic and optical properties of double perovskite Ba2VMoO6: FP-LAPW study

NASA Astrophysics Data System (ADS)

Hnamte, Lalhriatpuia; Sandeep, Joshi, Himanshu; Thapa, R. K.

2018-05-01

The calculation is carried out using the FPLAPW method in the DFT framework within mBJ and LDA using the WIEN2k code. The investigation of electronic properties showed Ba2VMoO6 to be semi-metal in spin-up and insulation in spin down. In both spin up and spin down channel, direct band gap along with indirect band gap in ΓX direction was observed. For investigation of the optical transitions in this compound, the real and imaginary parts of the dielectric function, reflectivity, refractive index and optical conductivity of real and imaginary parts are calculated and analysed.

Laser anemometry for hot flows

NASA Astrophysics Data System (ADS)

Kugler, P.; Langer, G.

1987-07-01

The fundamental principles, instrumentation, and practical operation of LDA and laser-transit-anemometry systems for measuring velocity profiles and the degree of turbulence in high-temperature flows are reviewed and illustrated with diagrams, drawings and graphs of typical data. Consideration is given to counter, tracker, spectrum-analyzer and correlation methods of LDA signal processing; multichannel analyzer and cross correlation methods for LTA data; LTA results for a small liquid fuel rocket motor; and experiments demonstrating the feasibility of an optoacoustic demodulation scheme for LDA signals from unsteady flows.

Processing techniques for correlation of LDA and thermocouple signals

NASA Astrophysics Data System (ADS)

Nina, M. N. R.; Pita, G. P. A.

1986-11-01

A technique was developed to enable the evaluation of the correlation between velocity and temperature, with laser Doppler anemometer (LDA) as the source of velocity signals and fine wire thermocouple as that of flow temperature. The discontinuous nature of LDA signals requires a special technique for correlation, in particular when few seeding particles are present in the flow. The thermocouple signal was analog compensated in frequency and the effect of the value of time constant on the velocity temperature correlation was studied.

Velocity precision measurements using laser Doppler anemometry

NASA Astrophysics Data System (ADS)

Dopheide, D.; Taux, G.; Narjes, L.

1985-07-01

A Laser Doppler Anemometer (LDA) was calibrated to determine its applicability to high pressure measurements (up to 10 bars) for industrial purposes. The measurement procedure with LDA and the experimental computerized layouts are presented. The calibration procedure is based on absolute accuracy of Doppler frequency and calibration of interference strip intervals. A four-quadrant detector allows comparison of the interference strip distance measurements and computer profiles. Further development of LDA is recommended to increase accuracy (0.1% inaccuracy) and to apply the method industrially.

Barbier Continuous Flow Preparation and Reactions of Carbamoyllithiums for Nucleophilic Amidation.

PubMed

Ganiek, Maximilian A; Becker, Matthias R; Berionni, Guillaume; Zipse, Hendrik; Knochel, Paul

2017-08-01

An ambient temperature continuous flow method for nucleophilic amidation and thioamidation is described. Deprotonation of formamides by lithium diisopropylamine (LDA) affords carbamoyllithium intermediates that are quenched in situ with various electrophiles such as ketones, allyl bromides, Weinreb and morpholino amides. The nature of the reactive lithium intermediates and the thermodynamics of the metalation were further investigated by ab initio calculations and kinetic experiments. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Iron Spin Crossover in the New Hexagonal Aluminous (NAL) Phase

NASA Astrophysics Data System (ADS)

Hsu, H.

2017-12-01

The new hexagonal aluminous (NAL) phase, chemical formula AB2C6O12 (A = Na+, K+, Ca2+; B = Mg2+, Fe2+, Fe3+; C = Al3+, Si4+, Fe3+), is considered a major component ( 20 vol%) of mid-ocean ridge basalt (MORB) at lower-mantle conditions. Given that MORB can be transported back into the Earth's lower mantle via subduction, a thorough knowledge of the NAL phase is essential to fully understand the fate of subducted MORB and its role in mantle dynamics and heterogeneity. In this presentation, the complicated spin crossover of the Fe-bearing NAL phase will be discussed based on a series of first-principles calculations [1], in which the local density approximation + self-consistent Hubbard U (LDA+Usc) method was adopted. As revealed by these calculations, only the ferric iron (Fe3+) substituting Al/Si in the octahedral (C) site undergoes a crossover from the high-spin (HS) to the low-spin (LS) state at 40 GPa, while iron substituting Mg in the trigonal-prismatic (B) site remains in the HS state, regardless of its oxidation state (Fe2+ or Fe3+). The volume/elastic anomalies, iron nuclear quadrupole splittings, and crystal field spltting determined by calculations are in great agreement with experiments [2,3]. The calculations further predict that the HS-LS transition pressure of the NAL phase barely increases with temperature due to the three nearly degenerate LS states of Fe3+, suggesting that the elastic anomalies of this mineral can occur at the top lower mantle. [1] H. Hsu, Phys. Rev. B 95, 020406(R) (2017). [2] Y. Wu et al. Earth Planet. Sci. Lett. 434, 91-100 (2016). [3] S. S. Lobanov et al., J. Geophys. Res. Solid Earth 122, 3565 (2017).

Novel Method for Differentiating Histological Types of Gastric Adenocarcinoma by Using Confocal Raman Microspectroscopy

PubMed Central

Hsu, Chih-Wei; Huang, Chia-Chi; Sheu, Jeng-Horng; Lin, Chia-Wen; Lin, Lien-Fu; Jin, Jong-Shiaw; Chau, Lai-Kwan; Chen, Wenlung

2016-01-01

Gastric adenocarcinoma, a single heterogeneous disease with multiple epidemiological and histopathological characteristics, accounts for approximately 10% of cancers worldwide. It is categorized into four histological types: papillary adenocarcinoma (PAC), tubular adenocarcinoma (TAC), mucinous adenocarcinoma (MAC), and signet ring cell adenocarcinoma (SRC). Effective differentiation of the four types of adenocarcinoma will greatly improve the treatment of gastric adenocarcinoma to increase its five-year survival rate. We reported here the differentiation of the four histological types of gastric adenocarcinoma from the molecularly structural viewpoint of confocal Raman microspectroscopy. In total, 79 patients underwent laparoscopic or open radical gastrectomy during 2008–2011: 21 for signet ring cell carcinoma, 21 for tubular adenocarcinoma, 14 for papillary adenocarcinoma, 6 for mucinous carcinoma, and 17 for normal gastric mucosas obtained from patients underwent operation for other benign lesions. Clinical data were retrospectively reviewed from medical charts, and Raman data were processed and analyzed by using principal component analysis (PCA) and linear discriminant analysis (LDA). Two-dimensional plots of PCA and LDA clearly demonstrated that the four histological types of gastric adenocarcinoma could be differentiated, and confocal Raman microspectroscopy provides potentially a rapid and effective method for differentiating SRC and MAC from TAC or PAC. PMID:27472385

General Rule of Negative Effective Ueff System & Materials Design of High-Tc Superconductors by ab initio Calculations

NASA Astrophysics Data System (ADS)

Katayama-Yoshida, Hiroshi; Nakanishi, Akitaka; Uede, Hiroki; Takawashi, Yuki; Fukushima, Tetsuya; Sato, Kazunori

2014-03-01

Based upon ab initio electronic structure calculation, I will discuss the general rule of negative effective U system by (1) exchange-correlation-induced negative effective U caused by the stability of the exchange-correlation energy in Hund's rule with high-spin ground states of d5 configuration, and (2) charge-excitation-induced negative effective U caused by the stability of chemical bond in the closed-shell of s2, p6, and d10 configurations. I will show the calculated results of negative effective U systems such as hole-doped CuAlO2 and CuFeS2. Based on the total energy calculations of antiferromagnetic and ferromagnetic states, I will discuss the magnetic phase diagram and superconductivity upon hole doping. I also discuss the computational materials design method of high-Tc superconductors by ab initio calculation to go beyond LDA and multi-scale simulations.

Detecting Hotspot Information Using Multi-Attribute Based Topic Model

PubMed Central

Wang, Jing; Li, Li; Tan, Feng; Zhu, Ying; Feng, Weisi

2015-01-01

Microblogging as a kind of social network has become more and more important in our daily lives. Enormous amounts of information are produced and shared on a daily basis. Detecting hot topics in the mountains of information can help people get to the essential information more quickly. However, due to short and sparse features, a large number of meaningless tweets and other characteristics of microblogs, traditional topic detection methods are often ineffective in detecting hot topics. In this paper, we propose a new topic model named multi-attribute latent dirichlet allocation (MA-LDA), in which the time and hashtag attributes of microblogs are incorporated into LDA model. By introducing time attribute, MA-LDA model can decide whether a word should appear in hot topics or not. Meanwhile, compared with the traditional LDA model, applying hashtag attribute in MA-LDA model gives the core words an artificially high ranking in results meaning the expressiveness of outcomes can be improved. Empirical evaluations on real data sets demonstrate that our method is able to detect hot topics more accurately and efficiently compared with several baselines. Our method provides strong evidence of the importance of the temporal factor in extracting hot topics. PMID:26496635

The relation between high-density and very-high-density amorphous ice.

PubMed

Loerting, Thomas; Salzmann, Christoph G; Winkel, Katrin; Mayer, Erwin

2006-06-28

The exact nature of the relationship between high-density (HDA) and very-high-density (VHDA) amorphous ice is unknown at present. Here we review the relation between HDA and VHDA, concentrating on experimental aspects and discuss these with respect to the relation between low-density amorphous ice (LDA) and HDA. On compressing LDA at 125 K up to 1.5 GPa, two distinct density steps are observable in the pressure-density curves which correspond to the LDA --> HDA and HDA --> VHDA conversion. This stepwise formation process LDA --> HDA --> VHDA at 125 K is the first unambiguous observation of a stepwise amorphous-amorphous-amorphous transformation sequence. Density values of amorphous ice obtained in situ between 0.3 and 1.9 GPa on isobaric heating up to the temperatures of crystallization show a pronounced change of slope at ca. 0.8 GPa which could indicate formation of a distinct phase. We infer that the relation between HDA and VHDA is very similar to that between LDA and HDA except for a higher activation barrier between the former. We further discuss the two options of thermodynamic phase transition versus kinetic densification for the HDA --> VHDA conversion.

Local Symmetry Effects in Actinide 4f X-ray Absorption in Oxides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Butorin, Sergei M.; Modin, Anders; Vegelius, Johan R.

2016-03-23

A systematic X-ray absorption study at actinide N 6,7 (4f → 6d transitions) edges was performed for light-actinide oxides including data obtained for the first time for NpO 2, PuO 2, and UO 3. The measurements were supported by ab initio calculations based on local-density-approximation with added 5f-5f Coulomb interaction (LDA+U). Improved energy resolution compared to common experiments at actinide L 2,3 (2p → 6d transitions) edges allowed us to resolve the major structures of the unoccupied 6d density of states (DOS) and estimate the crystal-field splittings in the 6d shell directly from the spectra of light-actinide dioxides. The measurementsmore » demonstrated an enhanced sensitivity of the N 6,7 spectral shape to changes in the compound crystal structure. Finally, for nonstoichiometric NpO 2-x, the filling of the entire band gap with Np 6d states was observed thus supporting a phase coexistence of Np metal and stoichiometric NpO 2 which is in agreement with the tentative Np-O phase diagram.« less

Atomic resolution chemical bond analysis of oxygen in La2CuO4

NASA Astrophysics Data System (ADS)

Haruta, M.; Nagai, T.; Lugg, N. R.; Neish, M. J.; Nagao, M.; Kurashima, K.; Allen, L. J.; Mizoguchi, T.; Kimoto, K.

2013-08-01

The distorted CuO6 octahedron in La2CuO4 was studied using aberration-corrected scanning transmission electron microscopy at atomic resolution. The near-edge structure in the oxygen K-edge electron energy-loss spectrum was recorded as a function of the position of the electron probe. After background subtraction, the measured spectrum image was processed using a recently developed inversion process to remove the mixing of signals on the atomic columns due to elastic and thermal scattering. The spectra were then compared with first-principles band structure calculations based on the local-density approximation plus on-site Coulomb repulsion (LDA + U) approach. In this article, we describe in detail not only anisotropic chemical bonding of the oxygen 2p state with the Cu 3d state but also with the Cu 4p and La 5d/4f states. Furthermore, it was found that buckling of the CuO2 plane was also detectable at the atomic resolution oxygen K-edge. Lastly, it was found that the effects of core-hole in the O K-edge were strongly dependent on the nature of the local chemical bonding, in particular, whether it is ionic or covalent.

Importance of strong-correlation on the lattice dynamics of light-actinides Th-Pa alloy

NASA Astrophysics Data System (ADS)

de La Peã+/-A Seaman, Omar; Heid, Rolf; Bohnen, Klaus-Peter

We have studied the structural, electronic, and lattice dynamics of the Th1-xPax actinide alloy. This system have been analyzed within the framework of density functional perturbation theory, using a mixed-basis pseudopotential method and the virtual crystal approximation (VCA) for modeling the alloy. In particular, the energetics is analyzed as the ground-state crystal structure is changed form fcc to bct, as well as the electronic density of states (DOS), and the phonon frequencies. Such properties have been calculated with and without strong correlations effects through the LDA+U formalism. Although the strong-correlation does not influence on a great manner the Th properties, such effects are more important as the content increases towards Pa, affecting even the definition of the ground-state crystal structure for Pa (experimentally determined as bct). The evolution of the density of states at the Fermi level (N (EF)) and the phonon frequencies as a function of Pa-content are presented and discussed in detail, aiming to understand their influence on the electron-phonon coupling for the Th-Pa alloy. This research was supported by Conacyt-México under project No. CB2013-221807-F.

Study of ice-related flow features around Tanaica Montes, Mars: Implications for late amazonian debris-covered glaciation

NASA Astrophysics Data System (ADS)

Sinha, Rishitosh K.; Vijayan, S.; Bharti, Rajiv R.

2017-11-01

Lobate debris aprons (LDA) and lineated valley fill (LVF) have been broadly recognized in the mid-latitudes of Mars and their subsequent analyses using data from the SHAllow RADar (SHARAD) instrument has suggested evidence for contemporary ice preserved beneath these features. In this study, we conduct detailed characterization of newly identified LDA flow units within the Tanaica Montes region (39.55˚ N, 269.17˚ E) of Mars to assess and understand the similarities in their emplacement with respect to LDA flow units mapped in other regions of Mars. We utilize the Mars Reconnaissance Orbiter (MRO) Context Camera (CTX) images and SHAllow RADar (SHARAD) datasets for geomorphic and subsurface analysis and Mars Global Surveyor (MGS) Mars Orbiter Laser Altimeter (MOLA) point tracks for topographic analysis. Geomorphic observation of LDA flow units surrounding the montes flanks and massif walls reveal integrated pattern of convergence and divergence and evidence of bending and deflection within the flow lines that resulted in concentric, loop-like flow patterns in the downslope. Brain-terrain texture and craters with varying morphological characteristics (ring-mold type) is suggestive that LDAs may be similar to ice-rich, debris-covered glaciers. MOLA point track based convex-up topographic profiles of LDAs suggest that their thickness vary in the range of ∼100-200 m in both the northwestern and southeastern portions of study region. Further, the slope values of mapped LDA surfaces within the study region are within ∼0.1˚-4˚. The extent of mapped LDAs within the study region is such that some of the low elevation (∼0.8-1.3 km) portions of montes flanks are surrounded by relatively less extent (up to ∼0.5-0.8 km) of LDA flow units. Geomorphic and topographic evidence for flow units that appear to be superposed on the main LDA body collectively suggest the possibility of episodic glacial activity in the region. Furthermore, based on the alignment of subsurface reflectors with the surrounding plains when a permittivity of ice (3.2) is assumed and the radargram is depth-corrected, we infer that some of the portions of LDA flow units have preserved ice in their subsurface up to ∼300-500 m depth. Crater size frequency distribution of craters counted on LDA surface indicates that the best-fit age is ∼110 Ma. In addition, the LDA surfaces exhibit different best-fit ages for different types of crater morphologies (bowl-shaped, ring-mold and infilled craters) included in the crater count statistics. Together, these observations and the interpretations suggest that most, if not all, of the LDAs in the study region are like classical LDAs mapped in other regions of Mars (e.g. along the mid-latitude dichotomy boundary and eastern Hellas region). These results indicate that a widespread accumulation and preservation of ice has occurred during the Late Amazonian as suggested in previous studies.

Multispectral imaging burn wound tissue classification system: a comparison of test accuracies between several common machine learning algorithms

NASA Astrophysics Data System (ADS)

Squiers, John J.; Li, Weizhi; King, Darlene R.; Mo, Weirong; Zhang, Xu; Lu, Yang; Sellke, Eric W.; Fan, Wensheng; DiMaio, J. Michael; Thatcher, Jeffrey E.

2016-03-01

The clinical judgment of expert burn surgeons is currently the standard on which diagnostic and therapeutic decisionmaking regarding burn injuries is based. Multispectral imaging (MSI) has the potential to increase the accuracy of burn depth assessment and the intraoperative identification of viable wound bed during surgical debridement of burn injuries. A highly accurate classification model must be developed using machine-learning techniques in order to translate MSI data into clinically-relevant information. An animal burn model was developed to build an MSI training database and to study the burn tissue classification ability of several models trained via common machine-learning algorithms. The algorithms tested, from least to most complex, were: K-nearest neighbors (KNN), decision tree (DT), linear discriminant analysis (LDA), weighted linear discriminant analysis (W-LDA), quadratic discriminant analysis (QDA), ensemble linear discriminant analysis (EN-LDA), ensemble K-nearest neighbors (EN-KNN), and ensemble decision tree (EN-DT). After the ground-truth database of six tissue types (healthy skin, wound bed, blood, hyperemia, partial injury, full injury) was generated by histopathological analysis, we used 10-fold cross validation to compare the algorithms' performances based on their accuracies in classifying data against the ground truth, and each algorithm was tested 100 times. The mean test accuracy of the algorithms were KNN 68.3%, DT 61.5%, LDA 70.5%, W-LDA 68.1%, QDA 68.9%, EN-LDA 56.8%, EN-KNN 49.7%, and EN-DT 36.5%. LDA had the highest test accuracy, reflecting the bias-variance tradeoff over the range of complexities inherent to the algorithms tested. Several algorithms were able to match the current standard in burn tissue classification, the clinical judgment of expert burn surgeons. These results will guide further development of an MSI burn tissue classification system. Given that there are few surgeons and facilities specializing in burn care, this technology may improve the standard of burn care for patients without access to specialized facilities.

Pressure-induced transformations in computer simulations of glassy water.

PubMed

Chiu, Janet; Starr, Francis W; Giovambattista, Nicolas

2013-11-14

Glassy water occurs in at least two broad categories: low-density amorphous (LDA) and high-density amorphous (HDA) solid water. We perform out-of-equilibrium molecular dynamics simulations to study the transformations of glassy water using the ST2 model. Specifically, we study the known (i) compression-induced LDA-to-HDA, (ii) decompression-induced HDA-to-LDA, and (iii) compression-induced hexagonal ice-to-HDA transformations. We study each transformation for a broad range of compression/decompression temperatures, enabling us to construct a "P-T phase diagram" for glassy water. The resulting phase diagram shows the same qualitative features reported from experiments. While many simulations have probed the liquid-state phase behavior, comparatively little work has examined the transitions of glassy water. We examine how the glass transformations relate to the (first-order) liquid-liquid phase transition previously reported for this model. Specifically, our results support the hypothesis that the liquid-liquid spinodal lines, between a low-density and high-density liquid, are extensions of the LDA-HDA transformation lines in the limit of slow compression. Extending decompression runs to negative pressures, we locate the sublimation lines for both LDA and hyperquenched glassy water (HGW), and find that HGW is relatively more stable to the vapor. Additionally, we observe spontaneous crystallization of HDA at high pressure to ice VII. Experiments have also seen crystallization of HDA, but to ice XII. Finally, we contrast the structure of LDA and HDA for the ST2 model with experiments. We find that while the radial distribution functions (RDFs) of LDA are similar to those observed in experiments, considerable differences exist between the HDA RDFs of ST2 water and experiment. The differences in HDA structure, as well as the formation of ice VII (a tetrahedral crystal), are a consequence of ST2 overemphasizing the tetrahedral character of water.

Pressure-induced transformations in computer simulations of glassy water

NASA Astrophysics Data System (ADS)

Chiu, Janet; Starr, Francis W.; Giovambattista, Nicolas

2013-11-01

Glassy water occurs in at least two broad categories: low-density amorphous (LDA) and high-density amorphous (HDA) solid water. We perform out-of-equilibrium molecular dynamics simulations to study the transformations of glassy water using the ST2 model. Specifically, we study the known (i) compression-induced LDA-to-HDA, (ii) decompression-induced HDA-to-LDA, and (iii) compression-induced hexagonal ice-to-HDA transformations. We study each transformation for a broad range of compression/decompression temperatures, enabling us to construct a "P-T phase diagram" for glassy water. The resulting phase diagram shows the same qualitative features reported from experiments. While many simulations have probed the liquid-state phase behavior, comparatively little work has examined the transitions of glassy water. We examine how the glass transformations relate to the (first-order) liquid-liquid phase transition previously reported for this model. Specifically, our results support the hypothesis that the liquid-liquid spinodal lines, between a low-density and high-density liquid, are extensions of the LDA-HDA transformation lines in the limit of slow compression. Extending decompression runs to negative pressures, we locate the sublimation lines for both LDA and hyperquenched glassy water (HGW), and find that HGW is relatively more stable to the vapor. Additionally, we observe spontaneous crystallization of HDA at high pressure to ice VII. Experiments have also seen crystallization of HDA, but to ice XII. Finally, we contrast the structure of LDA and HDA for the ST2 model with experiments. We find that while the radial distribution functions (RDFs) of LDA are similar to those observed in experiments, considerable differences exist between the HDA RDFs of ST2 water and experiment. The differences in HDA structure, as well as the formation of ice VII (a tetrahedral crystal), are a consequence of ST2 overemphasizing the tetrahedral character of water.

A comparison of effectiveness among frequent treatments of recurrent spontaneous abortion: A Bayesian network meta-analysis.

PubMed

Lv, Sha; Yu, Jing; Xu, Xiaoxiao

2018-04-30

A comprehensive network meta-analysis was designed to clarify contradictions and offer valuable clinical guidance in the treatment of recurrent spontaneous abortion (RSA). The included clinical trials were selected from the relevant medical journal databases and screened. Treatments were ranked by the surface under the cumulative ranking curve. Heat plots were constructed to analyze the inconsistency between direct data and network results, and adjusted funnel plots were constructed to assess publication bias. Forty-nine randomized controlled trials involving a total of 8496 RSA patients were selected. With placebo as control, corticosteroid plus low dose aspirin (LDA) plus unfractionated heparin (UFH), granulocyte colony-stimulating factor (G-CSF) alone, and LDA plus low molecular weight heparin (LMWH) all demonstrated effectiveness in increasing successful live birth rates and reducing the incidences of miscarriage. However, no treatment was demonstrably superior to placebo in terms of pregnancy success. For all 3 endpoints (live birth, abortion and success pregnancy), the adjusted funnel plots were symmetric to zero and indicated no publication bias. In terms of live birth and abortion rates, no treatment outperformed placebo in patients with antiphospholipid syndrome. In consideration of live birth and abortion rates, corticosteroid plus LDA plus UFH appeared to be the optimum treatment strategy; G-CSF was second, followed by LDA with LMWH, LDA plus LMWH plus intravenous immunoglobulin, corticosteroid with LDA and others. Subgroup analysis demonstrated no benefit of antithrombotic therapy in patients with antiphospholipid syndrome. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Local linear discriminant analysis framework using sample neighbors.

PubMed

Fan, Zizhu; Xu, Yong; Zhang, David

2011-07-01

The linear discriminant analysis (LDA) is a very popular linear feature extraction approach. The algorithms of LDA usually perform well under the following two assumptions. The first assumption is that the global data structure is consistent with the local data structure. The second assumption is that the input data classes are Gaussian distributions. However, in real-world applications, these assumptions are not always satisfied. In this paper, we propose an improved LDA framework, the local LDA (LLDA), which can perform well without needing to satisfy the above two assumptions. Our LLDA framework can effectively capture the local structure of samples. According to different types of local data structure, our LLDA framework incorporates several different forms of linear feature extraction approaches, such as the classical LDA and principal component analysis. The proposed framework includes two LLDA algorithms: a vector-based LLDA algorithm and a matrix-based LLDA (MLLDA) algorithm. MLLDA is directly applicable to image recognition, such as face recognition. Our algorithms need to train only a small portion of the whole training set before testing a sample. They are suitable for learning large-scale databases especially when the input data dimensions are very high and can achieve high classification accuracy. Extensive experiments show that the proposed algorithms can obtain good classification results.

Experimental study of the polyamorphism of water. I. The isobaric transitions from amorphous ices to LDA at 4 MPa.

PubMed

Handle, Philip H; Loerting, Thomas

2018-03-28

The existence of more than one solid amorphous state of water is an extraordinary feature. Since polyamorphism might be connected to the liquid-liquid critical point hypothesis, it is particularly important to study the relations amongst the different amorphous ices. Here we study the polyamorphic transformations of several high pressure amorphous ices to low-density amorphous ice (LDA) at 4 MPa by isobaric heating utilising in situ volumetry and ex situ X-ray diffraction. We find that very-high density amorphous ice (VHDA) and unannealed high density amorphous ice (HDA) show significant relaxation before transforming to LDA, whereby VHDA is seen to relax toward HDA. By contrast, expanded HDA shows almost no relaxation prior to the transformation. The transition to LDA itself obeys criteria for a first-order-like transition in all cases. In the case of VHDA, even macroscopic phase separation is observed. These findings suggest that HDA and LDA are two clearly distinct polyamorphs. We further present evidence that HDA reaches the metastable equilibrium at 140 K and 0.1 GPa but only comes close to that at 140 K and 0.2 GPa. The most important is the path independence of the amorphous phase reached at 140 K and 0.1 GPa.

Modeling virtual organizations with Latent Dirichlet Allocation: a case for natural language processing.

PubMed

Gross, Alexander; Murthy, Dhiraj

2014-10-01

This paper explores a variety of methods for applying the Latent Dirichlet Allocation (LDA) automated topic modeling algorithm to the modeling of the structure and behavior of virtual organizations found within modern social media and social networking environments. As the field of Big Data reveals, an increase in the scale of social data available presents new challenges which are not tackled by merely scaling up hardware and software. Rather, they necessitate new methods and, indeed, new areas of expertise. Natural language processing provides one such method. This paper applies LDA to the study of scientific virtual organizations whose members employ social technologies. Because of the vast data footprint in these virtual platforms, we found that natural language processing was needed to 'unlock' and render visible latent, previously unseen conversational connections across large textual corpora (spanning profiles, discussion threads, forums, and other social media incarnations). We introduce variants of LDA and ultimately make the argument that natural language processing is a critical interdisciplinary methodology to make better sense of social 'Big Data' and we were able to successfully model nested discussion topics from forums and blog posts using LDA. Importantly, we found that LDA can move us beyond the state-of-the-art in conventional Social Network Analysis techniques. Copyright © 2014 Elsevier Ltd. All rights reserved.

Experimental study of the polyamorphism of water. I. The isobaric transitions from amorphous ices to LDA at 4 MPa

NASA Astrophysics Data System (ADS)

Handle, Philip H.; Loerting, Thomas

2018-03-01

The existence of more than one solid amorphous state of water is an extraordinary feature. Since polyamorphism might be connected to the liquid-liquid critical point hypothesis, it is particularly important to study the relations amongst the different amorphous ices. Here we study the polyamorphic transformations of several high pressure amorphous ices to low-density amorphous ice (LDA) at 4 MPa by isobaric heating utilising in situ volumetry and ex situ X-ray diffraction. We find that very-high density amorphous ice (VHDA) and unannealed high density amorphous ice (HDA) show significant relaxation before transforming to LDA, whereby VHDA is seen to relax toward HDA. By contrast, expanded HDA shows almost no relaxation prior to the transformation. The transition to LDA itself obeys criteria for a first-order-like transition in all cases. In the case of VHDA, even macroscopic phase separation is observed. These findings suggest that HDA and LDA are two clearly distinct polyamorphs. We further present evidence that HDA reaches the metastable equilibrium at 140 K and 0.1 GPa but only comes close to that at 140 K and 0.2 GPa. The most important is the path independence of the amorphous phase reached at 140 K and 0.1 GPa.

Non-targeted 1H NMR fingerprinting and multivariate statistical analyses for the characterisation of the geographical origin of Italian sweet cherries.

PubMed

Longobardi, F; Ventrella, A; Bianco, A; Catucci, L; Cafagna, I; Gallo, V; Mastrorilli, P; Agostiano, A

2013-12-01

In this study, non-targeted (1)H NMR fingerprinting was used in combination with multivariate statistical techniques for the classification of Italian sweet cherries based on their different geographical origins (Emilia Romagna and Puglia). As classification techniques, Soft Independent Modelling of Class Analogy (SIMCA), Partial Least Squares Discriminant Analysis (PLS-DA), and Linear Discriminant Analysis (LDA) were carried out and the results were compared. For LDA, before performing a refined selection of the number/combination of variables, two different strategies for a preliminary reduction of the variable number were tested. The best average recognition and CV prediction abilities (both 100.0%) were obtained for all the LDA models, although PLS-DA also showed remarkable performances (94.6%). All the statistical models were validated by observing the prediction abilities with respect to an external set of cherry samples. The best result (94.9%) was obtained with LDA by performing a best subset selection procedure on a set of 30 principal components previously selected by a stepwise decorrelation. The metabolites that mostly contributed to the classification performances of such LDA model, were found to be malate, glucose, fructose, glutamine and succinate. Copyright © 2013 Elsevier Ltd. All rights reserved.

Electric Double-Layer Structure in Primitive Model Electrolytes. Comparing Molecular Dynamics with Local-Density Approximations

DOE PAGES

Giera, Brian; Lawrence Livermore National Lab.; Henson, Neil; ...

2015-02-27

We evaluate the accuracy of local-density approximations (LDAs) using explicit molecular dynamics simulations of binary electrolytes comprised of equisized ions in an implicit solvent. The Bikerman LDA, which considers ions to occupy a lattice, poorly captures excluded volume interactions between primitive model ions. Instead, LDAs based on the Carnahan–Starling (CS) hard-sphere equation of state capture simulated values of ideal and excess chemical potential profiles extremely well, as is the relationship between surface charge density and electrostatic potential. Excellent agreement between the EDL capacitances predicted by CS-LDAs and computed in molecular simulations is found even in systems where ion correlations drivemore » strong density and free charge oscillations within the EDL, despite the inability of LDAs to capture the oscillations in the detailed EDL profiles.« less

A novel procedure on next generation sequencing data analysis using text mining algorithm.

PubMed

Zhao, Weizhong; Chen, James J; Perkins, Roger; Wang, Yuping; Liu, Zhichao; Hong, Huixiao; Tong, Weida; Zou, Wen

2016-05-13

Next-generation sequencing (NGS) technologies have provided researchers with vast possibilities in various biological and biomedical research areas. Efficient data mining strategies are in high demand for large scale comparative and evolutional studies to be performed on the large amounts of data derived from NGS projects. Topic modeling is an active research field in machine learning and has been mainly used as an analytical tool to structure large textual corpora for data mining. We report a novel procedure to analyse NGS data using topic modeling. It consists of four major procedures: NGS data retrieval, preprocessing, topic modeling, and data mining using Latent Dirichlet Allocation (LDA) topic outputs. The NGS data set of the Salmonella enterica strains were used as a case study to show the workflow of this procedure. The perplexity measurement of the topic numbers and the convergence efficiencies of Gibbs sampling were calculated and discussed for achieving the best result from the proposed procedure. The output topics by LDA algorithms could be treated as features of Salmonella strains to accurately describe the genetic diversity of fliC gene in various serotypes. The results of a two-way hierarchical clustering and data matrix analysis on LDA-derived matrices successfully classified Salmonella serotypes based on the NGS data. The implementation of topic modeling in NGS data analysis procedure provides a new way to elucidate genetic information from NGS data, and identify the gene-phenotype relationships and biomarkers, especially in the era of biological and medical big data. The implementation of topic modeling in NGS data analysis provides a new way to elucidate genetic information from NGS data, and identify the gene-phenotype relationships and biomarkers, especially in the era of biological and medical big data.

Splitting Fermi Surfaces and Heavy Electronic States in Non-Centrosymmetric U3Ni3Sn4

NASA Astrophysics Data System (ADS)

Maurya, Arvind; Harima, Hisatomo; Nakamura, Ai; Shimizu, Yusei; Homma, Yoshiya; Li, DeXin; Honda, Fuminori; Sato, Yoshiki J.; Aoki, Dai

2018-04-01

We report the single-crystal growth of the non-centrosymmetric paramagnet U3Ni3Sn4 by the Bridgman method and the Fermi surface properties detected by de Haas-van Alphen (dHvA) experiments. We have also investigated single-crystal U3Ni3Sn4 by single-crystal X-ray diffraction, magnetization, electrical resistivity, and heat capacity measurements. The angular dependence of the dHvA frequencies reveals many closed Fermi surfaces, which are nearly spherical in topology. The experimental results are in good agreement with local density approximation (LDA) band structure calculations based on the 5f-itinerant model. The band structure calculation predicts many Fermi surfaces, mostly with spherical shape, derived from 12 bands crossing the Fermi energy. To our knowledge, the splitting of Fermi surfaces due to the non-centrosymmetric crystal in 5f-electron systems is experimentally detected for the first time. The temperature dependence of the dHvA amplitude reveals a large cyclotron effective mass of up to 35 m0, indicating the heavy electronic state of U3Ni3Sn4 due to the proximity of the quantum critical point. From the field dependence of the dHvA amplitude, a mean free path of conduction electrons of up to 1950 Å is detected, reflecting the good quality of the grown crystal. The small splitting energy related to the antisymmetric spin-orbit interaction is most likely due to the large cyclotron effective mass.

Structural and vibrational properties of transition-metal oxides from first-principles calculations

NASA Astrophysics Data System (ADS)

Cococcioni, M.; Floris, A.; Himmetoglu, B.

2010-12-01

The calculation of the vibrational spectrum of minerals is of fundamental importance to assess their behavior (e.g. their elastic properties, or possible structural phase transitions) under the high-temperature, high-pressure conditions of the Earth’s interior. The ubiquitous presence of transition metals and the consequent importance of electronic correlations make the study of these materials quite difficult to approach with approximate DFT functionals (as LDA or GGA). The DFT+U, consisting in a Hubbard-modeled correction to the DFT energy functionals, has been successfully used to study the electronic, structural, and magnetic properties of several Fe-bearing minerals. However, the vibrational spectrum of these systems has never been determined entirely (frozen- phonon techniques are overly expensive except for zone-center phonons). In this work we introduce the extension of Density-Functional-Perturbation-Theory to DFT+U, that allows to efficiently compute the phonon spectrum of transition-metal compounds from their correlated ground states. A comparative analysis between the vibrational properties of MnO, FeO, CoO, and NiO (in the undistorted cubic cell) highlights a marked dependence of several features of their phonon spectrum on the occupancy of localized d orbitals and thus, on elec- tronic correlation. The new computational tool is also employed to evaluate the rhombohedral distortion of FeO (particularly abundant in the Earth’s lower mantle) and to assess the stability of its B1 phase in different conditions of pressure and temperature.

First-Principles Study of the Self-Assembled Pentacene Molecules on Metal Surfaces

NASA Astrophysics Data System (ADS)

Lee, Kyuho; Han, Myung-Joon; Yu, Jaejun

2003-03-01

Oriented thin films of organic semiconducting small molecules have received considerable attention as active semiconductors for device applications such as Schottky diodes and thin-film transistors (TFTs). Among these organic materials, pentacene has been found to have the highest mobilities for hole transport. Understanding the formation of self-organized ad-layers of pentacene would contribute to the fabrication of nanostructures and possibly highly oriented pentacene layers by epitaxy for use in electronic devices. To understand the ordering patterns of pentacene ad-layers on metal surfaces, we investigated the energetics between pentacene molecules with and without metal substrates and analyzed its electronic structure. We used a self-consistent first-principles calculation method based on the density functional theory (DFT) within local density approximation (LDA). The localized pseudo-atomic orbitals (PAO) are employed for a real-space numerical basis set, which was suggested by Sankey and Niklewski, and the Troullier-Martins-type pseudo-potential is used. As results, we found that the ordering patterns can be explained by the energetics between pentacene molecules, and the metal substrates appears not to influence too much on the interaction between pentacenes. To investigate the nature of the self-assembled structure, we calculated the total energies of various configurations for the molecule pattern, e.g., side-by-side and head-to-head ordering or on-top stacking. Depending on its direction, extremely different interaction character between two pentacenes is found and explained by its electronic structure analysis.

Structural, electronic and optical properties of LiNbO3 using GGA-PBE and TB-mBJ functionals: A DFT study

NASA Astrophysics Data System (ADS)

Arshad Javid, M.; Khan, Zafar Ullah; Mehmood, Zahid; Nabi, Azeem; Hussain, Fayyaz; Imran, M.; Nadeem, Muhammad; Anjum, Naeem

2018-06-01

In the present work, first-principles calculations were performed to obtain the structural, electronic and optical properties of lithium niobate crystal using two exchange-correlation functionals (GGA-PBE and TB-mBJ). The calculated structural parameters were very close to the experimental values. TB-mBJ functional was found to be good when compared to LDA and GGA functionals in case of bandgap energy of 3.715 eV of lithium niobate. It was observed that the upper valence and lower conduction bands consist mainly the O-2p and Nb-4d states, respectively. Furthermore, calculations for real and imaginary parts of frequency-dependent dielectric function 𝜀(ω) of lithium niobate crystal were performed using TD-DFT method. The ordinary refractive index no(ω), extraordinary refractive index ne(ω), its birefringence and absorption peaks in imaginary dielectric function 𝜀2(ω) were also calculated.

Mid-Infrared Vibrational Spectra of Discrete Acetone-Ligated Cerium Hydroxide Cations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Groenewold, G. S.; Gianotto, Anita K.; Cossel, Kevin C.

2007-02-15

Cerium (III) hydroxy reactive sites are responsible for several important heterogeneous catalysis processes, and understanding the reaction chemistry of substrate molecules like CO, H2O, and CH3OH as they occur in heterogeneous media is a challenging task. We report here the first infrared spectra of model gas-phase cerium complexes and use the results as a benchmark to assist evaluation of the accuracy of ab initio calculations. Complexes containing [CeOH]2+ ligated by three- and four-acetone molecules were generated by electrospray ionization and characterized using wavelength-selective infrared multiple photon dissociation (IRMPD). The C=O stretching frequency for the [CeOH(acetone)4]2+ species appeared at 1650 cm-1more » and was red-shifted by 90 cm-1 compared to unligated acetone. The magnitude of this shift for the carbonyl frequency was even greater for the [CeOH(acetone)3]2+ complex: the IRMPD peak consisted of two dissociation channels, an initial elimination of acetone at 1635 cm-1, and elimination of acetone accompanied by a serial charge separation producing [CeO(acetone)]+ at 1599 cm-1, with the overall frequency centered at 1616 cm-1. The increasing red shift observed as the number of acetone ligands decreases from four to three is consistent with transfer of more electron density per ligand in the less coordinated complexes. The lower frequency measured for the elimination/charge separation process is likely due to anharmonicity resulting from population of higher vibrational states. The C-C stretching frequency in the complexes is also influenced by coordination to the metal: it is blue-shifted compared to bare acetone, indicating a slight strengthening of the C-C bond in the complex, with the intensity of the absorption decreasing with decreasing ligation. Density functional theory (DFT) calculations using three different functionals (LDA, B3LYP, and PBE0) are used to predict the infrared spectra of the complexes. Calculated frequencies for the carbonyl stretch are within 40 cm-1 of the IRMPD of the three-acetone complex measured using the single acetone loss, and within 60 cm-1 of the measurement for the four-acetone complexes. The B3LYP and LDA functionals provided the best agreement with the measured spectra. The C-C stretching frequencies calculated using B3LYP are higher in energy than the measured values by ~ 30 cm-1, and reproduce the observed trend which shows that the C-C stretching frequency decreases with increasing ligation. Agreement between C-C frequency and calculation was not as good using the LDA functional, but still within 70 cm-1. The results provide an evaluation of changes in the acceptor properties of the metal center as ligands are added, and of the utility of DFT for modeling f-block coordination complexes.« less

Waterlike glass polyamorphism in a monoatomic isotropic Jagla model.

PubMed

Xu, Limei; Giovambattista, Nicolas; Buldyrev, Sergey V; Debenedetti, Pablo G; Stanley, H Eugene

2011-02-14

We perform discrete-event molecular dynamics simulations of a system of particles interacting with a spherically-symmetric (isotropic) two-scale Jagla pair potential characterized by a hard inner core, a linear repulsion at intermediate separations, and a weak attractive interaction at larger separations. This model system has been extensively studied due to its ability to reproduce many thermodynamic, dynamic, and structural anomalies of liquid water. The model is also interesting because: (i) it is very simple, being composed of isotropically interacting particles, (ii) it exhibits polyamorphism in the liquid phase, and (iii) its slow crystallization kinetics facilitate the study of glassy states. There is interest in the degree to which the known polyamorphism in glassy water may have parallels in liquid water. Motivated by parallels between the properties of the Jagla potential and those of water in the liquid state, we study the metastable phase diagram in the glass state. Specifically, we perform the computational analog of the protocols followed in the experimental studies of glassy water. We find that the Jagla potential calculations reproduce three key experimental features of glassy water: (i) the crystal-to-high-density amorphous solid (HDA) transformation upon isothermal compression, (ii) the low-density amorphous solid (LDA)-to-HDA transformation upon isothermal compression, and (iii) the HDA-to-very-high-density amorphous solid (VHDA) transformation upon isobaric annealing at high pressure. In addition, the HDA-to-LDA transformation upon isobaric heating, observed in water experiments, can only be reproduced in the Jagla model if a free surface is introduced in the simulation box. The HDA configurations obtained in cases (i) and (ii) are structurally indistinguishable, suggesting that both processes result in the same glass. With the present parametrization, the evolution of density with pressure or temperature is remarkably similar to the corresponding experimental measurements on water. Our simulations also suggest that the Jagla potential may reproduce features of the HDA-VHDA transformations observed in glassy water upon compression and decompression. Snapshots of the system during the HDA-VHDA and HDA-LDA transformations reveal a clear segregation between LDA and HDA but not between HDA and VHDA, consistent with the possibility that LDA and HDA are separated by a first order transformation as found experimentally, whereas HDA and VHDA are not. Our results demonstrate that a system of particles with simple isotropic pair interactions, a Jagla potential with two characteristic length scales, can present polyamorphism in the glass state as well as reproducing many of the distinguishing properties of liquid water. While most isotropic pair potential models crystallize readily on simulation time scales at the low temperatures investigated here, the Jagla potential is an exception, and is therefore a promising model system for the study of glass phenomenology.

Impact of Soil Moisture Assimilation on Land Surface Model Spin-Up and Coupled LandAtmosphere Prediction

NASA Technical Reports Server (NTRS)

Santanello, Joseph A., Jr.; Kumar, Sujay V.; Peters-Lidard, Christa D.; Lawston, P.

2016-01-01

Advances in satellite monitoring of the terrestrial water cycle have led to a concerted effort to assimilate soil moisture observations from various platforms into offline land surface models (LSMs). One principal but still open question is that of the ability of land data assimilation (LDA) to improve LSM initial conditions for coupled short-term weather prediction. In this study, the impact of assimilating Advanced Microwave Scanning Radiometer for EOS (AMSR-E) soil moisture retrievals on coupled WRF Model forecasts is examined during the summers of dry (2006) and wet (2007) surface conditions in the southern Great Plains. LDA is carried out using NASAs Land Information System (LIS) and the Noah LSM through an ensemble Kalman filter (EnKF) approach. The impacts of LDA on the 1) soil moisture and soil temperature initial conditions for WRF, 2) land-atmosphere coupling characteristics, and 3) ambient weather of the coupled LIS-WRF simulations are then assessed. Results show that impacts of soil moisture LDA during the spin-up can significantly modify LSM states and fluxes, depending on regime and season. Results also indicate that the use of seasonal cumulative distribution functions (CDFs) is more advantageous compared to the traditional annual CDF bias correction strategies. LDA performs consistently regardless of atmospheric forcing applied, with greater improvements seen when using coarser, global forcing products. Downstream impacts on coupled simulations vary according to the strength of the LDA impact at the initialization, where significant modifications to the soil moisture flux- PBL-ambient weather process chain are observed. Overall, this study demonstrates potential for future, higher-resolution soil moisture assimilation applications in weather and climate research.

Metabolic Profile and Inflammatory Responses in Dairy Cows with Left Displaced Abomasum Kept under Small-Scaled Farm Conditions

PubMed Central

Klevenhusen, Fenja; Humer, Elke; Metzler-Zebeli, Barbara; Podstatzky-Lichtenstein, Leopold; Wittek, Thomas; Zebeli, Qendrim

2015-01-01

Simple Summary This research established an association between lactation number and milk production and metabolic and inflammatory responses in high-producing dairy cows affected by left abomasal displacement in small-scaled dairy farms. The study showed metabolic alterations, liver damage, and inflammation in the sick cows, which were further exacerbated with increasing lactation number and milk yield of the cows. Abstract Left displaced abomasum (LDA) is a severe metabolic disease of cattle with a strong negative impact on production efficiency of dairy farms. Metabolic and inflammatory alterations associated with this disease have been reported in earlier studies, conducted mostly in large dairy farms. This research aimed to: (1) evaluate metabolic and inflammatory responses in dairy cows affected by LDA in small-scaled dairy farms; and (2) establish an association between lactation number and milk production with the outcome of metabolic variables. The cows with LDA had lower serum calcium (Ca), but greater concentrations of non-esterified fatty acids (NEFA) and beta-hydroxy-butyrate (BHBA), in particular when lactation number was >2. Cows with LDA showed elevated levels of aspartate aminotransferase, glutamate dehydrogenase, and serum amyloid A (SAA), regardless of lactation number. In addition, this study revealed strong associations between milk yield and the alteration of metabolic profile but not with inflammation in the sick cows. Results indicate metabolic alterations, liver damage, and inflammation in LDA cows kept under small-scale farm conditions. Furthermore, the data suggest exacerbation of metabolic profile and Ca metabolism but not of inflammation and liver health with increasing lactation number and milk yield in cows affected by LDA. PMID:26479481

Improved Maturity and Ripeness Classifications of Magnifera Indica cv. Harumanis Mangoes through Sensor Fusion of an Electronic Nose and Acoustic Sensor

PubMed Central

Zakaria, Ammar; Shakaff, Ali Yeon Md; Masnan, Maz Jamilah; Saad, Fathinul Syahir Ahmad; Adom, Abdul Hamid; Ahmad, Mohd Noor; Jaafar, Mahmad Nor; Abdullah, Abu Hassan; Kamarudin, Latifah Munirah

2012-01-01

In recent years, there have been a number of reported studies on the use of non-destructive techniques to evaluate and determine mango maturity and ripeness levels. However, most of these reported works were conducted using single-modality sensing systems, either using an electronic nose, acoustics or other non-destructive measurements. This paper presents the work on the classification of mangoes (Magnifera Indica cv. Harumanis) maturity and ripeness levels using fusion of the data of an electronic nose and an acoustic sensor. Three groups of samples each from two different harvesting times (week 7 and week 8) were evaluated by the e-nose and then followed by the acoustic sensor. Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA) were able to discriminate the mango harvested at week 7 and week 8 based solely on the aroma and volatile gases released from the mangoes. However, when six different groups of different maturity and ripeness levels were combined in one classification analysis, both PCA and LDA were unable to discriminate the age difference of the Harumanis mangoes. Instead of six different groups, only four were observed using the LDA, while PCA showed only two distinct groups. By applying a low level data fusion technique on the e-nose and acoustic data, the classification for maturity and ripeness levels using LDA was improved. However, no significant improvement was observed using PCA with data fusion technique. Further work using a hybrid LDA-Competitive Learning Neural Network was performed to validate the fusion technique and classify the samples. It was found that the LDA-CLNN was also improved significantly when data fusion was applied. PMID:22778629

Attention-deficit hyperactivity disorder symptoms add risk to circadian rhythm sleep problems in depression and anxiety.

PubMed

Bron, T I; Bijlenga, D; Kooij, J J S; Vogel, S W N; Wynchank, D; Beekman, A T F; Penninx, B W J H

2016-08-01

Comorbid ADHD symptoms may partly account for circadian rhythm disturbances in depression and anxiety disorders. Self-reported sleep characteristics of 2090 participants in the Netherlands Study of Depression and Anxiety were assessed using the Munich Chronotype Questionnaire. We defined 3 groups: healthy controls (HC), persons with lifetime depression and/or anxiety disorders (LDA), and those with both LDA and high ADHD symptoms (LDA+ADHD), using the Conner's Adult ADHD Rating Scale. Sleep characteristics were least favorable in the LDA+ADHD group. Important group differences between LDA+ADHD, LDA and HC were found for extremely late chronotype (12% vs. 5% vs. 3%; p<.001), sleep duration <6h (15% vs. 5% vs. 4%; p<.001), and for an indication of the Delayed Sleep Phase Syndrome (DSPS; 16% vs. 8% vs. 5%; p<.001). After adjustment for covariates, including depression and anxiety, presence of ADHD symptoms increased the odds ratio for late chronotype (OR=2.6; p=.003), indication of DSPS (OR=2.4; p=.002), and sleep duration <6h (OR=2.7; p=.007). ADHD conceptually overlaps with symptom presentation of depression and anxiety. We used a cross-sectional study design, and used self reported sleep characteristics. High ADHD symptoms were associated with an increased rate of circadian rhythm sleep disturbances in an already at-risk population of people with depression and/or anxiety disorders. Circadian rhythm sleep disorders, as often seen in ADHD are not entirely due to any comorbid depression and/or anxiety disorder. Adequate treatment of such sleep problems is needed and may prevent serious health conditions in the long term. Copyright © 2016 Elsevier B.V. All rights reserved.

Lafutidine prevents low-dose aspirin and loxoprofen induced gastric injury: a randomized, double-blinded, placebo controlled study.

PubMed

Kato, Mototsugu; Kamada, Go; Yamamoto, Keiko; Nishida, Urara; Imai, Aki; Yoshida, Takeshi; Ono, Shouko; Nakagawa, Manabu; Nakagawa, Soichi; Shimizu, Yuichi; Asaka, Masahiro

2010-10-01

The concomitant use of non-steroidal anti-inflammatory drugs is a risk factor for low-dose aspirin (LDA)-associated upper gastrointestinal toxicity. Lafutidine is an H2-receptor antagonist with gastroprotective activity, produced by acting on capsaicin-sensitive afferent neurons. To evaluate the preventive effect of lafutidine on gastric damage caused by LDA alone and by the combination of both LDA and loxoprofen, we conducted a clinical study using healthy volunteers. A randomized, double-blinded, placebo-controlled, crossover study was carried out. Sixteen healthy volunteers without Helicobacter pylori infection were randomly assigned to two groups. Both groups received 81 mg of aspirin once daily for 14 days (on days 1 to 14) and 60 mg of loxoprofen three times daily for the last 7 days (on days 8 to 14). Placebo or 10 mg of lafutidine was administered twice daily for 14 days in each group. After a 2-week washout period, placebo and lafutidine were crossed over. Endoscopic findings of gastric mucosal damage were evaluated according to the modified Lanza score. The mean modified Lanza score was 2.19 ± 1.06 (SD) for aspirin plus placebo as compared with 0.50 ± 0.77 for aspirin plus lafutidine (P < 0.001), and 3.00 ± 1.56 for aspirin plus loxoprofen and placebo as compared with 1.25 ± 1.37 for aspirin plus loxoprofen and lafutidine (P < 0.01). The addition of loxoprofen to LDA increases gastric mucosal damage. Standard-dose lafutidine significantly prevents gastric mucosal damage induced by LDA alone or LDA plus loxoprofen in H. pylori-negative volunteers. Larger controlled studies are needed to strengthen these findings. © 2010 Journal of Gastroenterology and Hepatology Foundation and Blackwell Publishing Asia Pty Ltd.

Improved maturity and ripeness classifications of Magnifera Indica cv. Harumanis mangoes through sensor fusion of an electronic nose and acoustic sensor.

PubMed

Zakaria, Ammar; Shakaff, Ali Yeon Md; Masnan, Maz Jamilah; Saad, Fathinul Syahir Ahmad; Adom, Abdul Hamid; Ahmad, Mohd Noor; Jaafar, Mahmad Nor; Abdullah, Abu Hassan; Kamarudin, Latifah Munirah

2012-01-01

In recent years, there have been a number of reported studies on the use of non-destructive techniques to evaluate and determine mango maturity and ripeness levels. However, most of these reported works were conducted using single-modality sensing systems, either using an electronic nose, acoustics or other non-destructive measurements. This paper presents the work on the classification of mangoes (Magnifera Indica cv. Harumanis) maturity and ripeness levels using fusion of the data of an electronic nose and an acoustic sensor. Three groups of samples each from two different harvesting times (week 7 and week 8) were evaluated by the e-nose and then followed by the acoustic sensor. Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA) were able to discriminate the mango harvested at week 7 and week 8 based solely on the aroma and volatile gases released from the mangoes. However, when six different groups of different maturity and ripeness levels were combined in one classification analysis, both PCA and LDA were unable to discriminate the age difference of the Harumanis mangoes. Instead of six different groups, only four were observed using the LDA, while PCA showed only two distinct groups. By applying a low level data fusion technique on the e-nose and acoustic data, the classification for maturity and ripeness levels using LDA was improved. However, no significant improvement was observed using PCA with data fusion technique. Further work using a hybrid LDA-Competitive Learning Neural Network was performed to validate the fusion technique and classify the samples. It was found that the LDA-CLNN was also improved significantly when data fusion was applied.

On the Performance of Local Density Approximation in Describing the Adsorption of Electron Donating/Accepting Molecules on Graphene

PubMed Central

Wang, Yixuan; Xu, Zhenfeng; Moe, Yin N.

2012-01-01

In order to asses performance of the LDA in describing physisorption on graphene, adsorptions of TCNE, TCNQ, TNF, TTF, and DMPD as well as four benzene derivatives on C54H18 and C110H30 were explored with a variety of DFTs such as MPWB1K, M06-2X, PBE-D and LSDA. Although it is well known that the LDA considerably overestimate non-covalent interaction, the LSDA predicted adsorption energies except for TCNE on C110H30 are systematically lower than those from the M06-2X by 0.4–3.2 kcal/mol, and they are more significantly lower than those from the PBE-D for all the molecules by 3–6 kcal/mol. However, the LSDA adsorption energy sequence is consistent with that from the PBE-D, TNF~TCNQ>TCNE~DMPD>TTF. Moreover, the domain interaction between the electron donor and acceptor molecules with graphene through cooperative π···π, C-H···π and N-H···π were visualized with sign(λ2)×ρ, and the relationships between the binding energy with London force, molecular electronegativity, and frontier orbital level were extensively discussed. PMID:23180902

Improving the analysis of near-spectroscopy data with multivariate classification of hemodynamic patterns: a theoretical formulation and validation.

PubMed

Gemignani, Jessica; Middell, Eike; Barbour, Randall L; Graber, Harry L; Blankertz, Benjamin

2018-04-04

The statistical analysis of functional near infrared spectroscopy (fNIRS) data based on the general linear model (GLM) is often made difficult by serial correlations, high inter-subject variability of the hemodynamic response, and the presence of motion artifacts. In this work we propose to extract information on the pattern of hemodynamic activations without using any a priori model for the data, by classifying the channels as 'active' or 'not active' with a multivariate classifier based on linear discriminant analysis (LDA). This work is developed in two steps. First we compared the performance of the two analyses, using a synthetic approach in which simulated hemodynamic activations were combined with either simulated or real resting-state fNIRS data. This procedure allowed for exact quantification of the classification accuracies of GLM and LDA. In the case of real resting-state data, the correlations between classification accuracy and demographic characteristics were investigated by means of a Linear Mixed Model. In the second step, to further characterize the reliability of the newly proposed analysis method, we conducted an experiment in which participants had to perform a simple motor task and data were analyzed with the LDA-based classifier as well as with the standard GLM analysis. The results of the simulation study show that the LDA-based method achieves higher classification accuracies than the GLM analysis, and that the LDA results are more uniform across different subjects and, in contrast to the accuracies achieved by the GLM analysis, have no significant correlations with any of the demographic characteristics. Findings from the real-data experiment are consistent with the results of the real-plus-simulation study, in that the GLM-analysis results show greater inter-subject variability than do the corresponding LDA results. The results obtained suggest that the outcome of GLM analysis is highly vulnerable to violations of theoretical assumptions, and that therefore a data-driven approach such as that provided by the proposed LDA-based method is to be favored.

Glass and liquid phase diagram of a polyamorphic monatomic system

NASA Astrophysics Data System (ADS)

Reisman, Shaina; Giovambattista, Nicolas

2013-02-01

We perform out-of-equilibrium molecular dynamics (MD) simulations of a monatomic system with Fermi-Jagla (FJ) pair potential interactions. This model system exhibits polyamorphism both in the liquid and glass state. The two liquids, low-density (LDL) and high-density liquid (HDL), are accessible in equilibrium MD simulations and can form two glasses, low-density (LDA) and high-density amorphous (HDA) solid, upon isobaric cooling. The FJ model exhibits many of the anomalous properties observed in water and other polyamorphic liquids and thus, it is an excellent model system to explore qualitatively the thermodynamic properties of such substances. The liquid phase behavior of the FJ model system has been previously characterized. In this work, we focus on the glass behavior of the FJ system. Specifically, we perform systematic isothermal compression and decompression simulations of LDA and HDA at different temperatures and determine "phase diagrams" for the glass state; these phase diagrams varying with the compression/decompression rate used. We obtain the LDA-to-HDA and HDA-to-LDA transition pressure loci, PLDA-HDA(T) and PHDA-LDA(T), respectively. In addition, the compression-induced amorphization line, at which the low-pressure crystal (LPC) transforms to HDA, PLPC-HDA(T), is determined. As originally proposed by Poole et al. [Phys. Rev. E 48, 4605 (1993)], 10.1103/PhysRevE.48.4605 simulations suggest that the PLDA-HDA(T) and PHDA-LDA(T) loci are extensions of the LDL-to-HDL and HDL-to-LDL spinodal lines into the glass domain. Interestingly, our simulations indicate that the PLPC-HDA(T) locus is an extension, into the glass domain, of the LPC metastability limit relative to the liquid. We discuss the effects of compression/decompression rates on the behavior of the PLDA-HDA(T), PHDA-LDA(T), PLPC-HDA(T) loci. The competition between glass polyamorphism and crystallization is also addressed. At our "fast rate," crystallization can be partially suppressed and the glass phase diagram can be related directly with the liquid phase diagram. However, at our "slow rate," crystallization cannot be prevented at intermediate temperatures, within the glass region. In these cases, multiple crystal-crystal transformations are found upon compression/decompression (polymorphism).

Clinical features of gastroduodenal injury associated with long-term low-dose aspirin therapy

PubMed Central

Iwamoto, Junichi; Saito, Yoshifumi; Honda, Akira; Matsuzaki, Yasushi

2013-01-01

Low-dose aspirin (LDA) is clinically used for the prevention of cardiovascular and cerebrovascular events with the advent of an aging society. On the other hand, a very low dose of aspirin (10 mg daily) decreases the gastric mucosal prostaglandin levels and causes significant gastric mucosal damage. The incidence of LDA-induced gastrointestinal mucosal injury and bleeding has increased. It has been noticed that the incidence of LDA-induced gastrointestinal hemorrhage has increased more than that of non-aspirin non-steroidal anti-inflammatory drug (NSAID)-induced lesions. The pathogenesis related to inhibition of cyclooxygenase (COX)-1 includes reduced mucosal flow, reduced mucus and bicarbonate secretion, and impaired platelet aggregation. The pathogenesis related to inhibition of COX-2 involves reduced angiogenesis and increased leukocyte adherence. The pathogenic mechanisms related to direct epithelial damage are acid back diffusion and impaired platelet aggregation. The factors associated with an increased risk of upper gastrointestinal (GI) complications in subjects taking LDA are aspirin dose, history of ulcer or upper GI bleeding, age > 70 years, concomitant use of non-aspirin NSAIDs including COX-2-selective NSAIDs, and Helicobacter pylori (H. pylori) infection. Moreover, no significant differences have been found between ulcer and non-ulcer groups in the frequency and severity of symptoms such as nausea, acid regurgitation, heartburn, and bloating. It has been shown that the ratios of ulcers located in the body, fundus and cardia are significantly higher in bleeding patients than the ratio of gastroduodenal ulcers in patients taking LDA. Proton pump inhibitors reduce the risk of developing gastric and duodenal ulcers. In contrast to NSAID-induced gastrointestinal ulcers, a well-tolerated histamine H2-receptor antagonist is reportedly effective in prevention of LDA-induced gastrointestinal ulcers. The eradication of H. pylori is equivalent to treatment with omeprazole in preventing recurrent bleeding. Continuous aspirin therapy for patients with gastrointestinal bleeding may increase the risk of recurrent bleeding but potentially reduces the mortality rates, as stopping aspirin therapy is associated with higher mortality rates. It is very important to prevent LDA-induced gastroduodenal ulcer complications including bleeding, and every effort should be exercised to prevent the bleeding complications. PMID:23555156

Using color histograms and SPA-LDA to classify bacteria.

PubMed

de Almeida, Valber Elias; da Costa, Gean Bezerra; de Sousa Fernandes, David Douglas; Gonçalves Dias Diniz, Paulo Henrique; Brandão, Deysiane; de Medeiros, Ana Claudia Dantas; Véras, Germano

2014-09-01

In this work, a new approach is proposed to verify the differentiating characteristics of five bacteria (Escherichia coli, Enterococcus faecalis, Streptococcus salivarius, Streptococcus oralis, and Staphylococcus aureus) by using digital images obtained with a simple webcam and variable selection by the Successive Projections Algorithm associated with Linear Discriminant Analysis (SPA-LDA). In this sense, color histograms in the red-green-blue (RGB), hue-saturation-value (HSV), and grayscale channels and their combinations were used as input data, and statistically evaluated by using different multivariate classifiers (Soft Independent Modeling by Class Analogy (SIMCA), Principal Component Analysis-Linear Discriminant Analysis (PCA-LDA), Partial Least Squares Discriminant Analysis (PLS-DA) and Successive Projections Algorithm-Linear Discriminant Analysis (SPA-LDA)). The bacteria strains were cultivated in a nutritive blood agar base layer for 24 h by following the Brazilian Pharmacopoeia, maintaining the status of cell growth and the nature of nutrient solutions under the same conditions. The best result in classification was obtained by using RGB and SPA-LDA, which reached 94 and 100 % of classification accuracy in the training and test sets, respectively. This result is extremely positive from the viewpoint of routine clinical analyses, because it avoids bacterial identification based on phenotypic identification of the causative organism using Gram staining, culture, and biochemical proofs. Therefore, the proposed method presents inherent advantages, promoting a simpler, faster, and low-cost alternative for bacterial identification.

Effect of starvation and refeeding on the hepatopancreas of whiteleg shrimp Penaeus vannamei (Boone) using computer-assisted image analysis.

PubMed

Cervellione, F; McGurk, C; Berger Eriksen, T; Van den Broeck, W

2017-11-01

Under normal farming conditions, shrimp can experience starvation periods attributable to disease outbreaks or adverse environmental conditions. Starvation leads to significant morphological changes in the hepatopancreas (HP), being the main organ for absorption and storage of nutrients. In the literature, limited research has described the effect on the HP of periods of starvation followed by refeeding and none in whiteleg shrimp (Penaeus vannamei) using computer-assisted image analysis (CAIA). This study describes the effect of starvation and starvation followed by refeeding on the HP of whiteleg shrimp using CAIA. Visiopharm ® software was used to quantify the following morphological parameters, measured as ratio to the total tissue area (TLA): total lumen area (TLA:TTA), haemocytic infiltration area in the intertubular spaces (HIA:TTA), B-cell vacuole area (VBA:TTA), lipid droplet area within R cells (LDA:TTA) and F-cell area (FCA:TTA). Significant changes were measured for HIA:TTA and LDA:TTA during starvation (increase in HIA:TTA associated with decrease in LDA:TTA) and starvation followed by refeeding (decrease in HIA:TTA associated with increase in LDA:TTA). In the future, HIA:TTA and LDA:TTA have the potential to be used in a pre-emptive manner to monitor the health of the HP, facilitate early diagnosis of diseases and study the pathophysiology of the organ. © 2017 John Wiley & Sons Ltd.

Effect of intravenous amino acids on interdigestive antroduodenal motility and small bowel transit time.

PubMed

Gielkens, H A; van den Biggelaar, A; Vecht, J; Onkenhout, W; Lamers, C B; Masclee, A A

1999-02-01

Patients on total parenteral nutrition have an increased risk of developing gallstones because of gall bladder hypomotility. High dose amino acids may prevent biliary stasis by stimulating gall bladder emptying. To investigate whether intravenous amino acids also influence antroduodenal motility. Eight healthy volunteers received, on three separate occasions, intravenous saline (control), low dose amino acids (LDA), or high dose amino acids (HDA). Antroduodenal motility was recorded by perfusion manometry and duodenocaecal transit time (DCTT) using the lactulose breath hydrogen test. DCTT was significantly prolonged during LDA and HDA treatment compared with control. The interdigestive motor pattern was maintained and migrating motor complex (MMC) cycle length was significantly reduced during HDA compared with control and LDA due to a significant reduction in phase II duration. Significantly fewer phase IIIs originated in the gastric antrum during LDA and HDA compared with control. Duodenal phase II motility index was significantly reduced during HDA, but not during LDA, compared with control. Separate intravenous infusion of high doses of amino acids in healthy volunteers: (1) modulates interdigestive antroduodenal motility; (2) shortens MMC cycle length due to a reduced duration of phase II with a lower contractile incidence both in the antrum and duodenum (phase I remains unchanged whereas the effect on phase III is diverse: in the antrum phase III is suppressed and in the duodenum the frequency is increased); and (3) prolongs interdigestive DCTT.

Tetrahedrality and hydrogen bonds in water

NASA Astrophysics Data System (ADS)

Székely, Eszter; Varga, Imre K.; Baranyai, András

2016-06-01

We carried out extensive calculations of liquid water at different temperatures and pressures using the BK3 model suggested recently [P. T. Kiss and A. Baranyai, J. Chem. Phys. 138, 204507 (2013)]. In particular, we were interested in undercooled regions to observe the propensity of water to form tetrahedral coordination of closest neighbors around a central molecule. We compared the found tetrahedral order with the number of hydrogen bonds and with the partial pair correlation functions unfolded as distributions of the closest, the second closest, etc. neighbors. We found that contrary to the number of hydrogen bonds, tetrahedrality changes substantially with state variables. Not only the number of tetrahedral arrangements increases with lowering the pressure, the density, and the temperature but the domain size of connecting tetrahedral structures as well. The difference in tetrahedrality is very pronounced between the two sides of the Widom line and even more so between the low density amorphous (LDA) and high density amorphous (HDA) phases. We observed that in liquid water and in HDA, the 5th water molecule, contrary to ice and LDA, is positioned between the first and the second coordination shell. We found no convincing evidence of structural heterogeneity or regions referring to structural transition.

Predicting the aquatic toxicity mode of action using logistic regression and linear discriminant analysis.

PubMed

Ren, Y Y; Zhou, L C; Yang, L; Liu, P Y; Zhao, B W; Liu, H X

2016-09-01

The paper highlights the use of the logistic regression (LR) method in the construction of acceptable statistically significant, robust and predictive models for the classification of chemicals according to their aquatic toxic modes of action. Essentials accounting for a reliable model were all considered carefully. The model predictors were selected by stepwise forward discriminant analysis (LDA) from a combined pool of experimental data and chemical structure-based descriptors calculated by the CODESSA and DRAGON software packages. Model predictive ability was validated both internally and externally. The applicability domain was checked by the leverage approach to verify prediction reliability. The obtained models are simple and easy to interpret. In general, LR performs much better than LDA and seems to be more attractive for the prediction of the more toxic compounds, i.e. compounds that exhibit excess toxicity versus non-polar narcotic compounds and more reactive compounds versus less reactive compounds. In addition, model fit and regression diagnostics was done through the influence plot which reflects the hat-values, studentized residuals, and Cook's distance statistics of each sample. Overdispersion was also checked for the LR model. The relationships between the descriptors and the aquatic toxic behaviour of compounds are also discussed.

A multiple maximum scatter difference discriminant criterion for facial feature extraction.

PubMed

Song, Fengxi; Zhang, David; Mei, Dayong; Guo, Zhongwei

2007-12-01

Maximum scatter difference (MSD) discriminant criterion was a recently presented binary discriminant criterion for pattern classification that utilizes the generalized scatter difference rather than the generalized Rayleigh quotient as a class separability measure, thereby avoiding the singularity problem when addressing small-sample-size problems. MSD classifiers based on this criterion have been quite effective on face-recognition tasks, but as they are binary classifiers, they are not as efficient on large-scale classification tasks. To address the problem, this paper generalizes the classification-oriented binary criterion to its multiple counterpart--multiple MSD (MMSD) discriminant criterion for facial feature extraction. The MMSD feature-extraction method, which is based on this novel discriminant criterion, is a new subspace-based feature-extraction method. Unlike most other subspace-based feature-extraction methods, the MMSD computes its discriminant vectors from both the range of the between-class scatter matrix and the null space of the within-class scatter matrix. The MMSD is theoretically elegant and easy to calculate. Extensive experimental studies conducted on the benchmark database, FERET, show that the MMSD out-performs state-of-the-art facial feature-extraction methods such as null space method, direct linear discriminant analysis (LDA), eigenface, Fisherface, and complete LDA.

Fermi surface measurements in YBa2Cu3O(7-x) and La(1.874)Sr(126)CuO4

NASA Astrophysics Data System (ADS)

Howell, R. H.; Sterne, P. A.; Solal, F.; Fluss, M. J.; Haghighi, H.; Kaiser, J. H.; Rayner, S. L.; West, R. N.; Liu, J. Z.; Shelton, R.

1991-06-01

We report new, ultra high precision measurements of the electron-positron momentum spectra of YBa2Cu3O(7-x) and La(1.874)Sr(126)CuO4. The YBCO experiments were performed on twin free, single crystals and show discontinuities with the symmetry of the Fermi surface of the CuO chain bands. Conduction band and underlying features in LSCO share the same symmetry and can only be separated with the aid of LDA calculations.

Fermi surface measurements in YBa 2Cu 3O 7- x and La 1.874Sr .126CuO 4

NASA Astrophysics Data System (ADS)

Howell, R. H.; Sterne, P. A.; Solal, F.; Fluss, M. J.; Haghight, H.; Kaiser, J. H.; Rayner, S. L.; West, R. N.; Liu, J. Z.; Shelton, R.; Kojima, H.; Kitazawa, K.

1991-12-01

We report new, ultra high precision measurements of the electron-positron momentum spectra of YBa 2Cu 3O 7- x and La 1.874Sr .126CuO 4. The YBCO experiments were performed on twin free, single crystals and show discontinuities with the symmetry of the Fermi surface of the CuO chain bands. Conduction band and underlying features in LSCO share the same symmetry and can only be separated with the aid of LDA calculations.

LDA Assessments. Learning Times. Volume 7, Number 1

ERIC Educational Resources Information Center

LDA Minnesota, 2008

2008-01-01

This issue of "Learning Times" discusses how LDA assessments for children and adults provide self-understanding, renewed hope, and improved achievement. It also includes: (1) Where do Your Candidates Stand on Controlling Toxic Chemicals?; (2) ADHD (Attention Deficit Hyperactivity Disorder) Tips: Back-to-School (Ty Sassaman); (3) Healthy…

LDA-Mediated Synthesis of Triarylmethanes by Arylation of Diarylmethanes with Fluoroarenes at Room Temperature.

PubMed

Ji, Xinfei; Huang, Tao; Wu, Wei; Liang, Fang; Cao, Song

2015-10-16

A practical and convenient approach for the secondary C(sp(3))-H arylation of diarylmethanes with various fluoroarenes is described. The reaction proceeds smoothly in the presence of LDA (lithium diisopropylamide) at room temperature and affords triarylmethanes in moderate to high yields.

Electronic structure of clathrates Bax@AlySi46-y ; thermoelectric devices

NASA Astrophysics Data System (ADS)

Eguchi, Haruki; Nagano, Takatoshi; Takenaka, Hiroyuki; Tsumuraya, Kazuo

2002-03-01

Clathrates have received much attention as a candidate of high performance thermoelectric devices. This is because they have a) low thermal conductivity due to rattle effect of the alkali or heavy alkali-earth metals such as Ba atoms in the cages of clusters of the clathrates, and b) adjustablity of the Fermi levels through replacement of frame Si atoms with acceptor Al atoms and addition of the cage atoms as donors. We present the dispersion curves with LDA and GGA approximations for the exchange correlation of electrons using the planewave based pseudopotential methods and predict the electronic properties of the clathrates.

Apport de la microscopie a effet tunnel a la caracterisation d'interfaces molecule-metal a fort transfert de charge

NASA Astrophysics Data System (ADS)

Bedwani, Stephane

To assess the importance of charge-transfer on the interface properties, we studied the interaction of the tetracyanoethylene (TCNE) molecule with various copper surfaces. TCNE, a highly electrophilic molecule, appears as an ideal candidate to study the influence of high charge-transfer on the electronic and structural properties of molecule-surface interfaces. Indeed, various TCNE-transition metal complexes exhibit magnetism at room temperature, which is in agreement with a very significant change of the residual charge on the TCNE molecule. The adsorption of TCNE molecules on Cu(100) and Cu(111) surfaces was studied by scanning tunneling microscopy (STM) and by density functional theory (DFT) calculations with a local density approximation (LDA). DFT-LDA calculations were performed to determine the geometric and electronic structure of the studied interfaces. Mulliken analysis was used to evaluate the partial net charge on the adsorbed species. The density of states (DOS) diagrams provided informations on the nature of the frontier orbitals involved in the charge-transfer at molecule-metal interfaces. To validate the theoretical observations, a comparative study was conducted between our simulated STM images and experimental STM images provided by our collaborators. The theoretical STM images were obtained with the SPAGS-STM software using the Landauer-Buttiker formalism with a semi-empirical Hamiltonian based on the extended Huckel theory (EHT) and parameterized using DFT calculations. During the development of the SPAGS-STM software, we have created a discretization module allowing rapid generation of STM images. This module is based on an adaptive Delaunay meshing scheme to minimize the amount of tunneling current to be computed. The general idea consists into refining the mesh, and therefore the calculations, near large contrast zones rather than over the entire image. The adapted mesh provides an STM image resolution equivalent to that obtained with a conventional Cartesian grid but with a significantly smaller number of calculated pixels. This module is independent of the solver used to compute the tunneling current and can be transposed to different imaging techniques. Our work on the adsorption of TCNE molecules on Cu(100) surfaces revealed that the molecules assemble into a 1D chain, thereby buckling excessively a few Cu atoms from the surface. The large deformations observed at the molecule-metal interface show that the Cu atoms close to the TCNE nitrile groups assist the molecular assembly and show a distinct behavior compared with other Cu atoms. A strong charge-transfer is observed at the interface leading to an almost complete occupation of the state ascribed to the lowest unoccupied molecular orbital (LUMO) of TCNE in gas phase. In addition, a back-donation of charge from the molecule to the metal via the states associated with the highest occupied molecular orbitals (HOMO) of TCNE in gas phase may be seen. The magnitude of the charge-transfer between a TCNE molecule and Cu atoms is of the same order on the Cu(111) surface but causes much less buckling than that on the Cu(100) surface. However, experimental STM images of single TCNE molecules adsorbed on Cu(111) surfaces reveal a surprising electronic multistability. In addition, scanning tunneling spectroscopy (STS) reveals that one of these states has a magnetic nature and shows a Kondo resonance. STM simulations identified the source of two non-magnetic states. DFT-LDA calculations were able to ascribe the magnetic state to the partial occupation of a state corresponding to the LUMO+2 of TCNE. Moreover, the calculations showed that additional molecular deformations to those of TCNE in adsorbed phase, such the elongation of the C=C central bond and the bend of nitrile groups toward the surface, favor this charge-transfer to the LUMO+2. This suggested the presence of a Kondo state through the vibrational excitation of the stretching mode of the C=C central bond. The main results of this thesis led to the conclusion that strong charge-transfer between adsorbed molecules on a metallic surface may induce significant buckling of the surface. This surface reconstruction mechanism that involves a bidirectional charge-transfer between the species results into a partial net charge over the molecule. This mechanism is involved in the supramolecular self-assembly process that appears similar to a coordination network. Moreover, the adsorbed molecule presents some important geometric distortions that alter its electronic structure. Additional distortions on the adsorbed molecule induced by some molecular vibration modes seem to explain a stable magnetic state that can be switch on or off by an electrical impulse. (Abstract shortened by UMI.)

Glass polymorphism in amorphous germanium probed by first-principles computer simulations

NASA Astrophysics Data System (ADS)

Mancini, G.; Celino, M.; Iesari, F.; Di Cicco, A.

2016-01-01

The low-density (LDA) to high-density (HDA) transformation in amorphous Ge at high pressure is studied by first-principles molecular dynamics simulations in the framework of density functional theory. Previous experiments are accurately reproduced, including the presence of a well-defined LDA-HDA transition above 8 GPa. The LDA-HDA density increase is found to be about 14%. Pair and bond-angle distributions are obtained in the 0-16 GPa pressure range and allowed us a detailed analysis of the transition. The local fourfold coordination is transformed in an average HDA sixfold coordination associated with different local geometries as confirmed by coordination number analysis and shape of the bond-angle distributions.

On the peculiarities of LDA method in two-phase flows with high concentrations of particles

NASA Astrophysics Data System (ADS)

Poplavski, S. V.; Boiko, V. M.; Nesterov, A. U.

2016-10-01

Popular applications of laser Doppler anemometry (LDA) in gas dynamics are reviewed. It is shown that the most popular method cannot be used in supersonic flows and two-phase flows with high concentrations of particles. A new approach to implementation of the known LDA method based on direct spectral analysis, which offers better prospects for such problems, is presented. It is demonstrated that the method is suitable for gas-liquid jets. Owing to the progress in laser engineering, digital recording of spectra, and computer processing of data, the method is implemented at a higher technical level and provides new prospects of diagnostics of high-velocity dense two-phase flows.

On the transport coefficients of hydrogen in the inertial confinement fusion regime

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lambert, Flavien; Recoules, Vanina; Decoster, Alain

2011-05-15

Ab initio molecular dynamics is used to compute the thermal and electrical conductivities of hydrogen from 10 to 160 g cm{sup -3} and temperatures up to 800 eV, i.e., thermodynamical conditions relevant to inertial confinement fusion (ICF). The ionic structure is obtained using molecular dynamics simulations based on an orbital-free treatment for the electrons. The transport properties were computed using ab initio simulations in the DFT/LDA approximation. The thermal and electrical conductivities are evaluated using Kubo-Greenwood formulation. Particular attention is paid to the convergence of electronic transport properties with respect to the number of bands and atoms. These calculations aremore » then used to check various analytical models (Hubbard's, Lee-More's and Ichimaru's) widely used in hydrodynamics simulations of ICF capsule implosions. The Lorenz number, which is the ratio between thermal and electrical conductivities, is also computed and compared to the well-known Wiedemann-Franz law in different regimes ranging from the highly degenerate to the kinetic one. This allows us to deduce electrical conductivity from thermal conductivity for analytical model. We find that the coupling of Hubbard and Spitzer models gives a correct description of the behavior of electrical and thermal conductivities in the whole thermodynamic regime.« less

Oxygen holes and hybridization in the bismuthates

NASA Astrophysics Data System (ADS)

Khazraie, Arash; Foyevtsova, Kateryna; Elfimov, Ilya; Sawatzky, George A.

2018-02-01

Motivated by the recently renewed interest in the superconducting bismuth perovskites, we investigate the electronic structure of the parent compounds A BiO3 (A = Sr, Ba) using ab initio methods and tight-binding (TB) modeling. We use the density functional theory (DFT) in the local density approximation (LDA) to understand the role of various interactions in shaping the A BiO3 band structure near the Fermi level. It is established that interatomic hybridization involving Bi-6 s and O-2 p orbitals plays the most important role. Based on our DFT calculations, we derive a minimal TB model and demonstrate that it can describe the properties of the band structure as a function of lattice distortions, such as the opening of a charge gap with the onset of the breathing distortion and the associated condensation of holes onto a1 g-symmetric molecular orbitals formed by the O-2 pσ orbitals on collapsed octahedra. We also derive a single band model involving the hopping of an extended molecular orbital involving both Bi-6 s and a linear combination of six O-2 p orbitals which provides a very good description of the dispersion and band gaps of the low energy scale bands straddling the chemical potential.

Ab initio study of Pd carbonyls and CO/Pd(110)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramprasad, R.; Glassford, K.M.; Adams, J.B.

1994-12-31

Carbon monoxide chemisorption on transition metal surfaces has been one of the most extensively studied in surface science in past years due to its importance in a variety of catalytic processes, especially, automotive catalytic converters using Pt or Pd. The authors have performed ab initio studies to understand the electronic and geometric aspects of the Pd-CO bond in small carbonyl clusters and the CO covered (2 x 1)p2mg superstructure of the Pd(110) surface. They have used the standard quantum chemistry package Gaussian to study the former system and a LDA (local density approximation) formalism using ab initio pseudopotentials and amore » plane wave basis to study the latter. The latter results are preliminary; the authors intended to study thicker slabs in the future. The organization of the paper is as follows. The authors describe the methods used in their calculation in Sec. 2. In Sec. 3, they present results and discussion; here, they first look at the smallest possible clusters, viz, Pd{sub 2} and PdCO, take a brief look at the orbital chemistry involved and then move on to the study of the CO covered Pd(110) surface and examine the geometry of the near equilibrium structure.« less

The Sapphire (0001) Surface, Clean and with d-metal Overlayers: Density Functional - LDA Results

NASA Astrophysics Data System (ADS)

Verdozzi, C.; Jennison, D. R.; Schultz, P. A.; Sears, M. P.

1998-03-01

Previous theoretical work for the a-Al2O3(0001) surface mostly used very thin slabs, and limited theoretical information is available on the binding of metal overlayers. Also, no systematic information is available about the dependence of the metal-ceramic interaction on metal coverage. We present here results using the local density approximation for the structural and electronic properties of the a-Al2O3(0001) surface, with and without d-metal overlayers Pt, Ag, Cu, and with sufficiently thick slabs to find the bottom of the unusually large and deep surface relaxation in this material. Our thick slab site-optimized calculations are performed for 1, 2/3 and 1/3 monolayer (ML) coverage. The adhesion energy and the nature of the interfacial bond vary greatly with metal coverage and can be understood in terms of the relative roles of the surface Madelung potential and the strength of the lateral metal-metal bond. Our study should in principle succeed in bracketing the phenomenology of adhesion and wetting at least for the right-most part of the d-metal periodic table. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy under Contract DE-AC04-94AL85000. Corresponding author: claudio@sandia.gov.

First-principles study of defects and phase transition in UO(2).

PubMed

Yu, Jianguo; Devanathan, Ram; Weber, William J

2009-10-28

Defect properties and phase transition in UO(2) have been studied from first principles by the all-electron projector-augmented-wave (PAW) method. The generalized gradient approximation with empirical self-interaction correction, (GGA)+U, formalism has been used to account for the strong on-site Coulomb repulsion among the localized U 5f electrons. The Hubbard parameter U(eff), magnetic ordering, chemical potential and heat of formation have been systematically examined. By choosing an appropriate U(eff) = 3.0 eV it is possible to consistently describe structural properties of UO(2) and model the phase transition processes. The phase transition pressure for UO(2) is about 20 GPa, which is less than the experimental value of 42 GPa but better than the LDA+U value of 7.8 GPa. Meanwhile our results for the formation energies of intrinsic defects partly confirm earlier calculations for the intrinsic charge neutral defects but reveal large variations depending on the determination of the chemical potential and whether the environment is O-rich or U-rich. Moreover, the results for extrinsic defects of Xe, which are representative of mobile insoluble fission product in UO(2), are consistent with experimental data in which Xe prefers to be trapped by Schottky defects.

Using UV-Vis spectroscopy for simultaneous geographical and varietal classification of tea infusions simulating a home-made tea cup.

PubMed

Diniz, Paulo Henrique Gonçalves Dias; Barbosa, Mayara Ferreira; de Melo Milanez, Karla Danielle Tavares; Pistonesi, Marcelo Fabián; de Araújo, Mário César Ugulino

2016-02-01

In this work we proposed a method to verify the differentiating characteristics of simple tea infusions prepared in boiling water alone (simulating a home-made tea cup), which represents the final product as ingested by the consumers. For this purpose we used UV-Vis spectroscopy and variable selection through the Successive Projections Algorithm associated with Linear Discriminant Analysis (SPA-LDA) for simultaneous classification of the teas according to their variety and geographic origin. For comparison, KNN, CART, SIMCA, PLS-DA and PCA-LDA were also used. SPA-LDA and PCA-LDA provided significantly better results for tea classification of the five studied classes (Argentinean green tea; Brazilian green tea; Argentinean black tea; Brazilian black tea; and Sri Lankan black tea). The proposed methodology provides a simpler, faster and more affordable classification of simple tea infusions, and can be used as an alternative approach to traditional tea quality evaluation as made by skilful tasters, which is evidently partial and cannot assess geographic origins. Copyright © 2015 Elsevier Ltd. All rights reserved.

Independent components analysis to increase efficiency of discriminant analysis methods (FDA and LDA): Application to NMR fingerprinting of wine.

PubMed

Monakhova, Yulia B; Godelmann, Rolf; Kuballa, Thomas; Mushtakova, Svetlana P; Rutledge, Douglas N

2015-08-15

Discriminant analysis (DA) methods, such as linear discriminant analysis (LDA) or factorial discriminant analysis (FDA), are well-known chemometric approaches for solving classification problems in chemistry. In most applications, principle components analysis (PCA) is used as the first step to generate orthogonal eigenvectors and the corresponding sample scores are utilized to generate discriminant features for the discrimination. Independent components analysis (ICA) based on the minimization of mutual information can be used as an alternative to PCA as a preprocessing tool for LDA and FDA classification. To illustrate the performance of this ICA/DA methodology, four representative nuclear magnetic resonance (NMR) data sets of wine samples were used. The classification was performed regarding grape variety, year of vintage and geographical origin. The average increase for ICA/DA in comparison with PCA/DA in the percentage of correct classification varied between 6±1% and 8±2%. The maximum increase in classification efficiency of 11±2% was observed for discrimination of the year of vintage (ICA/FDA) and geographical origin (ICA/LDA). The procedure to determine the number of extracted features (PCs, ICs) for the optimum DA models was discussed. The use of independent components (ICs) instead of principle components (PCs) resulted in improved classification performance of DA methods. The ICA/LDA method is preferable to ICA/FDA for recognition tasks based on NMR spectroscopic measurements. Copyright © 2015 Elsevier B.V. All rights reserved.

Constraints on the formation and properties of a Martian lobate debris apron: Insights from high-resolution topography, SHARAD radar data, and a numerical ice flow model

NASA Astrophysics Data System (ADS)

Parsons, Reid; Holt, John

2016-03-01

Lobate debris aprons (LDAs) are midlatitude deposits of debris-covered ice formed during one or more periods of glaciation during the Amazonian period. However, little is known about the climate conditions that led to LDA formation. We explore a hypothesis in which a single, extended period of precipitation of ice on the steep slopes of Euripus Mons (45°S, 105°E—east of the Hellas Basin) produced a flowing ice deposit which was protected from subsequent ablation to produce the LDA found at this location. We test this hypothesis with a numerical ice flow model using an ice rheology based on low-temperature ice deformation experiments. The model simulates ice accumulation and flow for the northern and southern lobes of the Euripus Mons LDA using basal topography constrained by data from the Shallow Radar (SHARAD) and a range of ice viscosities (determined by ice temperature and ice grain size). Simulations for the northern lobe of the Euripus LDA produce good fits to the surface topography. Assuming an LDA age of ˜60 Myr and an expected temperature range of 200 to 204 K (for various obliquities) gives an ice grain size of ≈2 mm. Simulations of the southern section produce poor fits to surface topography and result in much faster flow timescales unless multiple ice deposition events or higher ice viscosities are considered.

Maintenance of Remission with Etanercept-DMARD Combination Therapy Compared with DMARDs Alone in African and Middle Eastern Patients with Active Rheumatoid Arthritis.

PubMed

Bassiouni, Hassan; Spargo, Catherine Elizabeth; Vlahos, Bonnie; Jones, Heather E; Pedersen, Ron; Shirazy, Khalid

2018-06-01

To compare etanercept (ETN) and placebo (PBO) for maintaining low disease activity (LDA) achieved with ETN in patients with rheumatoid arthritis (RA) from Africa and the Middle East. In this subset analysis of the Treat-to-Target trial (ClinicalTrials.gov identifier NCT01981473), 53 adult patients with moderate-to-severe RA nonresponsive to methotrexate were treated with 50 mg ETN/week for 24 weeks (Period 1). Patients achieving LDA were randomized to continue ETN treatment or switched to PBO for an additional 28 weeks (Period 2). The proportion of patients maintaining LDA or remission in each arm at the end of Period 2 was determined. Additional efficacy and patient-reported outcomes (PROs) were also evaluated. During Period 1, 51 patients achieved LDA according to the disease activity score-28 joints-erythrocyte sedimentation rate (DAS28-ESR LDA) and 30 achieved remission. At week 52, nine of 22 and eight of 29 in the ETN and PBO groups, respectively, remained in DAS28-ESR LDA without experiencing a flare. Additionally, six of 14 and five of 16 in the ETN and PBO groups, respectively, remained in remission. Among patients experiencing a flare during Period 2, 13 of 22 and 21 of 29 received ETN or PBO, respectively. The median time to flare was 193 and 87 days in the ETN and PBO groups, respectively. At week 52, consistently more patients in the ETN group than in the PBO group achieved predetermined efficacy and PRO endpoints. These data suggest continuing ETN maintenance therapy is beneficial to patients after they have achieved their treatment target. However, this subset analysis is limited by the small patient population and must be interpreted with caution. Pfizer. ClinicalTrials.gov identifier, NCT0198147.

A Beneficial Effect of Low-Dose Aspirin in a Murine Model of Active Tuberculosis

PubMed Central

Kroesen, Vera Marie; Rodríguez-Martínez, Paula; García, Eric; Rosales, Yaiza; Díaz, Jorge; Martín-Céspedes, Montse; Tapia, Gustavo; Sarrias, Maria Rosa; Cardona, Pere-Joan; Vilaplana, Cristina

2018-01-01

An excessive, non-productive host-immune response is detrimental in active, chronic tuberculosis (TB) disease as it typically leads to tissue damage. Given their anti-inflammatory effect, non-steroidal anti-inflammatory drugs can potentially attenuate excessive inflammation in active TB disease. As such, we investigated the prophylactic and therapeutic effect of low-dose aspirin (LDA) (3 mg/kg/day), either alone or in combination with common anti-TB treatment or BCG vaccination, on disease outcome in an experimental murine model of active TB. Survival rate, bacillary load (BL) in lungs, and lung pathology were measured. The possible mechanism of action of LDA on the host’s immune response was also evaluated by measuring levels of CD5L/AIM, selected cytokines/chemokines and other inflammatory markers in serum and lung tissue. LDA increased survival, had anti-inflammatory effects, reduced lung pathology, and decreased bacillary load in late-stage TB disease. Moreover, in combination with common anti-TB treatment, LDA enhanced survival and reduced lung pathology. Results from the immunological studies suggest the anti-inflammatory action of LDA at both a local and a systemic level. Our results showed a systemic decrease in neutrophilic recruitment, decreased levels of acute-phase reaction cytokines (IL-6, IL-1β, and TNF-α) at late stage and a delay in the decrease in T cell response (in terms of IFN-γ, IL-2, and IL-10 serum levels) that occurs during the course of Mycobacterium tuberculosis infection. An anti-inflammatory milieu was detected in the lung, with less neutrophil recruitment and lower levels of tissue factor. In conclusion, LDA may be beneficial as an adjunct to standard anti-TB treatment in the later stage of active TB by reducing excess, non-productive inflammation, while enhancing Th1-cell responses for elimination of the bacilli. PMID:29740435

Investigation of laser Doppler anemometry in developing a velocity-based measurement technique

NASA Astrophysics Data System (ADS)

Jung, Ki Won

2009-12-01

Acoustic properties, such as the characteristic impedance and the complex propagation constant, of porous materials have been traditionally characterized based on pressure-based measurement techniques using microphones. Although the microphone techniques have evolved since their introduction, the most general form of the microphone technique employs two microphones in characterizing the acoustic field for one continuous medium. The shortcomings of determining the acoustic field based on only two microphones can be overcome by using numerous microphones. However, the use of a number of microphones requires a careful and intricate calibration procedure. This dissertation uses laser Doppler anemometry (LDA) to establish a new measurement technique which can resolve issues that microphone techniques have: First, it is based on a single sensor, thus the calibration is unnecessary when only overall ratio of the acoustic field is required for the characterization of a system. This includes the measurements of the characteristic impedance and the complex propagation constant of a system. Second, it can handle multiple positional measurements without calibrating the signal at each position. Third, it can measure three dimensional components of velocity even in a system with a complex geometry. Fourth, it has a flexible adaptability which is not restricted to a certain type of apparatus only if the apparatus is transparent. LDA is known to possess several disadvantages, such as the requirement of a transparent apparatus, high cost, and necessity of seeding particles. The technique based on LDA combined with a curvefitting algorithm is validated through measurements on three systems. First, the complex propagation constant of the air is measured in a rigidly terminated cylindrical pipe which has very low dissipation. Second, the radiation impedance of an open-ended pipe is measured. These two parameters can be characterized by the ratio of acoustic field measured at multiple locations. Third, the power dissipated in a variable RLC load is measured. The three experiments validate the LDA technique proposed. The utility of the LDA method is then extended to the measurement of the complex propagation constant of the air inside a 100 ppi reticulated vitreous carbon (RVC) sample. Compared to measurements in the available studies, the measurement with the 100 ppi RVC sample supports the LDA technique in that it can achieve a low uncertainty in the determined quantity. This dissertation concludes with using the LDA technique for modal decomposition of the plane wave mode and the (1,1) mode that are driven simultaneously. This modal decomposition suggests that the LDA technique surpasses microphone-based techniques, because they are unable to determine the acoustic field based on an acoustic model with unconfined propagation constants for each modal component.

Elastic Properties of Orthoenstatite at Simultaneous High Pressure-Temperature Conditions and the Implication for the Origin of Low VP/VS Zones in the Mantle Wedge

NASA Astrophysics Data System (ADS)

Qian, W.; Wang, W.; Zou, F.; Wu, Z.

2017-12-01

The compositions of the Earth's interiors are critical in understanding the origin and evolution of the Earth and its geodynamics. Orthopyroxene is an important component for the upper mantle both in pyrolite model and in piclogite model. Furthermore, many evidences suggest the local enrichment of opx in the upper mantle. Therefore, its thermodynamic and elastic properties are fundamental for understanding of chemical compositions and dynamics of the upper mantle. We obtain the elastic properties of orthoenstatite (MgSiO3), Mg end-member orthopyroxene with space group Pbca, up to 20 GPa and 2000 K using first principles calculations with local density approximation (LDA). The calculated results are in good agreement with previous available experimental measurements and theoretical results. Both bulk and shear modulus show noticeable nonlinear pressure dependence, and the softening of shear wave velocities is prominent at high pressure. Meanwhile, orthoenstatite exhibits a negative temperature derivate of VP/VS ratios. This is different from other upper mantle minerals, such as olivine, ringwoodite and garnet, whose VP/VS increase with the increasing of the temperature. Compared to other major minerals in the upper mantle, orthoenstatite shows the lowest compressional velocities, shear velocities, and VP/VS (<1.7) ratio up to the depth of 200 km. Recently, many seismic studies have observed unusual low VP/VS (below 1.72) zones in subduction mantle wedge and orthopyroxene has been proposed to be a possible interpretation of this unusual observed. However, this explanation is still under debate because no experimental or calculated elastic data at the conditions of the upper mantle are available before. Our calculations show that VS and VP/VS ratio of orthoenstatite under the mantle wedge conditions (2-3 GPa and 1073-1723 K) are consistent of the unusual seismic observations of VP/VS in subduction mantle wedge. Therefore, the enrichment of orthopyroxene may potentially account for the observed low VP/VS in the mantle wedge.

Importance of finite-temperature exchange correlation for warm dense matter calculations.

PubMed

Karasiev, Valentin V; Calderín, Lázaro; Trickey, S B

2016-06-01

The effects of an explicit temperature dependence in the exchange correlation (XC) free-energy functional upon calculated properties of matter in the warm dense regime are investigated. The comparison is between the Karasiev-Sjostrom-Dufty-Trickey (KSDT) finite-temperature local-density approximation (TLDA) XC functional [Karasiev et al., Phys. Rev. Lett. 112, 076403 (2014)PRLTAO0031-900710.1103/PhysRevLett.112.076403] parametrized from restricted path-integral Monte Carlo data on the homogeneous electron gas (HEG) and the conventional Monte Carlo parametrization ground-state LDA XC [Perdew-Zunger (PZ)] functional evaluated with T-dependent densities. Both Kohn-Sham (KS) and orbital-free density-functional theories are used, depending upon computational resource demands. Compared to the PZ functional, the KSDT functional generally lowers the dc electrical conductivity of low-density Al, yielding improved agreement with experiment. The greatest lowering is about 15% for T=15 kK. Correspondingly, the KS band structure of low-density fcc Al from the KSDT functional exhibits a clear increase in interband separation above the Fermi level compared to the PZ bands. In some density-temperature regimes, the deuterium equations of state obtained from the two XC functionals exhibit pressure differences as large as 4% and a 6% range of differences. However, the hydrogen principal Hugoniot is insensitive to the explicit XC T dependence because of cancellation between the energy and pressure-volume work difference terms in the Rankine-Hugoniot equation. Finally, the temperature at which the HEG becomes unstable is T≥7200 K for the T-dependent XC, a result that the ground-state XC underestimates by about 1000 K.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, Brian B.; Kirkegaard, Marie C.; Miskowiec, Andrew J.

Uranyl fluoride (UO 2F 2) is a hygroscopic powder with two main structural phases: an anhydrous crystal and a partially hydrated crystal of the same R¯3m symmetry. The formally closed-shell electron structure of anhydrous UO 2F 2 is amenable to density functional theory calculations. We use density functional perturbation theory (DFPT) to calculate the vibrational frequencies of the anhydrous crystal structure and employ complementary inelastic neutron scattering and temperature-dependent Raman scattering to validate those frequencies. As a model closed-shell actinide, we investigated the effect of LDA, GGA, and non-local vdW functionals as well as the spherically-averaged Hubbard +U correction onmore » vibrational frequencies, electronic structure, and geometry of anhydrous UO 2F 2. A particular choice of U eff = 5.5 eV yields the correct U Oyl bond distance and vibrational frequencies for the characteristic Eg and A1g modes that are within the resolution of experiment. Inelastic neutron scattering and Raman scattering suggest a degree of water coupling to the lattice vibrations in the more experimentally accessible partially hydrated UO 2F 2 system, with the symmetric O-U-O stretching vibration shifted approximately 47 cm -1 lower in energy compared to the anhydrous structure. Evidence of water interaction with the uranyl ion is present from a two-peak decomposition of the uranyl stretching vibration in the Raman spectra and anion hydrogen stretching vibrations in the inelastic neutron scattering spectra. A first-order dehydration phase transition temperature is definitively identified to be 125 °C using temperature-dependent Raman scattering.« less

Vibrational Properties of Anhydrous and Partially Hydrated Uranyl Fluoride

DOE PAGES

Anderson, Brian B.; Kirkegaard, Marie C.; Miskowiec, Andrew J.; ...

2017-01-01

Uranyl fluoride (UO 2F 2) is a hygroscopic powder with two main structural phases: an anhydrous crystal and a partially hydrated crystal of the same R¯3m symmetry. The formally closed-shell electron structure of anhydrous UO 2F 2 is amenable to density functional theory calculations. We use density functional perturbation theory (DFPT) to calculate the vibrational frequencies of the anhydrous crystal structure and employ complementary inelastic neutron scattering and temperature-dependent Raman scattering to validate those frequencies. As a model closed-shell actinide, we investigated the effect of LDA, GGA, and non-local vdW functionals as well as the spherically-averaged Hubbard +U correction onmore » vibrational frequencies, electronic structure, and geometry of anhydrous UO 2F 2. A particular choice of U eff = 5.5 eV yields the correct U Oyl bond distance and vibrational frequencies for the characteristic Eg and A1g modes that are within the resolution of experiment. Inelastic neutron scattering and Raman scattering suggest a degree of water coupling to the lattice vibrations in the more experimentally accessible partially hydrated UO 2F 2 system, with the symmetric O-U-O stretching vibration shifted approximately 47 cm -1 lower in energy compared to the anhydrous structure. Evidence of water interaction with the uranyl ion is present from a two-peak decomposition of the uranyl stretching vibration in the Raman spectra and anion hydrogen stretching vibrations in the inelastic neutron scattering spectra. A first-order dehydration phase transition temperature is definitively identified to be 125 °C using temperature-dependent Raman scattering.« less

Interaction between benzenedithiolate and gold: Classical force field for chemical bonding

NASA Astrophysics Data System (ADS)

Leng, Yongsheng; Krstić, Predrag S.; Wells, Jack C.; Cummings, Peter T.; Dean, David J.

2005-06-01

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as ˜100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Assessing College-Level Learning Difficulties and "At Riskness" for Learning Disabilities and ADHD: Development and Validation of the Learning Difficulties Assessment

ERIC Educational Resources Information Center

Kane, Steven T.; Walker, John H.; Schmidt, George R.

2011-01-01

This article describes the development and validation of the "Learning Difficulties Assessment" (LDA), a normed and web-based survey that assesses perceived difficulties with reading, writing, spelling, mathematics, listening, concentration, memory, organizational skills, sense of control, and anxiety in college students. The LDA is designed to…

Decomposing biodiversity data using the Latent Dirichlet Allocation model, a probabilistic multivariate statistical method

Treesearch

Denis Valle; Benjamin Baiser; Christopher W. Woodall; Robin Chazdon; Jerome Chave

2014-01-01

We propose a novel multivariate method to analyse biodiversity data based on the Latent Dirichlet Allocation (LDA) model. LDA, a probabilistic model, reduces assemblages to sets of distinct component communities. It produces easily interpretable results, can represent abrupt and gradual changes in composition, accommodates missing data and allows for coherent estimates...

Communication: Disorder-suppressed vibrational relaxation in vapor-deposited high-density amorphous ice

NASA Astrophysics Data System (ADS)

Shalit, Andrey; Perakis, Fivos; Hamm, Peter

2014-04-01

We apply two-dimensional infrared spectroscopy to differentiate between the two polyamorphous forms of glassy water, low-density (LDA) and high-density (HDA) amorphous ices, that were obtained by slow vapor deposition at 80 and 11 K, respectively. Both the vibrational lifetime and the bandwidth of the 1-2 transition of the isolated OD stretch vibration of HDO in H2O exhibit characteristic differences when comparing hexagonal (Ih), LDA, and HDA ices, which we attribute to the different local structures - in particular the presence of interstitial waters in HDA ice - that cause different delocalization lengths of intermolecular phonon degrees of freedom. Moreover, temperature dependent measurements show that the vibrational lifetime closely follows the structural transition between HDA and LDA phases.

Short, intermediate and long range order in amorphous ices

NASA Astrophysics Data System (ADS)

Martelli, Fausto; Torquato, Salvatore; Giovanbattista, Nicolas; Car, Roberto

Water exhibits polyamorphism, i.e., it exists in more than one amorphous state. The most common forms of glassy water are the low-density amorphous (LDA) and the high-density amorphous (HDA) ices. LDA, the most abundant form of ice in the Universe, transforms into HDA upon isothermal compression. We model the transformation of LDA into HDA under isothermal compression with classical molecular dynamics simulations. We analyze the molecular structures with a recently introduced scalar order metric to measure short and intermediate range order. In addition, we rank the structures by their degree of hyperuniformity, i.e.,the extent to which long range density fluctuations are suppressed. F.M. and R.C. acknowledge support from the Department of Energy (DOE) under Grant No. DE-SC0008626.

Point defects in ZnO: an approach from first principles

PubMed Central

Oba, Fumiyasu; Choi, Minseok; Togo, Atsushi; Tanaka, Isao

2011-01-01

Recent first-principles studies of point defects in ZnO are reviewed with a focus on native defects. Key properties of defects, such as formation energies, donor and acceptor levels, optical transition energies, migration energies and atomic and electronic structure, have been evaluated using various approaches including the local density approximation (LDA) and generalized gradient approximation (GGA) to DFT, LDA+U/GGA+U, hybrid Hartree–Fock density functionals, sX and GW approximation. Results significantly depend on the approximation to exchange correlation, the simulation models for defects and the post-processes to correct shortcomings of the approximation and models. The choice of a proper approach is, therefore, crucial for reliable theoretical predictions. First-principles studies have provided an insight into the energetics and atomic and electronic structures of native point defects and impurities and defect-induced properties of ZnO. Native defects that are relevant to the n-type conductivity and the non-stoichiometry toward the O-deficient side in reduced ZnO have been debated. It is suggested that the O vacancy is responsible for the non-stoichiometry because of its low formation energy under O-poor chemical potential conditions. However, the O vacancy is a very deep donor and cannot be a major source of carrier electrons. The Zn interstitial and anti-site are shallow donors, but these defects are unlikely to form at a high concentration in n-type ZnO under thermal equilibrium. Therefore, the n-type conductivity is attributed to other sources such as residual impurities including H impurities with several atomic configurations, a metastable shallow donor state of the O vacancy, and defect complexes involving the Zn interstitial. Among the native acceptor-type defects, the Zn vacancy is dominant. It is a deep acceptor and cannot produce a high concentration of holes. The O interstitial and anti-site are high in formation energy and/or are electrically inactive and, hence, are unlikely to play essential roles in electrical properties. Overall defect energetics suggests a preference for the native donor-type defects over acceptor-type defects in ZnO. The O vacancy, Zn interstitial and Zn anti-site have very low formation energies when the Fermi level is low. Therefore, these defects are expected to be sources of a strong hole compensation in p-type ZnO. For the n-type doping, the compensation of carrier electrons by the native acceptor-type defects can be mostly suppressed when O-poor chemical potential conditions, i.e. low O partial pressure conditions, are chosen during crystal growth and/or doping. PMID:27877390

Ab-initio study of (Ga,Cr)N and (Ga,Mn)N DMSs: under hydrostatic pressure

NASA Astrophysics Data System (ADS)

Rani, Anita; Kumar, Ranjan

2018-03-01

The influence of hydrostatic pressure between 0-100 GPa on structural, electronic and magnetic properties of CrxGa1-xN and MnxGa1-xN (x = 0.25) diluted magnetic semiconductors has been studied. The calculations have been performed using DFT as implemented in code SIESTA. LDA + U as exchange-correlation (XC) potential have been used to study the parameters. Under external pressure, shifting in both valence band and conduction band energy levels from their actual positions has been observed, which lead to modification of electronic properties. Also, N0 α, s-d exchange constant and p-d exchange constants, N0 β have been calculated at different pressures. Both the compounds show half metallic nature at studied pressure range.

73Ge-NMR study on magnetic fluctuations of ferromagnetic superconductor UGe2

NASA Astrophysics Data System (ADS)

Noma, Y.; Kotegawa, H.; Kubo, T.; Tou, H.; Harima, H.; Haga, Y.; Yamamoto, E.; Ōnuki, Y.; Itoh, K. M.; Haller, E. E.; Nakamura, A.; Homma, Y.; Honda, F.; Aoki, D.

2018-05-01

We report 73Ge-NMR measurement on the ferromagnetic superconductor UGe2 at ambient pressure. The observed NMR spectrum supports that the electric field gradient at three inequivalent Ge sites is correctly deduced by a LDA calculation. The temperature dependences of the nuclear spin lattice relaxation rate 1 /T1 for H0 ⊥ a (easy axis) and H0 ∥ a were obtained for the oriented sample. The contrasting behavior in 1 /T1 for H0 ⊥ a and H0 ∥ a reveals that the magnetic fluctuation of UGe2 is highly anisotropic.

Titin strain contributes to the Frank–Starling law of the heart by structural rearrangements of both thin- and thick-filament proteins

PubMed Central

Ait-Mou, Younss; Hsu, Karen; Farman, Gerrie P.; Kumar, Mohit; Greaser, Marion L.; Irving, Thomas C.; de Tombe, Pieter P.

2016-01-01

The Frank–Starling mechanism of the heart is due, in part, to modulation of myofilament Ca2+ sensitivity by sarcomere length (SL) [length-dependent activation (LDA)]. The molecular mechanism(s) that underlie LDA are unknown. Recent evidence has implicated the giant protein titin in this cellular process, possibly by positioning the myosin head closer to actin. To clarify the role of titin strain in LDA, we isolated myocardium from either WT or homozygous mutant (HM) rats that express a giant splice isoform of titin, and subjected the muscles to stretch from 2.0 to 2.4 μm of SL. Upon stretch, HM compared with WT muscles displayed reduced passive force, twitch force, and myofilament LDA. Time-resolved small-angle X-ray diffraction measurements of WT twitching muscles during diastole revealed stretch-induced increases in the intensity of myosin (M2 and M6) and troponin (Tn3) reflections, as well as a reduction in cross-bridge radial spacing. Independent fluorescent probe analyses in relaxed permeabilized myocytes corroborated these findings. X-ray electron density reconstruction revealed increased mass/ordering in both thick and thin filaments. The SL-dependent changes in structure observed in WT myocardium were absent in HM myocardium. Overall, our results reveal a correlation between titin strain and the Frank–Starling mechanism. The molecular basis underlying this phenomenon appears not to involve interfilament spacing or movement of myosin toward actin but, rather, sarcomere stretch-induced simultaneous structural rearrangements within both thin and thick filaments that correlate with titin strain and myofilament LDA. PMID:26858417

Incorporating Topic Assignment Constraint and Topic Correlation Limitation into Clinical Goal Discovering for Clinical Pathway Mining.

PubMed

Xu, Xiao; Jin, Tao; Wei, Zhijie; Wang, Jianmin

2017-01-01

Clinical pathways are widely used around the world for providing quality medical treatment and controlling healthcare cost. However, the expert-designed clinical pathways can hardly deal with the variances among hospitals and patients. It calls for more dynamic and adaptive process, which is derived from various clinical data. Topic-based clinical pathway mining is an effective approach to discover a concise process model. Through this approach, the latent topics found by latent Dirichlet allocation (LDA) represent the clinical goals. And process mining methods are used to extract the temporal relations between these topics. However, the topic quality is usually not desirable due to the low performance of the LDA in clinical data. In this paper, we incorporate topic assignment constraint and topic correlation limitation into the LDA to enhance the ability of discovering high-quality topics. Two real-world datasets are used to evaluate the proposed method. The results show that the topics discovered by our method are with higher coherence, informativeness, and coverage than the original LDA. These quality topics are suitable to represent the clinical goals. Also, we illustrate that our method is effective in generating a comprehensive topic-based clinical pathway model.

Incorporating Topic Assignment Constraint and Topic Correlation Limitation into Clinical Goal Discovering for Clinical Pathway Mining

PubMed Central

Xu, Xiao; Wei, Zhijie

2017-01-01

Clinical pathways are widely used around the world for providing quality medical treatment and controlling healthcare cost. However, the expert-designed clinical pathways can hardly deal with the variances among hospitals and patients. It calls for more dynamic and adaptive process, which is derived from various clinical data. Topic-based clinical pathway mining is an effective approach to discover a concise process model. Through this approach, the latent topics found by latent Dirichlet allocation (LDA) represent the clinical goals. And process mining methods are used to extract the temporal relations between these topics. However, the topic quality is usually not desirable due to the low performance of the LDA in clinical data. In this paper, we incorporate topic assignment constraint and topic correlation limitation into the LDA to enhance the ability of discovering high-quality topics. Two real-world datasets are used to evaluate the proposed method. The results show that the topics discovered by our method are with higher coherence, informativeness, and coverage than the original LDA. These quality topics are suitable to represent the clinical goals. Also, we illustrate that our method is effective in generating a comprehensive topic-based clinical pathway model. PMID:29065617

Characterization and noninvasive diagnosis of bladder cancer with serum surface enhanced Raman spectroscopy and genetic algorithms

NASA Astrophysics Data System (ADS)

Li, Shaoxin; Li, Linfang; Zeng, Qiuyao; Zhang, Yanjiao; Guo, Zhouyi; Liu, Zhiming; Jin, Mei; Su, Chengkang; Lin, Lin; Xu, Junfa; Liu, Songhao

2015-05-01

This study aims to characterize and classify serum surface-enhanced Raman spectroscopy (SERS) spectra between bladder cancer patients and normal volunteers by genetic algorithms (GAs) combined with linear discriminate analysis (LDA). Two group serum SERS spectra excited with nanoparticles are collected from healthy volunteers (n = 36) and bladder cancer patients (n = 55). Six diagnostic Raman bands in the regions of 481-486, 682-687, 1018-1034, 1313-1323, 1450-1459 and 1582-1587 cm-1 related to proteins, nucleic acids and lipids are picked out with the GAs and LDA. By the diagnostic models built with the identified six Raman bands, the improved diagnostic sensitivity of 90.9% and specificity of 100% were acquired for classifying bladder cancer patients from normal serum SERS spectra. The results are superior to the sensitivity of 74.6% and specificity of 97.2% obtained with principal component analysis by the same serum SERS spectra dataset. Receiver operating characteristic (ROC) curves further confirmed the efficiency of diagnostic algorithm based on GA-LDA technique. This exploratory work demonstrates that the serum SERS associated with GA-LDA technique has enormous potential to characterize and non-invasively detect bladder cancer through peripheral blood.

Extending information retrieval methods to personalized genomic-based studies of disease.

PubMed

Ye, Shuyun; Dawson, John A; Kendziorski, Christina

2014-01-01

Genomic-based studies of disease now involve diverse types of data collected on large groups of patients. A major challenge facing statistical scientists is how best to combine the data, extract important features, and comprehensively characterize the ways in which they affect an individual's disease course and likelihood of response to treatment. We have developed a survival-supervised latent Dirichlet allocation (survLDA) modeling framework to address these challenges. Latent Dirichlet allocation (LDA) models have proven extremely effective at identifying themes common across large collections of text, but applications to genomics have been limited. Our framework extends LDA to the genome by considering each patient as a "document" with "text" detailing his/her clinical events and genomic state. We then further extend the framework to allow for supervision by a time-to-event response. The model enables the efficient identification of collections of clinical and genomic features that co-occur within patient subgroups, and then characterizes each patient by those features. An application of survLDA to The Cancer Genome Atlas ovarian project identifies informative patient subgroups showing differential response to treatment, and validation in an independent cohort demonstrates the potential for patient-specific inference.

Two-dimensional statistical linear discriminant analysis for real-time robust vehicle-type recognition

NASA Astrophysics Data System (ADS)

Zafar, I.; Edirisinghe, E. A.; Acar, S.; Bez, H. E.

2007-02-01

Automatic vehicle Make and Model Recognition (MMR) systems provide useful performance enhancements to vehicle recognitions systems that are solely based on Automatic License Plate Recognition (ALPR) systems. Several car MMR systems have been proposed in literature. However these approaches are based on feature detection algorithms that can perform sub-optimally under adverse lighting and/or occlusion conditions. In this paper we propose a real time, appearance based, car MMR approach using Two Dimensional Linear Discriminant Analysis that is capable of addressing this limitation. We provide experimental results to analyse the proposed algorithm's robustness under varying illumination and occlusions conditions. We have shown that the best performance with the proposed 2D-LDA based car MMR approach is obtained when the eigenvectors of lower significance are ignored. For the given database of 200 car images of 25 different make-model classifications, a best accuracy of 91% was obtained with the 2D-LDA approach. We use a direct Principle Component Analysis (PCA) based approach as a benchmark to compare and contrast the performance of the proposed 2D-LDA approach to car MMR. We conclude that in general the 2D-LDA based algorithm supersedes the performance of the PCA based approach.

A hybrid sensing approach for pure and adulterated honey classification.

PubMed

Subari, Norazian; Mohamad Saleh, Junita; Md Shakaff, Ali Yeon; Zakaria, Ammar

2012-10-17

This paper presents a comparison between data from single modality and fusion methods to classify Tualang honey as pure or adulterated using Linear Discriminant Analysis (LDA) and Principal Component Analysis (PCA) statistical classification approaches. Ten different brands of certified pure Tualang honey were obtained throughout peninsular Malaysia and Sumatera, Indonesia. Various concentrations of two types of sugar solution (beet and cane sugar) were used in this investigation to create honey samples of 20%, 40%, 60% and 80% adulteration concentrations. Honey data extracted from an electronic nose (e-nose) and Fourier Transform Infrared Spectroscopy (FTIR) were gathered, analyzed and compared based on fusion methods. Visual observation of classification plots revealed that the PCA approach able to distinct pure and adulterated honey samples better than the LDA technique. Overall, the validated classification results based on FTIR data (88.0%) gave higher classification accuracy than e-nose data (76.5%) using the LDA technique. Honey classification based on normalized low-level and intermediate-level FTIR and e-nose fusion data scored classification accuracies of 92.2% and 88.7%, respectively using the Stepwise LDA method. The results suggested that pure and adulterated honey samples were better classified using FTIR and e-nose fusion data than single modality data.

Validity of the rheumatoid arthritis impact of disease (RAID) score and definition of cut-off points for disease activity states in a population-based European cohort of patients with rheumatoid arthritis.

PubMed

Salaffi, Fausto; Di Carlo, Marco; Vojinovic, Jelena; Tincani, Angela; Sulli, Alberto; Soldano, Stefano; Andreoli, Laura; Dall'Ara, Francesca; Ionescu, Ruxandra; Simić Pašalić, Katarina; Balčune, Ineta; Ferraz-Amaro, Iván; Tlustochowicz, Malgorzata; Butrimienė, Irena; Punceviciene, Egle; Toroptsova, Natalia; Grazio, Simeon; Morović-Vergles, Jadranka; Masaryk, Pavol; Otsa, Kati; Bernardes, Miguel; Boyadzhieva, Vladimira; Cutolo, Maurizio

2018-05-01

To assess the validity of the rheumatoid arthritis impact of disease (RAID) for measuring disease activity of rheumatoid arthritis (RA) and to determine cut-off values for defining the disease activity states. A total of 622 RA patients from an European database have been included. Cross-validation was based on assessment of convergent and discriminant validity. Optimal cut-offs were determined against external criteria by calculating the respective 25th and 75th percentiles mean values of RAID. External criteria included definitions for remission (REM), low disease activity (LDA), moderate disease activity (MDA) and high disease activity (HDA), cut-offs of the 28-joint disease activity score-C-reactive protein (DAS28-CRP) score. The RAID showed a moderate degree of correlation with respect to DAS28-CRP (rho=0.417; P<0.0001). The receiver operating characteristic (ROC) curves to discriminate the ability of RAID to distinguish patients with active and non-active disease was very good with an area under the curve (AUC) of 0.847 (95% confidence interval [CI]: 0.816 to 0.878; P<0.0001). Based on the distributions of RAID in the different disease activity groups, we propose the following cut-off values for REM: RAID ≤3; for LDA: RAID >3 and ≤4; for MDA: RAID >4 and ≤6; for HDA: RAID >6. Mean RAID differed significantly between patients classified as REM, LDA, MDA or HDA (P=0.001). The cut-offs revealed good measurement characteristics in cross-validation analysis, had great discriminatory performance in distinguishing patients with different levels of disease activity and are suited for widespread use in everyday practice application and research. Copyright © 2017 Société française de rhumatologie. Published by Elsevier SAS. All rights reserved.

A new model of cavern diameter based on a validated CFD study on stirring of a highly shear-thinning fluid.

PubMed

Story, Anna; Jaworski, Zdzisław

2017-01-01

Results of numerical simulations of momentum transfer for a highly shear-thinning fluid (0.2% Carbopol) in a stirred tank equipped with a Prochem Maxflo T type impeller are presented. The simulation results were validated using LDA data and both tangential and axial force measurements in the laminar and early transitional flow range. A good agreement between the predicted and experimental results of the local fluid velocity components was found. From the predicted and experimental values of both tangential and axial forces, the power number, Po , and thrust number, Th , were also calculated. Values of the absolute relative deviations were below 4.0 and 10.5%, respectively, for Po and Th , which confirms a satisfactory agreement with experiments. An intensive mixing zone, known as cavern, was observed near the impeller. In this zone, the local values of fluid velocity, strain rate, Metzner-Otto coefficient, shear stress and intensity of energy dissipation were all characterized by strong variability. Based on the results of experimental study a new model using non-dimensional impeller force number was proposed to predict the cavern diameter. Comparative numerical simulations were also carried out for a Newtonian fluid (water) and their results were similarly well verified using LDA measurements, as well as experimental power number values.

Formation of lobate debris aprons on Mars: Assessment of regional ice sheet collapse and debris-cover armoring

NASA Astrophysics Data System (ADS)

Fastook, James L.; Head, James W.; Marchant, David R.

2014-01-01

Lobate debris aprons (LDA) are lobate-shaped aprons surrounding scarps and isolated massifs that are concentrated in the vicinity of the northern Dichotomy Boundary on Mars. LDAs have been interpreted as (1) ice-cemented talus aprons undergoing viscous flow, (2) local debris-covered alpine-like glaciers, or (3) remnants of the collapse of a regional retreating ice sheet. We investigate the plausibility that LDAs are remnants of a more extensive regional ice sheet by modeling this process. We find that as a regional ice sheet collapses, the surface drops below cliff and massif bedrock margins, exposing bedrock and regolith, and initiating debris deposition on the surface of a cold-based glacier. Reduced sublimation due to debris-cover armoring of the proto-LDA surface produces a surface slope and consequent ice flow that carries the armoring debris away from the rock outcrops. As collapse and ice retreat continue the debris train eventually reaches the substrate surface at the front of the glacier, leaving the entire LDA armored by debris cover. Using a simplified ice flow model we are able to characterize the temperature and sublimation rate that would be necessary to produce LDAs with a wide range of specified lateral extents and thicknesses. We then apply this method to a database of documented LDA parameters (height, lateral extent) from the Dichotomy Boundary region, and assess the implications for predicted climate conditions during their formation and the range of formation times implied by the model. We find that for the population examined here, typical temperatures are in the range of -85 to -40 °C and typical sublimation rates lie in the range of 6-14 mm/a. Lobate debris apron formation times (from the point of bedrock exposure to complete debris cover) cluster near 400-500 ka. These results show that LDA length and thickness characteristics are consistent with climate conditions and a formation scenario typical of the collapse of a regional retreating ice sheet and exposure of bedrock cliffs. This scenario helps resolve many of the unusual characteristics of lobate debris aprons (LDA) and lineated valley fill (LVF). For example, the distribution of LVF is very consistent with extensive flow of glacial ice from plateau icefields, and the acquisition of a debris cover in the waning stages of retreat of the regional cover as the bedrock scarps are exposed. The typical concentric development of LDA around massifs is much more consistent with ice sheet retreat than insolation-related local accumulation and flow. We thus conclude that the retreating ice-sheet model is robust and should be investigated and tested in more detail. In addition, these results clearly show that the lobate debris aprons in the vicinity of the Dichotomy Boundary could not have attained temperatures near or above the ice melting point and retained their current shape, a finding that supports subzero temperatures for the last several hundred million years, the age of the LDA surfaces. A further implication is that the LDA ice has been preserved for at least several hundred million years, and could potentially contain the record of the climate of Mars, preserved since that time below a sublimation lag deposit.

Fermi surfaces and electronic topological transitions in metallic solid solutions

NASA Astrophysics Data System (ADS)

Bruno, E.; Ginatempo, B.; Guiliano, E. S.; Ruban, A. V.; Vekilov, Yu. Kh.

1994-12-01

Notwithstanding the substitutional disorder, the Fermi surface of metallic alloys can be measured and computed. We show that, from the theoretical point of view, it is defined as the locus of the peaks of the Bloch Spectral Function (BSF). Such Fermi surfaces, on varying the atomic concentrations, may undergo changes of their topology, known as Electronic Topological Transitions (ETT). Thus, for instance, pockets of electrons or holes may appear or disappear, necks may open or close. ETTs cause anomalous behaviours of thermodynamic, transport and elastic properties of metals and constitute a fascinating field in the study of Fermi liquid systems. Although ETTs could be studied on pure systems as a function of the thermodynamic variables, nevertheless such a study would often require extreme conditions, and would lead to experimental difficulties. On the other hand, it is possible to explore the variations of atomic concentration, i.e. the valence electron per atom ratio, in metallic solid solutions with a relative experimental ease. In this paper we review the theoretical techniques for the determination of Fermi surfaces in metallic solid solutions and discuss some examples of ETTs, namely LiMg, ZrNb, NbMo, MoRe, AgPd, CdMg, NiW and NiTi alloys, also in connection with experimental data as thermoelectric power, resistivity, elastic constants and electron-phonon coupling and with the determinations of the electron momentum distribution function from Compton scattering and positron annihilation experiments. We show that the ab initio calculations of the electronic structure for the quoted systems, together with a careful determination of the BSF, are able to predict quantitatively ETTs at those concentrations where physical quantities display anomalies, so confirming directly ETT theory. Although it is not the purpose of the present review to give a full account of electronic structure calculation schemes, however, we briefly discuss the ideas and the main physical approximations underlying theories of substitutional disorder in alloys. We shall pay some more attention to the Coherent Potential Approximation (CPA) in the Korringa-Kohn-Rostoker (KKR) multiple scattering framework and the Hohenberg and Kohn Density Functional Theory in the Local Density Approximation (LDA) for the exchange-correlation potential. The above choice is supported by the numerical versatility of the LDAKKRCPA theory, and, more important, by the a fortiori evidence that essentially equivalent results are obtained from different theoretical frameworks, provided the same basic physical approximations are used. Accordingly, when convenient, we present new LDAKKRCPA determinations of the Fermi surfaces, as for the ZrNbMoRe series.

Detecting Spatial Patterns of Natural Hazards from the Wikipedia Knowledge Base

NASA Astrophysics Data System (ADS)

Fan, J.; Stewart, K.

2015-07-01

The Wikipedia database is a data source of immense richness and variety. Included in this database are thousands of geotagged articles, including, for example, almost real-time updates on current and historic natural hazards. This includes usercontributed information about the location of natural hazards, the extent of the disasters, and many details relating to response, impact, and recovery. In this research, a computational framework is proposed to detect spatial patterns of natural hazards from the Wikipedia database by combining topic modeling methods with spatial analysis techniques. The computation is performed on the Neon Cluster, a high performance-computing cluster at the University of Iowa. This work uses wildfires as the exemplar hazard, but this framework is easily generalizable to other types of hazards, such as hurricanes or flooding. Latent Dirichlet Allocation (LDA) modeling is first employed to train the entire English Wikipedia dump, transforming the database dump into a 500-dimension topic model. Over 230,000 geo-tagged articles are then extracted from the Wikipedia database, spatially covering the contiguous United States. The geo-tagged articles are converted into an LDA topic space based on the topic model, with each article being represented as a weighted multidimension topic vector. By treating each article's topic vector as an observed point in geographic space, a probability surface is calculated for each of the topics. In this work, Wikipedia articles about wildfires are extracted from the Wikipedia database, forming a wildfire corpus and creating a basis for the topic vector analysis. The spatial distribution of wildfire outbreaks in the US is estimated by calculating the weighted sum of the topic probability surfaces using a map algebra approach, and mapped using GIS. To provide an evaluation of the approach, the estimation is compared to wildfire hazard potential maps created by the USDA Forest service.

Maintenance of remission with combination etanercept-DMARD therapy versus DMARDs alone in active rheumatoid arthritis: results of an international treat-to-target study conducted in regions with limited biologic access.

PubMed

Pavelka, Karel; Akkoç, Nurullah; Al-Maini, Mustafa; Zerbini, Cristiano A F; Karateev, Dmitry E; Nasonov, Evgeny L; Rahman, Mahboob U; Pedersen, Ronald; Dinh, Andrew; Shen, Qi; Vasilescu, Radu; Kotak, Sameer; Mahgoub, Ehab; Vlahos, Bonnie

2017-09-01

In this transglobal, randomized, double-blind, placebo-controlled, treat-to-target study, the maintenance of efficacy was compared between biologic-and biologic-free-disease-modifying antirheumatic drug (DMARD) combination regimens after low disease activity (LDA) was achieved with biologic DMARD induction therapy. Patients with moderate-to-severe rheumatoid arthritis despite methotrexate therapy received open-label etanercept 50 mg subcutaneously once weekly plus methotrexate with or without other conventional synthetic (cs) DMARDs for 24 weeks. Patients achieving LDA [disease activity score in 28 joints based on erythrocyte sedimentation rate (DAS28-ESR) <3.2] at week 24 were randomized to receive etanercept-methotrexate combination therapy or placebo-methotrexate combination therapy, with or without other csDMARDs, for 28 weeks. In the open-label period, 72% of patients achieved DAS28-ESR LDA at week 24. Patients enrolled in the double-blind period had long-standing rheumatoid arthritis and high disease activity at baseline (mean duration, 8.1 years; DAS28-ESR, 6.4). In the etanercept and placebo combination groups, 44% versus 17% achieved DAS28-ESR LDA and 34 versus 13% achieved DAS28-ESR remission at week 52 (p < 0.001). Adverse events were reported in 37 and 43%, serious adverse events in 0 and 4%, and serious infections in 0 and 2% in these groups, respectively, in the double-blind period. After induction of response with etanercept combination therapy following a treat-to-target approach in patients with long-standing rheumatoid arthritis and high disease activity at baseline, the etanercept combination regimen was significantly more effective in maintaining LDA and remission than a biologic-free regimen. ClinicalTrials.gov identifier. NCT01578850.

FUN-LDA: A Latent Dirichlet Allocation Model for Predicting Tissue-Specific Functional Effects of Noncoding Variation: Methods and Applications.

PubMed

Backenroth, Daniel; He, Zihuai; Kiryluk, Krzysztof; Boeva, Valentina; Pethukova, Lynn; Khurana, Ekta; Christiano, Angela; Buxbaum, Joseph D; Ionita-Laza, Iuliana

2018-05-03

We describe a method based on a latent Dirichlet allocation model for predicting functional effects of noncoding genetic variants in a cell-type- and/or tissue-specific way (FUN-LDA). Using this unsupervised approach, we predict tissue-specific functional effects for every position in the human genome in 127 different tissues and cell types. We demonstrate the usefulness of our predictions by using several validation experiments. Using eQTL data from several sources, including the GTEx project, Geuvadis project, and TwinsUK cohort, we show that eQTLs in specific tissues tend to be most enriched among the predicted functional variants in relevant tissues in Roadmap. We further show how these integrated functional scores can be used for (1) deriving the most likely cell or tissue type causally implicated for a complex trait by using summary statistics from genome-wide association studies and (2) estimating a tissue-based correlation matrix of various complex traits. We found large enrichment of heritability in functional components of relevant tissues for various complex traits, and FUN-LDA yielded higher enrichment estimates than existing methods. Finally, using experimentally validated functional variants from the literature and variants possibly implicated in disease by previous studies, we rigorously compare FUN-LDA with state-of-the-art functional annotation methods and show that FUN-LDA has better prediction accuracy and higher resolution than these methods. In particular, our results suggest that tissue- and cell-type-specific functional prediction methods tend to have substantially better prediction accuracy than organism-level prediction methods. Scores for each position in the human genome and for each ENCODE and Roadmap tissue are available online (see Web Resources). Copyright © 2018 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Titin strain contributes to the Frank–Starling law of the heart by structural rearrangements of both thin- and thick-filament proteins

DOE PAGES

Ait-Mou, Younss; Hsu, Karen; Farman, Gerrie P.; ...

2016-02-08

The Frank–Starling mechanism of the heart is due, in part, to modulation of myofilament Ca 2+ sensitivity by sarcomere length (SL) [length-dependent activation (LDA)]. The molecular mechanism(s) that underlie LDA are unknown. Recent evidence has implicated the giant protein titin in this cellular process, possibly by positioning the myosin head closer to actin. To clarify the role of titin strain in LDA, we isolated myocardium from either WT or homozygous mutant (HM) rats that express a giant splice isoform of titin, and subjected the muscles to stretch from 2.0 to 2.4 μm of SL. Upon stretch, HM compared with WTmore » muscles displayed reduced passive force, twitch force, and myofilament LDA. Time-resolved small-angle X-ray diffraction measurements of WT twitching muscles during diastole revealed stretch-induced increases in the intensity of myosin (M2 and M6) and troponin (Tn3) reflections, as well as a reduction in cross-bridge radial spacing. Independent fluorescent probe analyses in relaxed permeabilized myocytes corroborated these findings. X-ray electron density reconstruction revealed increased mass/ordering in both thick and thin filaments. The SL-dependent changes in structure observed in WT myocardium were absent in HM myocardium. Overall, our results reveal a correlation between titin strain and the Frank–Starling mechanism. The molecular basis underlying this phenomenon appears not to involve interfilament spacing or movement of myosin toward actin but, rather, sarcomere stretch-induced simultaneous structural rearrangements within both thin and thick filaments that correlate with titin strain and myofilament LDA.« less

Titin strain contributes to the Frank–Starling law of the heart by structural rearrangements of both thin- and thick-filament proteins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ait-Mou, Younss; Hsu, Karen; Farman, Gerrie P.

The Frank–Starling mechanism of the heart is due, in part, to modulation of myofilament Ca 2+ sensitivity by sarcomere length (SL) [length-dependent activation (LDA)]. The molecular mechanism(s) that underlie LDA are unknown. Recent evidence has implicated the giant protein titin in this cellular process, possibly by positioning the myosin head closer to actin. To clarify the role of titin strain in LDA, we isolated myocardium from either WT or homozygous mutant (HM) rats that express a giant splice isoform of titin, and subjected the muscles to stretch from 2.0 to 2.4 μm of SL. Upon stretch, HM compared with WTmore » muscles displayed reduced passive force, twitch force, and myofilament LDA. Time-resolved small-angle X-ray diffraction measurements of WT twitching muscles during diastole revealed stretch-induced increases in the intensity of myosin (M2 and M6) and troponin (Tn3) reflections, as well as a reduction in cross-bridge radial spacing. Independent fluorescent probe analyses in relaxed permeabilized myocytes corroborated these findings. X-ray electron density reconstruction revealed increased mass/ordering in both thick and thin filaments. The SL-dependent changes in structure observed in WT myocardium were absent in HM myocardium. Overall, our results reveal a correlation between titin strain and the Frank–Starling mechanism. The molecular basis underlying this phenomenon appears not to involve interfilament spacing or movement of myosin toward actin but, rather, sarcomere stretch-induced simultaneous structural rearrangements within both thin and thick filaments that correlate with titin strain and myofilament LDA.« less

The glass transition in high-density amorphous ice

PubMed Central

Loerting, Thomas; Fuentes-Landete, Violeta; Handle, Philip H.; Seidl, Markus; Amann-Winkel, Katrin; Gainaru, Catalin; Böhmer, Roland

2015-01-01

There has been a long controversy regarding the glass transition in low-density amorphous ice (LDA). The central question is whether or not it transforms to an ultraviscous liquid state above 136 K at ambient pressure prior to crystallization. Currently, the most widespread interpretation of the experimental findings is in terms of a transformation to a superstrong liquid above 136 K. In the last decade some work has also been devoted to the study of the glass transition in high-density amorphous ice (HDA) which is in the focus of the present review. At ambient pressure HDA is metastable against both ice I and LDA, whereas at > 0.2 GPa HDA is no longer metastable against LDA, but merely against high-pressure forms of crystalline ice. The first experimental observation interpreted as the glass transition of HDA was made using in situ methods by Mishima, who reported a glass transition temperature Tg of 160 K at 0.40 GPa. Soon thereafter Andersson and Inaba reported a much lower glass transition temperature of 122 K at 1.0 GPa. Based on the pressure dependence of HDA's Tg measured in Innsbruck, we suggest that they were in fact probing the distinct glass transition of very high-density amorphous ice (VHDA). Very recently the glass transition in HDA was also observed at ambient pressure at 116 K. That is, LDA and HDA show two distinct glass transitions, clearly separated by about 20 K at ambient pressure. In summary, this suggests that three glass transition lines can be defined in the p–T plane for LDA, HDA, and VHDA. PMID:25641986

The glass transition in high-density amorphous ice.

PubMed

Loerting, Thomas; Fuentes-Landete, Violeta; Handle, Philip H; Seidl, Markus; Amann-Winkel, Katrin; Gainaru, Catalin; Böhmer, Roland

2015-01-01

There has been a long controversy regarding the glass transition in low-density amorphous ice (LDA). The central question is whether or not it transforms to an ultraviscous liquid state above 136 K at ambient pressure prior to crystallization. Currently, the most widespread interpretation of the experimental findings is in terms of a transformation to a superstrong liquid above 136 K. In the last decade some work has also been devoted to the study of the glass transition in high-density amorphous ice (HDA) which is in the focus of the present review. At ambient pressure HDA is metastable against both ice I and LDA, whereas at > 0.2 GPa HDA is no longer metastable against LDA, but merely against high-pressure forms of crystalline ice. The first experimental observation interpreted as the glass transition of HDA was made using in situ methods by Mishima, who reported a glass transition temperature T g of 160 K at 0.40 GPa. Soon thereafter Andersson and Inaba reported a much lower glass transition temperature of 122 K at 1.0 GPa. Based on the pressure dependence of HDA's T g measured in Innsbruck, we suggest that they were in fact probing the distinct glass transition of very high-density amorphous ice (VHDA). Very recently the glass transition in HDA was also observed at ambient pressure at 116 K. That is, LDA and HDA show two distinct glass transitions, clearly separated by about 20 K at ambient pressure. In summary, this suggests that three glass transition lines can be defined in the p-T plane for LDA, HDA, and VHDA.

Effect of Low-Dose Aspirin on Chronic Acid Reflux Esophagitis in Rats.

PubMed

Masuda, Takahiro; Yano, Fumiaki; Omura, Nobuo; Tsuboi, Kazuto; Hoshino, Masato; Yamamoto, Se Ryung; Akimoto, Shunsuke; Kashiwagi, Hideyuki; Yanaga, Katsuhiko

2018-01-01

Clinical role of low-dose aspirin (LDA) in pathogenesis of gastroesophageal reflux disease is by far controversial. This can be attributed to the paucity of basic research detailing the mechanism of LDA-induced esophageal mucosal injury (EI) on underlying chronic acid reflux esophagitis (RE). The aim of this study was to clarify the effect of LDA on chronic RE in rats. Esophagitis was induced in 8-week-old male Wistar rats by ligating the border between forestomach and glandular portion with a 2-0 silk tie and covering the duodenum with a small piece of 18-Fr Nélaton catheter. Seventy-eight chronic RE rat models were divided into five treatment groups, consisting of orally administered vehicle (controls), and aspirin doses of 2, 5, 50 or 100 mg/kg once daily for 28 days. EI was assessed by gross area of macroscopic mucosal injury, severity grade of esophagitis and microscopic depth of infiltration by inflammatory cells. Area of esophagitis in animals with aspirin dose of 100 mg/kg/day showed a 36.5% increase compared with controls, although it failed to achieve statistical significance (p = 0.812). Additionally, the rate of severe EI was increased in animals with aspirin dose of 100 mg/kg/day as compared with controls (p < 0.05). The grade of severity correlated with the depth of inflammation (r s  = 0.492, p < 0.001). Maximal dose aspirin (100 mg/kg/day) contributed in exacerbating preexisting EI. LDA (2 and 5 mg/kg/day), on the other hand, did not affect chronic RE in this model. LDA seems to be safe for use in patients with chronic RE.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Warmack, Robert J. Bruce; Wolf, Dennis A.; Frank, Steven Shane

Various apparatus and methods for smoke detection are disclosed. In one embodiment, a method of training a classifier for a smoke detector comprises inputting sensor data from a plurality of tests into a processor. The sensor data is processed to generate derived signal data corresponding to the test data for respective tests. The derived signal data is assigned into categories comprising at least one fire group and at least one non-fire group. Linear discriminant analysis (LDA) training is performed by the processor. The derived signal data and the assigned categories for the derived signal data are inputs to the LDAmore » training. The output of the LDA training is stored in a computer readable medium, such as in a smoke detector that uses LDA to determine, based on the training, whether present conditions indicate the existence of a fire.« less

Density-functional theory applied to d- and f-electron systems

NASA Astrophysics Data System (ADS)

Wu, Xueyuan

Density functional theory (DFT) has been applied to study the electronic and geometric structures of prototype d- and f-electron systems. For the d-electron system, all electron DFT with gradient corrections to the exchange and correlation functionals has been used to investigate the properties of small neutral and cationic vanadium clusters. Results are in good agreement with available experimental and other theoretical data. For the f-electron system, a hybrid DFT, namely, B3LYP (Becke's 3-parameter hybrid functional using the correlation functional of Lee, Yang and Parr) with relativistic effective core potentials and cluster models has been applied to investigate the nature of chemical bonding of both the bulk and the surfaces of plutonium monoxide and dioxide. Using periodic models, the electronic and geometric structures of PuO2 and its (110) surface, as well as water adsorption on this surface have also been investigated using DFT in both local density approximation (LDA) and generalized gradient approximation (GGA) formalisms.

78 FR 14010 - Standard Instrument Approach Procedures, and Takeoff Minimums and Obstacle Departure Procedures...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-04

... by reference in this amendment under 5 U.S.C. 552(a), 1 CFR part 51, and 14 CFR part 97.20. The... 97 continues to read as follows: Authority: 49 U.S.C. 106(g), 40103, 40106, 40113, 40114, 40120... Intl, LDA PRM RWY 6R, Amdt 1C, CANCELED Cleveland, OH, Cleveland-Hopkins Intl, LDA PRM RWY 24L, Orig-C...

Prediction of Potential Hit Song and Musical Genre Using Artificial Neural Networks

NASA Astrophysics Data System (ADS)

Monterola, Christopher; Abundo, Cheryl; Tugaff, Jeric; Venturina, Lorcel Ericka

Accurately quantifying the goodness of music based on the seemingly subjective taste of the public is a multi-million industry. Recording companies can make sound decisions on which songs or artists to prioritize if accurate forecasting is achieved. We extract 56 single-valued musical features (e.g. pitch and tempo) from 380 Original Pilipino Music (OPM) songs (190 are hit songs) released from 2004 to 2006. Based on an effect size criterion which measures a variable's discriminating power, the 20 highest ranked features are fed to a classifier tasked to predict hit songs. We show that regardless of musical genre, a trained feed-forward neural network (NN) can predict potential hit songs with an average accuracy of ΦNN = 81%. The accuracy is about +20% higher than those of standard classifiers such as linear discriminant analysis (LDA, ΦLDA = 61%) and classification and regression trees (CART, ΦCART = 57%). Both LDA and CART are above the proportional chance criterion (PCC, ΦPCC = 50%) but are slightly below the suggested acceptable classifier requirement of 1.25*ΦPCC = 63%. Utilizing a similar procedure, we demonstrate that different genres (ballad, alternative rock or rock) of OPM songs can be automatically classified with near perfect accuracy using LDA or NN but only around 77% using CART.

Habits with killer instincts: in vivo analysis on the severity of oral mucosal alterations using autofluorescence spectroscopy

NASA Astrophysics Data System (ADS)

Nazeer Shaiju, S.; Ariya, Saraswathy; Asish, Rajasekharan; Salim Haris, Padippurakkakath; Anita, Balan; Arun Kumar, Gupta; Jayasree, Ramapurath S.

2011-08-01

Oral habits like chewing and smoking are main causes of oral cancer, which has a higher mortality rate than many other cancer forms. Currently, the long term survival rate of oral cancer is less than 50%, as a majority of cases are detected very late. The clinician's main challenge is to differentiate among a multitude of red, white, or ulcerated lesions. Hence, new noninvasive, reliable, and fast techniques for the discrimination of oral cavity disorders are to be developed. This study includes autofluorescence spectroscopic screening of normal volunteers with and without lifestyle oral habits and patients with oral submucous fibrosis (OSF). The spectra from different sites of habitués, non-habitués, and OSF patients were analyzed using the intensity ratio, redox ratio, and linear discriminant analysis (LDA). The spectral disparities among these groups are well demonstrated in the emission regions of collagen and Flavin adenine dinucleotide. We observed that LDA gives better efficiency of classification than the intensity ratio technique. Even the differentiation of habitués and non-habitués could be well established with LDA. The study concludes that the clinical application of autofluorescence spectroscopy along with LDA, yields spontaneous screening among individuals, facilitating better patient management for clinicians and better quality of life for patients.

Component-based subspace linear discriminant analysis method for face recognition with one training sample

NASA Astrophysics Data System (ADS)

Huang, Jian; Yuen, Pong C.; Chen, Wen-Sheng; Lai, J. H.

2005-05-01

Many face recognition algorithms/systems have been developed in the last decade and excellent performances have also been reported when there is a sufficient number of representative training samples. In many real-life applications such as passport identification, only one well-controlled frontal sample image is available for training. Under this situation, the performance of existing algorithms will degrade dramatically or may not even be implemented. We propose a component-based linear discriminant analysis (LDA) method to solve the one training sample problem. The basic idea of the proposed method is to construct local facial feature component bunches by moving each local feature region in four directions. In this way, we not only generate more samples with lower dimension than the original image, but also consider the face detection localization error while training. After that, we propose a subspace LDA method, which is tailor-made for a small number of training samples, for the local feature projection to maximize the discrimination power. Theoretical analysis and experiment results show that our proposed subspace LDA is efficient and overcomes the limitations in existing LDA methods. Finally, we combine the contributions of each local component bunch with a weighted combination scheme to draw the recognition decision. A FERET database is used for evaluating the proposed method and results are encouraging.

The Simultaneous Abolition of Three Starch Hydrolases Blocks Transient Starch Breakdown in Arabidopsis*

PubMed Central

Streb, Sebastian; Eicke, Simona; Zeeman, Samuel C.

2012-01-01

In this study, we investigated which enzymes are involved in debranching amylopectin during transient starch degradation. Previous studies identified two debranching enzymes, isoamylase 3 (ISA3) and limit dextrinase (LDA), involved in this process. However, plants lacking both enzymes still degrade substantial amounts of starch. Thus, other enzymes/mechanisms must contribute to starch breakdown. We show that the chloroplastic α-amylase 3 (AMY3) also participates in starch degradation and provide evidence that all three enzymes can act directly at the starch granule surface. The isa3 mutant has a starch excess phenotype, reflecting impaired starch breakdown. In contrast, removal of AMY3, LDA, or both enzymes together has no impact on starch degradation. However, removal of AMY3 or LDA in addition to ISA3 enhances the starch excess phenotype. In plants lacking all three enzymes, starch breakdown is effectively blocked, and starch accumulates to the highest levels observed so far. This provides indirect evidence that the heteromultimeric debranching enzyme ISA1-ISA2 is not involved in starch breakdown. However, we illustrate that ISA1-ISA2 can hydrolyze small soluble branched glucans that accumulate when ISA3 and LDA are missing, albeit at a slow rate. Starch accumulation in the mutants correlates inversely with plant growth. PMID:23019330

A Hybrid Sensing Approach for Pure and Adulterated Honey Classification

PubMed Central

Subari, Norazian; Saleh, Junita Mohamad; Shakaff, Ali Yeon Md; Zakaria, Ammar

2012-01-01

This paper presents a comparison between data from single modality and fusion methods to classify Tualang honey as pure or adulterated using Linear Discriminant Analysis (LDA) and Principal Component Analysis (PCA) statistical classification approaches. Ten different brands of certified pure Tualang honey were obtained throughout peninsular Malaysia and Sumatera, Indonesia. Various concentrations of two types of sugar solution (beet and cane sugar) were used in this investigation to create honey samples of 20%, 40%, 60% and 80% adulteration concentrations. Honey data extracted from an electronic nose (e-nose) and Fourier Transform Infrared Spectroscopy (FTIR) were gathered, analyzed and compared based on fusion methods. Visual observation of classification plots revealed that the PCA approach able to distinct pure and adulterated honey samples better than the LDA technique. Overall, the validated classification results based on FTIR data (88.0%) gave higher classification accuracy than e-nose data (76.5%) using the LDA technique. Honey classification based on normalized low-level and intermediate-level FTIR and e-nose fusion data scored classification accuracies of 92.2% and 88.7%, respectively using the Stepwise LDA method. The results suggested that pure and adulterated honey samples were better classified using FTIR and e-nose fusion data than single modality data. PMID:23202033

Analysis of Flavonoid in Medicinal Plant Extract Using Infrared Spectroscopy and Chemometrics

PubMed Central

Retnaningtyas, Yuni; Nuri; Lukman, Hilmia

2016-01-01

Infrared (IR) spectroscopy combined with chemometrics has been developed for simple analysis of flavonoid in the medicinal plant extract. Flavonoid was extracted from medicinal plant leaves by ultrasonication and maceration. IR spectra of selected medicinal plant extract were correlated with flavonoid content using chemometrics. The chemometric method used for calibration analysis was Partial Last Square (PLS) and the methods used for classification analysis were Linear Discriminant Analysis (LDA), Soft Independent Modelling of Class Analogies (SIMCA), and Support Vector Machines (SVM). In this study, the calibration of NIR model that showed best calibration with R 2 and RMSEC value was 0.9916499 and 2.1521897, respectively, while the accuracy of all classification models (LDA, SIMCA, and SVM) was 100%. R 2 and RMSEC of calibration of FTIR model were 0.8653689 and 8.8958149, respectively, while the accuracy of LDA, SIMCA, and SVM was 86.0%, 91.2%, and 77.3%, respectively. PLS and LDA of NIR models were further used to predict unknown flavonoid content in commercial samples. Using these models, the significance of flavonoid content that has been measured by NIR and UV-Vis spectrophotometry was evaluated with paired samples t-test. The flavonoid content that has been measured with both methods gave no significant difference. PMID:27529051

Authenticity assessment of banknotes using portable near infrared spectrometer and chemometrics.

PubMed

da Silva Oliveira, Vanessa; Honorato, Ricardo Saldanha; Honorato, Fernanda Araújo; Pereira, Claudete Fernandes

2018-05-01

Spectra recorded using a portable near infrared (NIR) spectrometer, Soft Independent Modeling of Class Analogy (SIMCA) and Linear Discriminant Analysis (LDA) associated to Successive Projections Algorithm (SPA) models were applied to identify counterfeit and authentic Brazilian Real (R$20, R$50 and R$100) banknotes, enabling a simple field analysis. NIR spectra (950-1650nm) were recorded from seven different areas of the banknotes (two with fluorescent ink, one over watermark, three with intaglio printing process and one over the serial numbers with typography printing). SIMCA and SPA-LDA models were built using 1st derivative preprocessed spectral data from one of the intaglio areas. For the SIMCA models, all authentic (300) banknotes were correctly classified and the counterfeits (227) were not classified. For the two classes SPA-LDA models (authentic and counterfeit currencies), all the test samples were correctly classified into their respective class. The number of selected variables by SPA varied from two to nineteen for R$20, R$50 and R$100 currencies. These results show that the use of the portable near-infrared with SIMCA or SPA-LDA models can be a completely effective, fast, and non-destructive way to identify authenticity of banknotes as well as permitting field analysis. Copyright © 2018 Elsevier B.V. All rights reserved.

Computational study of hydroxyapatite structures, properties and defects

NASA Astrophysics Data System (ADS)

Bystrov, V. S.; Coutinho, J.; Bystrova, A. V.; Dekhtyar, Yu D.; Pullar, R. C.; Poronin, A.; Palcevskis, E.; Dindune, A.; Alkan, B.; Durucan, C.; Paramonova, E. V.

2015-03-01

Hydroxyapatite (HAp) was studied from a first principle approach using the local density approximation (LDA) method in AIMPRO code, in combination with various quantum mechanical (QM) and molecular mechanical (MM) methods from HypemChem 7.5/8.0. The data obtained were used for studies of HAp structures, the physical properties of HAp (density of electronic states—DOS, bulk modulus etc) and defects in HAp. Computed data confirmed that HAp can co-exist in different phases—hexagonal and monoclinic. Ordered monoclinic structures, which could reveal piezoelectric properties, are of special interest. The data obtained allow us to characterize the properties of the following defects in HAp: O, H and OH vacancies; H and OH interstitials; substitutions of Ca by Mg, Sr, Mn or Se, and P by Si. These properties reveal the appearance of additional energy levels inside the forbidden zone, shifts of the top of the valence band or the bottom of the conduction band, and subsequent changes in the width of the forbidden zone. The data computed are compared with other known data, both calculated and experimental, such as alteration of the electron work functions under different influences of various defects and treatments, obtained by photoelectron emission. The obtained data are very useful, and there is an urgent need for such analysis of modified HAp interactions with living cells and tissues, improvement of implant techniques and development of new nanomedical applications.

DFT +U Modeling of Hole Polarons in Organic Lead Halide Perovskites

NASA Astrophysics Data System (ADS)

Welch, Eric; Erhart, Paul; Scolfaro, Luisa; Zakhidov, Alex

Due to the ever present drive towards improved efficiencies in solar cell technology, new and improved materials are emerging rapidly. Organic halide perovskites are a promising prospect, yet a fundamental understanding of the organic perovskite structure and electronic properties is missing. Particularly, explanations of certain physical phenomena, specifically a low recombination rate and high mobility of charge carriers still remain controversial. We theoretically investigate possible formation of hole polarons adopting methodology used for oxide perovskites. The perovskite studied here is the ABX3structure, with A being an organic cation, B lead and C a halogen; the combinations studied allow for A1,xA2 , 1 - xBX1,xX2 , 3 - xwhere the alloy convention is used to show mixtures of the organic cations and/or the halogens. Two organic cations, methylammonium and formamidinium, and three halogens, iodine, chlorine and bromine are studied. Electronic structures and polaron behavior is studied through first principle density functional theory (DFT) calculations using the Vienna Ab Initio Simulation Package (VASP). Local density approximation (LDA) pseudopotentials are used and a +U Hubbard correction of 8 eV is added; this method was shown to work with oxide perovskites. It is shown that a localized state is realized with the Hubbard correction in systems with an electron removed, residing in the band gap of each different structure. Thus, hole polarons are expected to be seen in these perovskites.

Performance of quantum Monte Carlo for calculating molecular bond lengths

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cleland, Deidre M., E-mail: deidre.cleland@csiro.au; Per, Manolo C., E-mail: manolo.per@csiro.au

2016-03-28

This work investigates the accuracy of real-space quantum Monte Carlo (QMC) methods for calculating molecular geometries. We present the equilibrium bond lengths of a test set of 30 diatomic molecules calculated using variational Monte Carlo (VMC) and diffusion Monte Carlo (DMC) methods. The effect of different trial wavefunctions is investigated using single determinants constructed from Hartree-Fock (HF) and Density Functional Theory (DFT) orbitals with LDA, PBE, and B3LYP functionals, as well as small multi-configurational self-consistent field (MCSCF) multi-determinant expansions. When compared to experimental geometries, all DMC methods exhibit smaller mean-absolute deviations (MADs) than those given by HF, DFT, and MCSCF.more » The most accurate MAD of 3 ± 2 × 10{sup −3} Å is achieved using DMC with a small multi-determinant expansion. However, the more computationally efficient multi-determinant VMC method has a similar MAD of only 4.0 ± 0.9 × 10{sup −3} Å, suggesting that QMC forces calculated from the relatively simple VMC algorithm may often be sufficient for accurate molecular geometries.« less

A novel method for qualitative analysis of edible oil oxidation using an electronic nose.

PubMed

Xu, Lirong; Yu, Xiuzhu; Liu, Lei; Zhang, Rui

2016-07-01

An electronic nose (E-nose) was used for rapid assessment of the degree of oxidation in edible oils. Peroxide and acid values of edible oil samples were analyzed using data obtained by the American Oil Chemists' Society (AOCS) Official Method for reference. Qualitative discrimination between non-oxidized and oxidized oils was conducted using the E-nose technique developed in combination with cluster analysis (CA), principal component analysis (PCA), and linear discriminant analysis (LDA). The results from CA, PCA and LDA indicated that the E-nose technique could be used for differentiation of non-oxidized and oxidized oils. LDA produced slightly better results than CA and PCA. The proposed approach can be used as an alternative to AOCS Official Method as an innovative tool for rapid detection of edible oil oxidation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Improving Efficiency in Multi-Strange Baryon Reconstruction in d-Au at STAR

NASA Astrophysics Data System (ADS)

Leight, William

2003-10-01

We report preliminary multi-strange baryon measurements for d-Au collisions recorded at RHIC by the STAR experiment. After using classical topological analysis, in which cuts for each discriminating variable are adjusted by hand, we investigate improvements in signal-to-noise optimization using Linear Discriminant Analysis (LDA). LDA is an algorithm for finding, in the n-dimensional space of the n discriminating variables, the axis on which the signal and noise distributions are most separated. LDA is the first step in moving towards more sophisticated techniques for signal-to-noise optimization, such as Artificial Neural Nets. Due to the relatively low background and sufficiently high yields of d-Au collisions, they form an ideal system to study these possibilities for improving reconstruction methods. Such improvements will be extremely important for forthcoming Au-Au runs in which the size of the combinatoric background is a major problem in reconstruction efforts.

Finding complex biological relationships in recent PubMed articles using Bio-LDA.

PubMed

Wang, Huijun; Ding, Ying; Tang, Jie; Dong, Xiao; He, Bing; Qiu, Judy; Wild, David J

2011-03-23

The overwhelming amount of available scholarly literature in the life sciences poses significant challenges to scientists wishing to keep up with important developments related to their research, but also provides a useful resource for the discovery of recent information concerning genes, diseases, compounds and the interactions between them. In this paper, we describe an algorithm called Bio-LDA that uses extracted biological terminology to automatically identify latent topics, and provides a variety of measures to uncover putative relations among topics and bio-terms. Relationships identified using those approaches are combined with existing data in life science datasets to provide additional insight. Three case studies demonstrate the utility of the Bio-LDA model, including association predication, association search and connectivity map generation. This combined approach offers new opportunities for knowledge discovery in many areas of biology including target identification, lead hopping and drug repurposing.

Finding Complex Biological Relationships in Recent PubMed Articles Using Bio-LDA

PubMed Central

Wang, Huijun; Ding, Ying; Tang, Jie; Dong, Xiao; He, Bing; Qiu, Judy; Wild, David J.

2011-01-01

The overwhelming amount of available scholarly literature in the life sciences poses significant challenges to scientists wishing to keep up with important developments related to their research, but also provides a useful resource for the discovery of recent information concerning genes, diseases, compounds and the interactions between them. In this paper, we describe an algorithm called Bio-LDA that uses extracted biological terminology to automatically identify latent topics, and provides a variety of measures to uncover putative relations among topics and bio-terms. Relationships identified using those approaches are combined with existing data in life science datasets to provide additional insight. Three case studies demonstrate the utility of the Bio-LDA model, including association predication, association search and connectivity map generation. This combined approach offers new opportunities for knowledge discovery in many areas of biology including target identification, lead hopping and drug repurposing. PMID:21448266

Relaxation dynamics and transformation kinetics of deeply supercooled water: Temperature, pressure, doping, and proton/deuteron isotope effects.

PubMed

Lemke, Sonja; Handle, Philip H; Plaga, Lucie J; Stern, Josef N; Seidl, Markus; Fuentes-Landete, Violeta; Amann-Winkel, Katrin; Köster, Karsten W; Gainaru, Catalin; Loerting, Thomas; Böhmer, Roland

2017-07-21

Above its glass transition, the equilibrated high-density amorphous ice (HDA) transforms to the low-density pendant (LDA). The temperature dependence of the transformation is monitored at ambient pressure using dielectric spectroscopy and at elevated pressures using dilatometry. It is found that near the glass transition temperature of deuterated samples, the transformation kinetics is 300 times slower than the structural relaxation, while for protonated samples, the time scale separation is at least 30 000 and insensitive to doping. The kinetics of the HDA to LDA transformation lacks a proton/deuteron isotope effect, revealing that this process is dominated by the restructuring of the oxygen network. The x-ray diffraction experiments performed on samples at intermediate transition stages reflect a linear combination of the LDA and HDA patterns implying a macroscopic phase separation, instead of a local intermixing of the two amorphous states.

Spotting the difference in molecular dynamics simulations of biomolecules

NASA Astrophysics Data System (ADS)

Sakuraba, Shun; Kono, Hidetoshi

2016-08-01

Comparing two trajectories from molecular simulations conducted under different conditions is not a trivial task. In this study, we apply a method called Linear Discriminant Analysis with ITERative procedure (LDA-ITER) to compare two molecular simulation results by finding the appropriate projection vectors. Because LDA-ITER attempts to determine a projection such that the projections of the two trajectories do not overlap, the comparison does not suffer from a strong anisotropy, which is an issue in protein dynamics. LDA-ITER is applied to two test cases: the T4 lysozyme protein simulation with or without a point mutation and the allosteric protein PDZ2 domain of hPTP1E with or without a ligand. The projection determined by the method agrees with the experimental data and previous simulations. The proposed procedure, which complements existing methods, is a versatile analytical method that is specialized to find the "difference" between two trajectories.

A chromatochemometric approach for evaluating and selecting the perfume maceration time.

PubMed

López-Nogueroles, Marina; Chisvert, Alberto; Salvador, Amparo

2010-04-30

A chemometric treatment of the data obtained by gas chromatography (GC) with flame ionization detector (FID) has been proposed to study the maceration time involved in perfumes manufacture with the final purpose of reducing this time but preserving the organoleptic characteristics of the perfume that is being elaborated. In this sense, GC-FID chromatograms were used as a fingerprint of perfume samples subjected to different maceration times, and data were treated by linear discriminant analysis (LDA), by comparing to a set of samples known to be macerated or not, which were used as calibration objects. The GC-FID methodology combined with the treatment of data by LDA has been applied successfully to seven different perfumes. The constructed LDA models exhibited excellent Wilks' lambdas (0.013-0.118, depending on the perfume), and up to a reduction of 57% has been achieved with respect to the maceration time initially established. 2010 Elsevier B.V. All rights reserved.

Relaxation dynamics and transformation kinetics of deeply supercooled water: Temperature, pressure, doping, and proton/deuteron isotope effects

NASA Astrophysics Data System (ADS)

Lemke, Sonja; Handle, Philip H.; Plaga, Lucie J.; Stern, Josef N.; Seidl, Markus; Fuentes-Landete, Violeta; Amann-Winkel, Katrin; Köster, Karsten W.; Gainaru, Catalin; Loerting, Thomas; Böhmer, Roland

2017-07-01

Above its glass transition, the equilibrated high-density amorphous ice (HDA) transforms to the low-density pendant (LDA). The temperature dependence of the transformation is monitored at ambient pressure using dielectric spectroscopy and at elevated pressures using dilatometry. It is found that near the glass transition temperature of deuterated samples, the transformation kinetics is 300 times slower than the structural relaxation, while for protonated samples, the time scale separation is at least 30 000 and insensitive to doping. The kinetics of the HDA to LDA transformation lacks a proton/deuteron isotope effect, revealing that this process is dominated by the restructuring of the oxygen network. The x-ray diffraction experiments performed on samples at intermediate transition stages reflect a linear combination of the LDA and HDA patterns implying a macroscopic phase separation, instead of a local intermixing of the two amorphous states.

Predicting binary, discrete and continued lncRNA-disease associations via a unified framework based on graph regression.

PubMed

Shi, Jian-Yu; Huang, Hua; Zhang, Yan-Ning; Long, Yu-Xi; Yiu, Siu-Ming

2017-12-21

In human genomes, long non-coding RNAs (lncRNAs) have attracted more and more attention because their dysfunctions are involved in many diseases. However, the associations between lncRNAs and diseases (LDA) still remain unknown in most cases. While identifying disease-related lncRNAs in vivo is costly, computational approaches are promising to not only accelerate the possible identification of associations but also provide clues on the underlying mechanism of various lncRNA-caused diseases. Former computational approaches usually only focus on predicting new associations between lncRNAs having known associations with diseases and other lncRNA-associated diseases. They also only work on binary lncRNA-disease associations (whether the pair has an association or not), which cannot reflect and reveal other biological facts, such as the number of proteins involved in LDA or how strong the association is (i.e., the intensity of LDA). To address abovementioned issues, we propose a graph regression-based unified framework (GRUF). In particular, our method can work on lncRNAs, which have no previously known disease association and diseases that have no known association with any lncRNAs. Also, instead of only a binary answer for the association, our method tries to uncover more biological relationship between a pair of lncRNA and disease, which may provide better clues for researchers. We compared GRUF with three state-of-the-art approaches and demonstrated the superiority of GRUF, which achieves 5%~16% improvement in terms of the area under the receiver operating characteristic curve (AUC). GRUF also provides a predicted confidence score for the predicted LDA, which reveals the significant correlation between the score and the number of RNA-Binding Proteins involved in LDAs. Lastly, three out of top-5 LDA candidates generated by GRUF in novel prediction are verified indirectly by medical literature and known biological facts. The proposed GRUF has two advantages over existing approaches. Firstly, it can be used to work on lncRNAs that have no known disease association and diseases that have no known association with any lncRNAs. Secondly, instead of providing a binary answer (with or without association), GRUF works for both discrete and continued LDA, which help revealing the pathological implications between lncRNAs and diseases.

Etude, par principes premiers, des effets de la correlation entre electrons sur les proprietes electroniques et magnetiques de polymeres pontes et de supraconducteurs a haute temperature critique

NASA Astrophysics Data System (ADS)

Pesant, Simon

Description of complex systems by Density functional theory is treated in this thesis. First, the Density functional theory and a few functionals used to simulate cristals are presented. Specifically, the LDA and GGA functionnals are described and their limits are exposed. Furthermore, the Hubbard model as well as the LDA+U functionnal are addressed in this chapter. These methods enable the study of highly correlated materials. Then, results obtained on polymers are summarized in two articles. The first one treats the band gap variation of ladder-type polymers compared to non ladder type ones. The second article considers small band gap polymers. In this case, it will be shown that an hybrid functional, which contains exact exchange, is required to describe the electronic properties of the polymers under study. Finally, the last chapter address the study of cuprates superconductors. The LDA+U can account for the localization of electrons in copper orbitals. Consequently, a study of the impact of this functionnal on electronic properties of cuprates is conducted. The chapter is ended by an article treating magnetic orders in doped La 2CuO4. Supplementary materials of the second article and a description of the theory of superconductivity of Bardeen, Cooper and Schrieffer are put in annex. Keywords : Electronic correlation, DFT, LDA+U, cuprates, polymers, magnetic orders

Density Functional O(N) Calculations

NASA Astrophysics Data System (ADS)

Ordejón, Pablo

1998-03-01

We have developed a scheme for performing Density Functional Theory calculations with O(N) scaling.(P. Ordejón, E. Artacho and J. M. Soler, Phys. Rev. B, 53), 10441 (1996) The method uses arbitrarily flexible and complete Atomic Orbitals (AO) basis sets. This gives a wide range of choice, from extremely fast calculations with minimal basis sets, to greatly accurate calculations with complete sets. The size-efficiency of AO bases, together with the O(N) scaling of the algorithm, allow the application of the method to systems with many hundreds of atoms, in single processor workstations. I will present the SIESTA code,(D. Sanchez-Portal, P. Ordejón, E. Artacho and J. M. Soler, Int. J. Quantum Chem., 65), 453 (1997) in which the method is implemented, with several LDA, LSD and GGA functionals available, and using norm-conserving, non-local pseudopotentials (in the Kleinman-Bylander form) to eliminate the core electrons. The calculation of static properties such as energies, forces, pressure, stress and magnetic moments, as well as molecular dynamics (MD) simulations capabilities (including variable cell shape, constant temperature and constant pressure MD) are fully implemented. I will also show examples of the accuracy of the method, and applications to large-scale materials and biomolecular systems.

Theory of resonant x-ray emission spectra in compounds with localized f electrons

NASA Astrophysics Data System (ADS)

Kolorenč, Jindřich

2018-05-01

I discuss a theoretical description of the resonant x-ray emission spectroscopy (RXES) that is based on the Anderson impurity model. The parameters entering the model are determined from material-specific LDA+DMFT calculations. The theory is applicable across the whole f series, not only in the limits of nearly empty (La, Ce) or nearly full (Yb) valence f shell. Its performance is illustrated on the pressure-enhanced intermediate valency of elemental praseodymium. The obtained results are compared to the usual interpretation of RXES, which assumes that the spectrum is a superposition of several signals, each corresponding to one configuration of the 4f shell. The present theory simplifies to such superposition only if nearly all effects of hybridization of the 4f shell with the surrounding states are neglected. Although the assumption of negligible hybridization sounds reasonable for lanthanides, the explicit calculations show that it substantially distorts the analysis of the RXES data.

General tensor discriminant analysis and gabor features for gait recognition.

PubMed

Tao, Dacheng; Li, Xuelong; Wu, Xindong; Maybank, Stephen J

2007-10-01

The traditional image representations are not suited to conventional classification methods, such as the linear discriminant analysis (LDA), because of the under sample problem (USP): the dimensionality of the feature space is much higher than the number of training samples. Motivated by the successes of the two dimensional LDA (2DLDA) for face recognition, we develop a general tensor discriminant analysis (GTDA) as a preprocessing step for LDA. The benefits of GTDA compared with existing preprocessing methods, e.g., principal component analysis (PCA) and 2DLDA, include 1) the USP is reduced in subsequent classification by, for example, LDA; 2) the discriminative information in the training tensors is preserved; and 3) GTDA provides stable recognition rates because the alternating projection optimization algorithm to obtain a solution of GTDA converges, while that of 2DLDA does not. We use human gait recognition to validate the proposed GTDA. The averaged gait images are utilized for gait representation. Given the popularity of Gabor function based image decompositions for image understanding and object recognition, we develop three different Gabor function based image representations: 1) the GaborD representation is the sum of Gabor filter responses over directions, 2) GaborS is the sum of Gabor filter responses over scales, and 3) GaborSD is the sum of Gabor filter responses over scales and directions. The GaborD, GaborS and GaborSD representations are applied to the problem of recognizing people from their averaged gait images.A large number of experiments were carried out to evaluate the effectiveness (recognition rate) of gait recognition based on first obtaining a Gabor, GaborD, GaborS or GaborSD image representation, then using GDTA to extract features and finally using LDA for classification. The proposed methods achieved good performance for gait recognition based on image sequences from the USF HumanID Database. Experimental comparisons are made with nine state of the art classification methods in gait recognition.

Effects of Achieving Target Measures in Rheumatoid Arthritis on Functional Status, Quality of Life, and Resource Utilization: Analysis of Clinical Practice Data.

PubMed

Alemao, Evo; Joo, Seongjung; Kawabata, Hugh; Al, Maiwenn J; Allison, Paul D; Rutten-van Mölken, Maureen P M H; Frits, Michelle L; Iannaccone, Christine K; Shadick, Nancy A; Weinblatt, Michael E

2016-03-01

To evaluate associations between achieving guideline-recommended targets of disease activity, defined by the Disease Activity Score in 28 joints using C-reactive protein level (DAS28-CRP) <2.6, the Simplified Disease Activity Index (SDAI) ≤3.3, or the Clinical Disease Activity Index (CDAI) ≤2.8, and other health outcomes in a longitudinal observational study. Other defined thresholds included low disease activity (LDA), moderate (MDA), or severe disease activity (SDA). To control for intraclass correlation and estimate effects of independent variables on outcomes of the modified Health Assessment Questionnaire (M-HAQ), the EuroQol 5-domain (EQ-5D; a quality-of-life measure), hospitalization, and durable medical equipment (DME) use, we employed mixed models for continuous outcomes and generalized estimating equations for binary outcomes. Among 1,297 subjects, achievement (versus nonachievement) of recommended disease targets was associated with enhanced physical functioning and lower health resource utilization. After controlling for baseline covariates, achievement of disease targets (versus LDA) was associated with significantly enhanced physical functioning based on SDAI ≤3.3 (ΔM-HAQ -0.047; P = 0.0100) and CDAI ≤2.8 (-0.073; P = 0.0003) but not DAS28-CRP <2.6 (-0.022; P = 0.1735). Target attainment was associated with significantly improved EQ-5D (0.022-0.096; P < 0.0030 versus LDA, MDA, or SDA). Patients achieving guideline-recommended disease targets were 36-45% less likely to be hospitalized (P < 0.0500) and 23-45% less likely to utilize DME (P < 0.0100). Attaining recommended target disease-activity measures was associated with enhanced physical functioning and health-related quality of life. Some health outcomes were similar in subjects attaining guideline targets versus LDA. Achieving LDA is a worthy clinical objective in some patients. © 2016 The Authors. Arthritis Care & Research published by Wiley Periodicals, Inc. on behalf of the American College of Rheumatology.

Q-mode versus R-mode principal component analysis for linear discriminant analysis (LDA)

NASA Astrophysics Data System (ADS)

Lee, Loong Chuen; Liong, Choong-Yeun; Jemain, Abdul Aziz

2017-05-01

Many literature apply Principal Component Analysis (PCA) as either preliminary visualization or variable con-struction methods or both. Focus of PCA can be on the samples (R-mode PCA) or variables (Q-mode PCA). Traditionally, R-mode PCA has been the usual approach to reduce high-dimensionality data before the application of Linear Discriminant Analysis (LDA), to solve classification problems. Output from PCA composed of two new matrices known as loadings and scores matrices. Each matrix can then be used to produce a plot, i.e. loadings plot aids identification of important variables whereas scores plot presents spatial distribution of samples on new axes that are also known as Principal Components (PCs). Fundamentally, the scores matrix always be the input variables for building classification model. A recent paper uses Q-mode PCA but the focus of analysis was not on the variables but instead on the samples. As a result, the authors have exchanged the use of both loadings and scores plots in which clustering of samples was studied using loadings plot whereas scores plot has been used to identify important manifest variables. Therefore, the aim of this study is to statistically validate the proposed practice. Evaluation is based on performance of external error obtained from LDA models according to number of PCs. On top of that, bootstrapping was also conducted to evaluate the external error of each of the LDA models. Results show that LDA models produced by PCs from R-mode PCA give logical performance and the matched external error are also unbiased whereas the ones produced with Q-mode PCA show the opposites. With that, we concluded that PCs produced from Q-mode is not statistically stable and thus should not be applied to problems of classifying samples, but variables. We hope this paper will provide some insights on the disputable issues.

Efficacy of ABT-116, an antagonist of transient receptor potential vanilloid type 1, in providing analgesia for dogs with chemically induced synovitis.

PubMed

Cathcart, Curtis J; Johnston, Spencer A; Reynolds, Lisa R; Al-Nadaf, Sami; Budsberg, Steven C

2012-01-01

To investigate the ability of ABT-116 (a proprietary antagonist of transient receptor potential vanilloid type 1) administered at 2 doses to attenuate lameness in dogs with experimentally induced urate synovitis. 8 purpose-bred mixed-breed dogs. In a 4-way crossover study, dogs orally received each of low-dose ABT-116 treatment (LDA; 10 mg/kg), high-dose ABT-116 treatment (HDA; 30 mg/kg), firocoxib (5 mg/kg), and no treatment (nontreatment) once a day for 2 days, in a randomly assigned order. Synovitis was induced on the second day of each treatment period by intra-articular injection of either stifle joint with sodium urate, alternating between joints for each treatment period, beginning with the left stifle joint. Ground reaction forces, clinical lameness scores, and rectal temperature were assessed before the injection (baseline) and at various points afterward. Lameness scores at the 2-, 6-, and 12-hour assessment points were higher than baseline scores for HDA and nontreatment, whereas scores at the 2- and 6-hour points were higher than baseline scores for LDA. For firocoxib, there was no difference from baseline scores in lameness scores at any point. Compared with baseline values, peak vertical force and vertical impulse were lower at 2 and 6 hours for HDA and nontreatment and at 2 hours for LDA. No changes in these values were evident for firocoxib. The HDA or LDA resulted in higher rectal temperatures than did treatment with firocoxib or nothing, but those temperatures did not differ among treatments. HDA had no apparent effect on sodium urate-induced lameness; LDA did attenuate the lameness but not as completely as firocoxib treatment. High rectal temperature is an adverse effect of oral ABT-116 administration that may be of clinical concern.

Key determinants of the fungal and bacterial microbiomes in homes.

PubMed

Kettleson, Eric M; Adhikari, Atin; Vesper, Stephen; Coombs, Kanistha; Indugula, Reshmi; Reponen, Tiina

2015-04-01

The microbiome of the home is of great interest because of its possible impact on health. Our goal was to identify some of the factors that determine the richness, evenness and diversity of the home's fungal and bacterial microbiomes. Vacuumed settled dust from homes (n=35) in Cincinnati, OH, were analyzed by pyrosequencing to determine the fungal and bacterial relative sequence occurrence. The correlation coefficients between home environmental characteristics, including age of home, Environmental Relative Moldiness Index (ERMI) values, occupant number, relative humidity and temperature, as well as pets (dog and cat) were evaluated for their influence on fungal and bacterial communities. In addition, linear discriminant analysis (LDA) was used for identifying fungal and bacterial genera and species associated with those housing determinants found to be significant. The fungal richness was found to be positively correlated with age of home (p=0.002), ERMI value (p=0.003), and relative humidity (p=0.015) in the home. However, fungal evenness and diversity were only correlated with the age of home (p=0.001). Diversity and evenness (not richness) of the bacterial microbiome in the homes were associated with dog ownership. Linear discriminant analysis showed total of 39 putative fungal genera/species with significantly higher LDA scores in high ERMI homes and 47 genera/species with significantly higher LDA scores in homes with high relative humidity. When categorized according to the age of the home, a total of 67 fungal genera/species had LDA scores above the significance threshold. Dog ownership appeared to have the most influence on the bacterial microbiome, since a total of 130 bacterial genera/species had significantly higher LDA scores in homes with dogs. Some key determinants of the fungal and bacterial microbiome appear to be excess moisture, age of the home and dog ownership. Copyright © 2015 Elsevier Inc. All rights reserved.

First-principles study of the covalently functionalized graphene

NASA Astrophysics Data System (ADS)

Jha, Sanjiv Kumar

Theoretical investigations of nanoscale systems, such as functionalized graphene, present major challenges to conventional computational methods employed in quantum chemistry and solid state physics. The properties of graphene can be affected by chemical functionalization. The surface functionalization of graphene offers a promising way to increase the solubility and reactivity of graphene for use in nanocomposites and chemical sensors. Covalent functionalization is an efficient way to open band-gap in graphene for applications in nanoelectronics. We apply ab initio computational methods based on density functional theory to study the covalent functionalization of graphene with benzyne (C6H4), tetracyanoethylene oxide (TCNEO), and carboxyl (COOH) groups. Our calculations are carried out using the SIESTA and Quantum-ESPRESSO electronic structure codes combined with the generalized gradient (GGA) and local density approximations (LDA) for the exchange correlation functionals and norm-conserving Troullier-Martins pseudopotentials. Calculated binding energies, densities of states (DOS), band structures, and vibrational spectra of functionalized graphene are analyzed in comparison with the available experimental data. Our calculations show that the reactions of [2 + 2] and [2 + 4] cycloaddition of C6H4 to the surface of pristine graphene are exothermic, with binding energies of --0.73 eV and --0.58 eV, respectively. Calculated band structures indicate that the [2 + 2] and [2 + 4] attachments of benzyne results in opening small band gap in graphene. The study of graphene--TCNEO interactions suggests that the reaction of cycloaddition of TCNEO to the surface of pristine graphene is endothermic. On the other hand, the reaction of cycloaddition of TCNEO is found to be exothermic for the edge of an H-terminated graphene sheet. Simulated Raman and infrared spectra of graphene functionalized with TCNEO are consistent with experimental results. The Raman (non-resonant) and infrared (IR) spectra of graphene functionalized with carboxyl (COON) groups are studied in graphene with no surface defects, di-vacancies (DV), and Stone-Wales (SW) defects. Simulated Raman and IR spectra of carboxylated graphene are consistent with available experimental results. Computed vibrational spectra of carboxylated graphene show that the presence of point defects near the functionalization site affect the Raman and IR spectroscopic signatures of the functionalized graphene.

Towards a Simple and Efficient Web Search Framework

DTIC Science & Technology

2014-11-01

any useful information about the various aspects of a topic. For example, for the query “ raspberry pi ”, it covers topics such as “what is raspberry pi ...topics generated by the LDA topic model for query ” raspberry pi ”. One simple explanation is that web texts are too noisy and unfocused for the LDA process...making a rasp- berry pi ”. However, the topics generated based on the 10 top ranked documents do not make much sense to us in terms of their keywords

REVIEW ARTICLE: Phonons and magnetoelectric interactions in Ni3V2O8

NASA Astrophysics Data System (ADS)

Yildirim, T.; Vergara, L. I.; Íñiguez, Jorge; Musfeldt, J. L.; Harris, A. B.; Rogado, N.; Cava, R. J.; Yen, F.; Chaudhury, R. P.; Lorenz, B.

2008-10-01

We present a detailed study of the zone-center phonons and magnetoelectric interactions in Ni3V2O8. Using combined neutron scattering, polarized infrared (IR) measurements and first-principles LDA+U calculations, we successfully assigned all IR-active modes, including eleven B2u phonons which can induce the observed spontaneous electric polarization. We also calculated the Born-effective charges and the IR intensities which are in surprisingly good agreement with the experimental data. Among the eleven B2u phonons, we find that only a few of them can actually induce a significant dipole moment. The exchange interactions up to a cutoff of 6.5 Å are also calculated within the LDA+U approach with different values of U for Ni, V and O atoms. We find that LSDA (i.e. U = 0) gives excellent results concerning the optimized atomic positions, bandgap and phonon energies. However, the magnitudes of the exchange constants are too large compared to the experimental Curie-Weiss constant, Θ. Including U for Ni corrects the magnitude of the superexchange constants but opens a too large electronic bandgap. We observe that including correlation at the O site is very important to get simultaneously the correct phonon energies, bandgap and exchange constants. In particular, the nearest and next-nearest exchange constants along the Ni-spine sites result in incommensurate spin ordering with a wavevector that is consistent with the experimental data. Our results also explain how the antiferromagnetic coupling between sublattices in the b and c directions is consistent with the relatively small observed value of Θ. We also find that, regardless of the values of U used, we always get the same five exchange constants that are significantly larger than the rest. Finally, we discuss how the B2u phonons and the spin structure combine to yield the observed spontaneous polarization. We present a simple phenomenological model which shows how trilinear (and quartic) couplings of one (or two) phonons to two spin operators perturbatively affects the magnon (i.e. electromagnon) and phonon energies.

The dispersion of particles in a separated backward-facing step flow

NASA Astrophysics Data System (ADS)

Ruck, B.; Makiola, B.

1991-05-01

Flows in technical and natural circuits often involve a particulate phase. To measure the dynamics of suspended, naturally resident or artificially seeded particles in the flow, optical measuring techniques, e.g., laser Doppler anemometry (LDA) can be used advantageously. In this paper the dispersion of particles in a single-sided backward-facing step flow is investigated by LDA. The investigation is of relevance for both, two-phase flow problems in separated flows with the associated particle diameter range of 1-70 μm and the accuracy of LDA with tracer particles of different sizes. The latter is of interest for all LDA applications to measure continuous phase properties, where interest for experimental restraints require tracer diameters in the upper micrometer range, e.g., flame resistant particles for measurements inside reactors, cylinders, etc. For the experiments, a closed-loop wind tunnel with a step expansion was used. Part of this tunnel, the test section, was made of glass. The step had a height H=25 mm (channel height before the step 25 mm, after 50 mm, i.e., an expansion ratio of 2). The width of the channel was 500 mm. The length of the glass test section was chosen as 116 step heights. The wind tunnel, driven by a radial fan, allowed flow velocities up to 50 m/sec which is equivalent to ReH=105. Seeding was performed with particles of well-known size: 1, 15, 30, and 70 μm in diameter. As 1 μm tracers oil droplets were used, whereas for the upper micron range starch particles (density 1.500 kg/m3) were chosen. Starch particles have a spherical shape and are not soluble in cold water. Particle velocities were measured locally using a conventional 1-D LDA system. The measurements deliver the resultant ``flow'' field information stemming from different particle size classes. Thus, the particle behavior in the separated flow field can be resolved. The results show that with increasing particle size, the particle velocity field differs increasingly from the flow field of the continuous phase (inferred from the smallest tracers used). The velocity fluctuations successively decrease with increasing particle diameter. In separation zones, bigger particles have a lower mean velocity than smaller ones. The opposite holds for the streamwise portions of the particle velocity field, where bigger particles show a higher velocity. The measurements give detailed insight into the particle dynamics in separated flow regions. LDA-measured dividing streamlines and lines of zero velocity of different particle classes in the recirculation region have been plotted and compared. In LDA the use of tracer particles in the upper micrometer size range leads to erroneous determinations of continuous phase flow characteristics. It turned out that the dimensions of the measured recirculation zones are reduced with increasing particle diameter. The physical reasons for these findings (relaxation time of particles, Stokes numbers, etc.) are explained in detail.

First-Principles Momentum-Dependent Local Ansatz Wavefunction and Momentum Distribution Function Bands of Iron

NASA Astrophysics Data System (ADS)

Kakehashi, Yoshiro; Chandra, Sumal

2016-04-01

We have developed a first-principles local ansatz wavefunction approach with momentum-dependent variational parameters on the basis of the tight-binding LDA+U Hamiltonian. The theory goes beyond the first-principles Gutzwiller approach and quantitatively describes correlated electron systems. Using the theory, we find that the momentum distribution function (MDF) bands of paramagnetic bcc Fe along high-symmetry lines show a large deviation from the Fermi-Dirac function for the d electrons with eg symmetry and yield the momentum-dependent mass enhancement factors. The calculated average mass enhancement m*/m = 1.65 is consistent with low-temperature specific heat data as well as recent angle-resolved photoemission spectroscopy (ARPES) data.

The impact of low-dose aspirin on preterm birth: secondary analysis of a randomized controlled trial.

PubMed

Allshouse, A A; Jessel, R H; Heyborne, K D

2016-06-01

The objective of this study is to determine whether low-dose aspirin (LDA) reduced the rate of preterm birth (PTB) in a cohort of women at high risk for preeclampsia. Secondary analysis of the Maternal-Fetal Medicine Units High-Risk Aspirin trial. Preterm births were categorized by phenotype: indicated, spontaneous or due to preterm premature rupture of membranes (PPROMs). Of 1789 randomized women, 30.5% delivered before 37 weeks (18.5% indicated, 5.8% spontaneous and 6.2% following preterm PPROMs). Among women randomized to LDA, we observed a trend favoring fewer PTBs due to spontaneous preterm labor and preterm PPROMs, odds ratio (OR: 0.826 (0.620, 1.099)); the incidence of indicated PTBs appeared unchanged, OR: 0.999 (0.787, 1.268). Although not reaching significance, we observed an effect size similar to other studies of both low- and high-risk women. These results support findings from other studies assessing LDA as a PTB prevention strategy.

Assessing college-level learning difficulties and "at riskness" for learning disabilities and ADHD: development and validation of the learning difficulties assessment.

PubMed

Kane, Steven T; Walker, John H; Schmidt, George R

2011-01-01

This article describes the development and validation of the Learning Difficulties Assessment (LDA), a normed and web-based survey that assesses perceived difficulties with reading, writing, spelling, mathematics, listening, concentration, memory, organizational skills, sense of control, and anxiety in college students. The LDA is designed to (a) map individual learning strengths and weaknesses, (b) provide users with a comparative sense of their academic skills, (c) integrate research in user-interface design to assist those with reading and learning challenges, and (d) identify individuals who may be at risk for learning disabilities and attention-deficit/hyperactivity disorder (ADHD) and who should thus be further assessed. Data from a large-scale 5-year study describing the instrument's validity as a screening tool for learning disabilities and ADHD are presented. This article also describes unique characteristics of the LDA including its user-interface design, normative characteristics, and use as a no-cost screening tool for identifying college students at risk for learning disorders and ADHD.

Mapping annotations with textual evidence using an scLDA model.

PubMed

Jin, Bo; Chen, Vicky; Chen, Lujia; Lu, Xinghua

2011-01-01

Most of the knowledge regarding genes and proteins is stored in biomedical literature as free text. Extracting information from complex biomedical texts demands techniques capable of inferring biological concepts from local text regions and mapping them to controlled vocabularies. To this end, we present a sentence-based correspondence latent Dirichlet allocation (scLDA) model which, when trained with a corpus of PubMed documents with known GO annotations, performs the following tasks: 1) learning major biological concepts from the corpus, 2) inferring the biological concepts existing within text regions (sentences), and 3) identifying the text regions in a document that provides evidence for the observed annotations. When applied to new gene-related documents, a trained scLDA model is capable of predicting GO annotations and identifying text regions as textual evidence supporting the predicted annotations. This study uses GO annotation data as a testbed; the approach can be generalized to other annotated data, such as MeSH and MEDLINE documents.

Supervised chemical pattern recognition in almond ( Prunus dulcis ) Portuguese PDO cultivars: PCA- and LDA-based triennial study.

PubMed

Barreira, João C M; Casal, Susana; Ferreira, Isabel C F R; Peres, António M; Pereira, José Alberto; Oliveira, M Beatriz P P

2012-09-26

Almonds harvested in three years in Trás-os-Montes (Portugal) were characterized to find differences among Protected Designation of Origin (PDO) Amêndoa Douro and commercial non-PDO cultivars. Nutritional parameters, fiber (neutral and acid detergent fibers, acid detergent lignin, and cellulose), fatty acids, triacylglycerols (TAG), and tocopherols were evaluated. Fat was the major component, followed by carbohydrates, protein, and moisture. Fatty acids were mostly detected as monounsaturated and polyunsaturated forms, with relevance of oleic and linoleic acids. Accordingly, 1,2,3-trioleoylglycerol and 1,2-dioleoyl-3-linoleoylglycerol were the major TAG. α-Tocopherol was the leading tocopherol. To verify statistical differences among PDO and non-PDO cultivars independent of the harvest year, data were analyzed through an analysis of variance, a principal component analysis, and a linear discriminant analysis (LDA). These differences identified classification parameters, providing an important tool for authenticity purposes. The best results were achieved with TAG analysis coupled with LDA, which proved its effectiveness to discriminate almond cultivars.

Palm vein recognition based on directional empirical mode decomposition

NASA Astrophysics Data System (ADS)

Lee, Jen-Chun; Chang, Chien-Ping; Chen, Wei-Kuei

2014-04-01

Directional empirical mode decomposition (DEMD) has recently been proposed to make empirical mode decomposition suitable for the processing of texture analysis. Using DEMD, samples are decomposed into a series of images, referred to as two-dimensional intrinsic mode functions (2-D IMFs), from finer to large scale. A DEMD-based 2 linear discriminant analysis (LDA) for palm vein recognition is proposed. The proposed method progresses through three steps: (i) a set of 2-D IMF features of various scale and orientation are extracted using DEMD, (ii) the 2LDA method is then applied to reduce the dimensionality of the feature space in both the row and column directions, and (iii) the nearest neighbor classifier is used for classification. We also propose two strategies for using the set of 2-D IMF features: ensemble DEMD vein representation (EDVR) and multichannel DEMD vein representation (MDVR). In experiments using palm vein databases, the proposed MDVR-based 2LDA method achieved recognition accuracy of 99.73%, thereby demonstrating its feasibility for palm vein recognition.

[Validity evidence of the Health-Related Quality of Life for Drug Abusers Test based on the Biaxial Model of Addiction].

PubMed

Lozano, Oscar M; Rojas, Antonio J; Pérez, Cristino; González-Sáiz, Francisco; Ballesta, Rosario; Izaskun, Bilbao

2008-05-01

The aim of this work is to show evidence of the validity of the Health-Related Quality of Life for Drug Abusers Test (HRQoLDA Test). This test was developed to measure specific HRQoL for drugs abusers, within the theoretical addiction framework of the biaxial model. The sample comprised 138 patients diagnosed with opiate drug dependence. In this study, the following constructs and variables of the biaxial model were measured: severity of dependence, physical health status, psychological adjustment and substance consumption. Results indicate that the HRQoLDA Test scores are related to dependency and consumption-related problems. Multiple regression analysis reveals that HRQoL can be predicted from drug dependence, physical health status and psychological adjustment. These results contribute empirical evidence of the theoretical relationships established between HRQoL and the biaxial model, and they support the interpretation of the HRQoLDA Test to measure HRQoL in drug abusers, thus providing a test to measure this specific construct in this population.

Interplay of the Glass Transition and the Liquid-Liquid Phase Transition in Water

PubMed Central

Giovambattista, Nicolas; Loerting, Thomas; Lukanov, Boris R.; Starr, Francis W.

2012-01-01

Water has multiple glassy states, often called amorphous ices. Low-density (LDA) and high-density (HDA) amorphous ice are separated by a dramatic, first-order like phase transition. It has been argued that the LDA-HDA transformation connects to a first-order liquid-liquid phase transition (LLPT) above the glass transition temperature Tg. Direct experimental evidence of the LLPT is challenging to obtain, since the LLPT occurs at conditions where water rapidly crystallizes. In this work, we explore the implications of a LLPT on the pressure dependence of Tg(P) for LDA and HDA by performing computer simulations of two water models – one with a LLPT, and one without. In the absence of a LLPT, Tg(P) for all glasses nearly coincide. When there is a LLPT, different glasses exhibit dramatically different Tg(P) which are directly linked with the LLPT. Available experimental data for Tg(P) are only consistent with the scenario including a LLPT. PMID:22550566

Interplay of the Glass Transition and the Liquid-Liquid Phase Transition in Water

NASA Astrophysics Data System (ADS)

Giovambattista, Nicolas; Loerting, Thomas; Lukanov, Boris R.; Starr, Francis W.

2012-05-01

Water has multiple glassy states, often called amorphous ices. Low-density (LDA) and high-density (HDA) amorphous ice are separated by a dramatic, first-order like phase transition. It has been argued that the LDA-HDA transformation connects to a first-order liquid-liquid phase transition (LLPT) above the glass transition temperature Tg. Direct experimental evidence of the LLPT is challenging to obtain, since the LLPT occurs at conditions where water rapidly crystallizes. In this work, we explore the implications of a LLPT on the pressure dependence of Tg(P) for LDA and HDA by performing computer simulations of two water models - one with a LLPT, and one without. In the absence of a LLPT, Tg(P) for all glasses nearly coincide. When there is a LLPT, different glasses exhibit dramatically different Tg(P) which are directly linked with the LLPT. Available experimental data for Tg(P) are only consistent with the scenario including a LLPT.

Mechanisms of anomalous compressibility of vitreous silica

NASA Astrophysics Data System (ADS)

Clark, Alisha N.; Lesher, Charles E.; Jacobsen, Steven D.; Sen, Sabyasachi

2014-11-01

The anomalous compressibility of vitreous silica has been known for nearly a century, but the mechanisms responsible for it remain poorly understood. Using GHz-ultrasonic interferometry, we measured longitudinal and transverse acoustic wave travel times at pressures up to 5 GPa in vitreous silica with fictive temperatures (Tf) ranging between 985 °C and 1500 °C. The maximum in ultrasonic wave travel times-corresponding to a minimum in acoustic velocities-shifts to higher pressure with increasing Tf for both acoustic waves, with complete reversibility below 5 GPa. These relationships reflect polyamorphism in the supercooled liquid, which results in a glassy state possessing different proportions of domains of high- and low-density amorphous phases (HDA and LDA, respectively). The relative proportion of HDA and LDA is set at Tf and remains fixed on compression below the permanent densification pressure. The bulk material exhibits compression behavior systematically dependent on synthesis conditions that arise from the presence of floppy modes in a mixture of HDA and LDA domains.

Mott Transition of MnO under Pressure: A Comparison of Correlated Band Theories

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kasinathan, Deepa; Kunes, Jan; Koepernik, K

The electronic structure, magnetic moment, and volume collapse of MnO under pressure are obtained from four different correlated band theory methods; local density approximation+Hubbard U (LDA+U), pseudopotential self-interaction correction (pseudo-SIC), the hybrid functional (combined local exchange plus Hartree-Fock exchange), and the local spin density SIC (SIC-LSD) method. Each method treats correlation among the five Mn 3d orbitals (per spin), including their hybridization with three O 2p orbitals in the valence bands and their changes with pressure. The focus is on comparison of the methods for rock salt MnO (neglecting the observed transition to the NiAs structure in the 90-100 GPamore » range). Each method predicts a first-order volume collapse, but with variation in the predicted volume and critical pressure. Accompanying the volume collapse is a moment collapse, which for all methods is from high-spin to low-spin ((5/2){yields}(1/2)), not to nonmagnetic as the simplest scenario would have. The specific manner in which the transition occurs varies considerably among the methods: pseudo-SIC and SIC-LSD give insulator-to-metal, while LDA+U gives insulator-to-insulator and the hybrid method gives an insulator-to-semimetal transition. Projected densities of states above and below the transition are presented for each of the methods and used to analyze the character of each transition. In some cases the rhombohedral symmetry of the antiferromagnetically ordered phase clearly influences the character of the transition.« less

Fourier transform infra-red spectroscopic signatures for lung cells' epithelial mesenchymal transition: A preliminary report

NASA Astrophysics Data System (ADS)

Sarkar, Atasi; Sengupta, Sanghamitra; Mukherjee, Anirban; Chatterjee, Jyotirmoy

2017-02-01

Infra red (IR) spectral characterization can provide label-free cellular metabolic signatures of normal and diseased circumstances in a rapid and non-invasive manner. Present study endeavoured to enlist Fourier transform infra red (FTIR) spectroscopic signatures for lung normal and cancer cells during chemically induced epithelial mesenchymal transition (EMT) for which global metabolic dimension is not well reported yet. Occurrence of EMT was validated with morphological and immunocytochemical confirmation. Pre-processed spectral data was analyzed using ANOVA and principal component analysis-linear discriminant analysis (PCA-LDA). Significant differences observed in peak area corresponding to biochemical fingerprint (900-1800 cm- 1) and high wave-number (2800-3800 cm- 1) regions contributed to adequate PCA-LDA segregation of cells undergoing EMT. The findings were validated by re-analysis of data using another in-house built binary classifier namely vector valued regularized kernel approximation (VVRKFA), in order to understand EMT progression. To improve the classification accuracy, forward feature selection (FFS) tool was employed in extracting potent spectral signatures by eliminating undesirable noise. Gradual increase in classification accuracy with EMT progression of both cell types indicated prominence of the biochemical alterations. Rapid changes in cellular metabolome noted in cancer cells within first 24 h of EMT induction along with higher classification accuracy for cancer cell groups in comparison to normal cells might be attributed to inherent differences between them. Spectral features were suggestive of EMT triggered changes in nucleic acid, protein, lipid and bound water contents which can emerge as the useful markers to capture EMT related cellular characteristics.

DFT study of the polarization behaviors of various distorted barium titanate crystals: The role of atomic displacements

NASA Astrophysics Data System (ADS)

Mirseraji, Mojtaba; Shahraki, Mehran Gholipour

2018-06-01

A Local Density Approximation (LDA) was employed to investigate the influence of applied strains on valence charge distributions, atomic displacements, Tisbnd O (3) bond distances and the total polarizations in barium titanate (BaTiO3). Four types of various strains were imposed on perfect tetragonal BaTiO3 along the a, c, ab and abc axial directions. Electromechanical properties of BaTiO3 were evaluated in LDA framework and a good agreement with previous results was achieved. The results show that, in the cases of a, ab strains, the values of polarization are almost constant in negative strains and increased by gradual increasing of the positive strains after a sudden enhancement at about +0.1% strain. In the case of c-strain, axial oxygen and Ti atoms underwent the highest displacements and the polarization linearly increased by applied strain. The case of abc-strain, represent the both types of features. In negative abc-strain show a similar polarization behavior like c-strain case and in positive region, polarization behavior is the same as a- and ab-strain cases. In the abc-strains of -0.3% and +0.1%, an abrupt jump in total polarization curve and a small change, are observed due to abnormal atomic displacements. In the most cases a direct relation between polarization and Tisbnd O (3) bond distance was also beheld. Finally, the effects of valence charge distributions on the atomic displacements and total polarizations are studied. It is found that there is a direct relation between polarization and Valence Charge Asymmetry of 3d -orbitals.

Discrimination of raw and processed Dipsacus asperoides by near infrared spectroscopy combined with least squares-support vector machine and random forests

NASA Astrophysics Data System (ADS)

Xin, Ni; Gu, Xiao-Feng; Wu, Hao; Hu, Yu-Zhu; Yang, Zhong-Lin

2012-04-01

Most herbal medicines could be processed to fulfill the different requirements of therapy. The purpose of this study was to discriminate between raw and processed Dipsacus asperoides, a common traditional Chinese medicine, based on their near infrared (NIR) spectra. Least squares-support vector machine (LS-SVM) and random forests (RF) were employed for full-spectrum classification. Three types of kernels, including linear kernel, polynomial kernel and radial basis function kernel (RBF), were checked for optimization of LS-SVM model. For comparison, a linear discriminant analysis (LDA) model was performed for classification, and the successive projections algorithm (SPA) was executed prior to building an LDA model to choose an appropriate subset of wavelengths. The three methods were applied to a dataset containing 40 raw herbs and 40 corresponding processed herbs. We ran 50 runs of 10-fold cross validation to evaluate the model's efficiency. The performance of the LS-SVM with RBF kernel (RBF LS-SVM) was better than the other two kernels. The RF, RBF LS-SVM and SPA-LDA successfully classified all test samples. The mean error rates for the 50 runs of 10-fold cross validation were 1.35% for RBF LS-SVM, 2.87% for RF, and 2.50% for SPA-LDA. The best classification results were obtained by using LS-SVM with RBF kernel, while RF was fast in the training and making predictions.

A Flow Cytometry-Based Assay for Quantifying Non-Plaque Forming Strains of Yellow Fever Virus

PubMed Central

Hammarlund, Erika; Amanna, Ian J.; Dubois, Melissa E.; Barron, Alex; Engelmann, Flora; Messaoudi, Ilhem; Slifka, Mark K.

2012-01-01

Primary clinical isolates of yellow fever virus can be difficult to quantitate by standard in vitro methods because they may not form discernable plaques or induce a measurable cytopathic effect (CPE) on cell monolayers. In our hands, the Dakar strain of yellow fever virus (YFV-Dakar) could not be measured by plaque assay (PA), focus-forming assay (FFA), or by measurement of CPE. For these reasons, we developed a YFV-specific monoclonal antibody (3A8.B6) and used it to optimize a highly sensitive flow cytometry-based tissue culture limiting dilution assay (TC-LDA) to measure levels of infectious virus. The TC-LDA was performed by incubating serial dilutions of virus in replicate wells of C6/36 cells and stained intracellularly for virus with MAb 3A8.B6. Using this approach, we could reproducibly quantitate YFV-Dakar in tissue culture supernatants as well as from the serum of viremic rhesus macaques experimentally infected with YFV-Dakar. Moreover, the TC-LDA approach was >10-fold more sensitive than standard plaque assay for quantitating typical plaque-forming strains of YFV including YFV-17D and YFV-FNV (French neurotropic vaccine). Together, these results indicate that the TC-LDA technique is effective for quantitating both plaque-forming and non-plaque-forming strains of yellow fever virus, and this methodology may be readily adapted for the study and quantitation of other non-plaque-forming viruses. PMID:23028428

A flow cytometry-based assay for quantifying non-plaque forming strains of yellow fever virus.

PubMed

Hammarlund, Erika; Amanna, Ian J; Dubois, Melissa E; Barron, Alex; Engelmann, Flora; Messaoudi, Ilhem; Slifka, Mark K

2012-01-01

Primary clinical isolates of yellow fever virus can be difficult to quantitate by standard in vitro methods because they may not form discernable plaques or induce a measurable cytopathic effect (CPE) on cell monolayers. In our hands, the Dakar strain of yellow fever virus (YFV-Dakar) could not be measured by plaque assay (PA), focus-forming assay (FFA), or by measurement of CPE. For these reasons, we developed a YFV-specific monoclonal antibody (3A8.B6) and used it to optimize a highly sensitive flow cytometry-based tissue culture limiting dilution assay (TC-LDA) to measure levels of infectious virus. The TC-LDA was performed by incubating serial dilutions of virus in replicate wells of C6/36 cells and stained intracellularly for virus with MAb 3A8.B6. Using this approach, we could reproducibly quantitate YFV-Dakar in tissue culture supernatants as well as from the serum of viremic rhesus macaques experimentally infected with YFV-Dakar. Moreover, the TC-LDA approach was >10-fold more sensitive than standard plaque assay for quantitating typical plaque-forming strains of YFV including YFV-17D and YFV-FNV (French neurotropic vaccine). Together, these results indicate that the TC-LDA technique is effective for quantitating both plaque-forming and non-plaque-forming strains of yellow fever virus, and this methodology may be readily adapted for the study and quantitation of other non-plaque-forming viruses.

Cheap streak camera based on the LD-S-10 intensifier tube

NASA Astrophysics Data System (ADS)

Dashevsky, Boris E.; Krutik, Mikhail I.; Surovegin, Alexander L.

1992-01-01

Basic properties of a new streak camera and its test results are reported. To intensify images on its screen, we employed modular G1 tubes, the LD-A-1.0 and LD-A-0.33, enabling magnification of 1.0 and 0.33, respectively. If necessary, the LD-A-0.33 tube may be substituted by any other image intensifier of the LDA series, the choice to be determined by the size of the CCD matrix with fiber-optical windows. The reported camera employs a 12.5- mm-long CCD strip consisting of 1024 pixels, each 12 X 500 micrometers in size. Registered radiation was imaged on a 5 X 0.04 mm slit diaphragm tightly connected with the LD-S- 10 fiber-optical input window. Electrons escaping the cathode are accelerated in a 5 kV electric field and focused onto a phosphor screen covering a fiber-optical plate as they travel between deflection plates. Sensitivity of the latter was 18 V/mm, which implies that the total deflecting voltage was 720 V per 40 mm of the screen surface, since reversed-polarity scan pulses +360 V and -360 V were applied across the deflection plate. The streak camera provides full scan times over the screen of 15, 30, 50, 100, 250, and 500 ns. Timing of the electrically or optically driven camera was done using a 10 ns step-controlled-delay (0 - 500 ns) circuit.

Orbital-Dependent-Functionals within Density Functional Theory: Methodology and Applications

NASA Astrophysics Data System (ADS)

Makmal, Adi

I have designed and implemented a new numerical scheme for solving Kohn-Sham (KS) equations for diatomic systems, together with a full solution of the OEP equation. The equations are solved on a real-space prolate spheroidal coordinate grid, such that all the system's electrons are taken into account. The OEP equation is solved via the S-iteration scheme. This newly developed software package is called DARSEC (DiAtomic Real-Space Electronic structure Calculations). It involves no approximation except for the one inherent in the XC functional. Thus it is especially suitable for examining new functionals of any kind, and ODFs in particular. It is also an ideal tool for assessing the validity of commonly used approximations, for the same reasons. One case for which this uniqueness of DARSEC was exploited in this thesis is the examination of the validity of the pseudopotential approximation for KS gaps that are calculated with EXX OEP (xOEP). Before this study, use of the pseudopotential approximation in such calculations was called into question. I have shown that KS gaps obtained with pseudopotentials that have been constructed in a manner consistent with the exact-exchange functional agree with the all-electron results (i.e. without the pseudopotential approximation), for the cases studied. This confirmed the reliability of the pseudopotential approximation for ODFs such as EXX. Explicit density-dependent XC functionals traditionally fail to obtain atomization-energy as well as charge-dissociation curves that are, at least qualitatively, correct for diatomic systems. On the other hand, Hartree-Fock (HF) theory encounters no such problem. Hence, an additional goal of this research was to study the performances of the EXX functional (being the DFT counterpart of HF) in describing binding energies and charge dissociations for stretched diatomic molecules. Moreover, I wanted to investigate the special features of the resulting single and local EXX KS potential, as opposed to the non-local orbital specific HF potentials. I asked the following questions: Is it at all possible to obtain correct binding energy curves and charge dissociation curves with the local exact-exchange KS potential? What are the main features of such a local KS potential? And how are they related to the spatial shapes of the KS orbitals? To answer these questions, I calculated the electronic structures of highly stretched H2, HF and LiF molecules with EXX, using the Krieger, Li, and Iafrate (KLI) scheme. All calculations were done with DARSEC, whose coordinate system is highly suitable for calculating such stretched diatomic molecules. By examining several electronic configurations in a systematic manner, low energy ones were identified, and qualitatively correct binding-energy curves were obtained. For the LiF molecule a qualitatively correct charge separation curve was also achieved. Once the local EXX KLI potential was obtained for highly stretched diatomic systems, I could study its properties. Specifically, I have identified and demonstrated the following features: (a) The location and size of a constant shift in the potential and its relation to orbital spatial shapes; (b) The dependence of the shift's position on the inter-atomic separation length; (c) The existence of multiple constant shifts of the same kind; (d) The relation between the eigenvalues of the highly stretched diatomic system and the corresponding eigenvalues of the separated atoms - and how this relation is correlated with the asymptotic shift of the local potential. Understanding this unique combination of features sheds light on the mechanism with which the EXX potential enforces the correct charge dissociation. Last, a study on a novel ODF was initiated. The new ODF, suggested by Stephan Kummel, has a local function that mixes a fraction of EXX with a complementary fraction of exchange of the homogenous electronic gas (LDA), where a different fraction is assigned for each point in space. To derive the corresponding potential, the functional derivative of the new energy expression with respect to the KS orbitals was analytically derived. The new energy and potential expressions were implemented into DARSEC, and preliminary examinations were carried out. (Abstract shortened by UMI.)

Global hybrids from the semiclassical atom theory satisfying the local density linear response.

PubMed

Fabiano, Eduardo; Constantin, Lucian A; Cortona, Pietro; Della Sala, Fabio

2015-01-13

We propose global hybrid approximations of the exchange-correlation (XC) energy functional which reproduce well the modified fourth-order gradient expansion of the exchange energy in the semiclassical limit of many-electron neutral atoms and recover the full local density approximation (LDA) linear response. These XC functionals represent the hybrid versions of the APBE functional [Phys. Rev. Lett. 2011, 106, 186406] yet employing an additional correlation functional which uses the localization concept of the correlation energy density to improve the compatibility with the Hartree-Fock exchange as well as the coupling-constant-resolved XC potential energy. Broad energetic and structural testing, including thermochemistry and geometry, transition metal complexes, noncovalent interactions, gold clusters and small gold-molecule interfaces, as well as an analysis of the hybrid parameters, show that our construction is quite robust. In particular, our testing shows that the resulting hybrid, including 20% of Hartree-Fock exchange and named hAPBE, performs remarkably well for a broad palette of systems and properties, being generally better than popular hybrids (PBE0 and B3LYP). Semiempirical dispersion corrections are also provided.

Thermoelasticity of (Mg,Fe)SiO3 perovskite

NASA Astrophysics Data System (ADS)

Shukla, Gaurav; Wu, Zhongqing; Hsu, Han; Cococcioni, Matteo; Wentzcovitch, Renata

2015-03-01

We present LDA+U calculations of high temperature elastic properties of (Mg(1 - x)Fex2+)SiO3 bridgemanite (0 <= x <= 0 . 125), the most abundant constituent of Earth's lower mantle. Calculations of aggregate elastic moduli and acoustic velocities for the Mg-end member (x=0) are in excellent agreement with the latest high pressure and high temperature experimental measurements. In the iron bearing system, we particularly focus on the change in thermoelastic parameters across the state change that occurs in ferrous iron above ~30 GPa, often attributed to a high-spin (HS) to intermediate spin (IS) crossover but explained by calculations as a lateral displacement of substitutional iron in the perovskite cage. We show that the measured effect on the equation of state of this change in the state of iron can be explained by the lateral displacement of substitutional iron, not by the HS to IS crossover. Calculated elastic properties of (Mg0.875 Fe0.125 2 +)SiO3 along an adiabatic mantle geotherm, somewhat overestimate longitudinal velocities but produce densities and shear velocities consistent with Preliminary Reference Earth Model data throughout most of the lower mantle. Research supported by NSF/EAR and NSF/CAREER.

Migratory resonances and Wigner timers in the photoionization of fullerene class of molecules

NASA Astrophysics Data System (ADS)

Chakraborty, Himadri

2017-04-01

Empty fullerenes and atom-encaging endofullerenes are quintessential symmetric molecules exhibiting near stability in the room temperature. This property endows them with the quality to be tested for spectroscopic information otherwise inaccessible with regular atoms and molecules. Probing the response of fullerenes and endofullerenes to electromagnetic radiations is one classic way to accomplish this. Conventional spectroscopy of determining the photoelectron count and kinetic energy, as the frequency of the incoming photons varies, predicts varieties of resonances for such molecules. These resonances fundamentally originate from either the correlated electronic motions leading to plasmons or from the molecule's structural symmetry inducing diffractions or even from the mixing of both these effects in tandem. A particularly exotic class of these resonances, which will be emphasized in the talk, includes photoexcitation at one site of the molecule but its subsequent decay at a different location, as well as a coherent admixture of this mechanism with localized Auger processes. The other part of the talk will be devoted to connect to a more contemporary form of spectroscopy by evaluating the time-of-flight of the photoelectron, starting from its production at the molecule to the detector. This utilizes a Wigner clock based on the knowledge of energy-dependent photoelectron quantum phase. It will be shown that the information that can be obtained from the knowledge of this time is often consistent with the underlying electron correlative dynamics, both at the energy region of the giant plasmon resonance and at the generic Cooper-type minima (or anti-resonances). A selection of the results will be presented which are computed by the density functional approximation. The ground state of the molecule is described in a local density approximation (LDA) framework with accurate exchange correlation potential. And a linear-response variant of LDA (TDLDA) is utilized to describe the interaction with the photon. Future research questions will be posed. Besides two postdocs, a PhD student, and the external collaborators, the program involved a large number of undergraduate students. The research is being funded by the US National Science Foundation.

A Theoretical Investigation of the Charge Transfer System TCNQ-F4 and Alpha-Sexithiophene

NASA Astrophysics Data System (ADS)

Braun, Kai-Felix

2005-03-01

The electronic and geometrical structures of the charge-transfer system of alpha-sexihiophene and tetrafluorotetracyanoquinodimethane are calculated self-consistently from first principles. By means of density functional theory (DFT) methods several configurations of the free molecules are calculated within LDA and B3LYP employing a plane wave basis and different atomic orbital sets. The combined system exhibits preferential binding of the center of the TCNQ-F4 on top of a c-c bond of the sexithiophene, thereby the central configuration having the lowest energy. As opposed to the periodic arrangement in a crystal of the related system dimethylquaterthiophene and TCNQ-F4, the free system exhibits a strong interaction going along with a substantial polarization of both molecules. For comparison with scanning tunneling spectroscopy results, the molecules were adsorbed in a parallel geometry on a Au(111) slab. To take into account the voltage applied to the STM tip the system was finally calculated within an electric field. This work is financially supported by the US-DOE grant no. DE-FG02-02ER46012.

Diffusion in liquid Germanium using ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Kulkarni, R. V.; Aulbur, W. G.; Stroud, D.

1996-03-01

We describe the results of calculations of the self-diffusion constant of liquid Ge over a range of temperatures. The calculations are carried out using an ab initio molecular dynamics scheme which combines an LDA model for the electronic structure with the Bachelet-Hamann-Schlüter norm-conserving pseudopotentials^1. The energies associated with electronic degrees of freedom are minimized using the Williams-Soler algorithm, and ionic moves are carried out using the Verlet algorithm. We use an energy cutoff of 10 Ry, which is sufficient to give results for the lattice constant and bulk modulus of crystalline Ge to within 1% and 12% of experiment. The program output includes not only the self-diffusion constant but also the structure factor, electronic density of states, and low-frequency electrical conductivity. We will compare our results with other ab initio and semi-empirical calculations, and discuss extension to impurity diffusion. ^1 We use the ab initio molecular dynamics code fhi94md, developed at 1cm the Fritz-Haber Institute, Berlin. ^2 Work supported by NASA, Grant NAG3-1437.

A theoretical study of structural and electronic properties of pentacene/Al(100) interface.

PubMed

Saranya, G; Nair, Shiny; Natarajan, V; Kolandaivel, P; Senthilkumar, K

2012-09-01

The first principle calculations within the framework of density functional theory have been performed for the pentacene molecule deposited on the aluminum Al(100) substrate to study the structural and electronic properties of the pentacene/Al(100) interface. The most stable configuration was found at bridge site with 45° rotation of the pentacene molecule on Al(100) surface with a vertical distance of 3.4 Å within LDA and 3.8 Å within GGA functionals. The calculated adsorption energy reveals that the adsorption of pentacene molecule on Al(100) surface is physisorption. For the stable adsorption geometry the electronic properties such as density of states (DOS), partial density of states (PDOS), Mulliken population analysis and Schottky barrier height are studied. The analysis of atomic charge, DOS and PDOS show that the charge is transferred from the Al(100) surface to pentacene molecule, and the transferred charge is about -0.05 electrons. For the adsorbed system, the calculated Schottky barrier height for hole and electron transport is 0.27 and 1.55 eV, respectively. Copyright © 2012 Elsevier Inc. All rights reserved.

WE-E-17A-02: Predictive Modeling of Outcome Following SABR for NSCLC Based On Radiomics of FDG-PET Images

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, R; Aguilera, T; Shultz, D

2014-06-15

Purpose: This study aims to develop predictive models of patient outcome by extracting advanced imaging features (i.e., Radiomics) from FDG-PET images. Methods: We acquired pre-treatment PET scans for 51 stage I NSCLC patients treated with SABR. We calculated 139 quantitative features from each patient PET image, including 5 morphological features, 8 statistical features, 27 texture features, and 100 features from the intensity-volume histogram. Based on the imaging features, we aim to distinguish between 2 risk groups of patients: those with regional failure or distant metastasis versus those without. We investigated 3 pattern classification algorithms: linear discriminant analysis (LDA), naive Bayesmore » (NB), and logistic regression (LR). To avoid the curse of dimensionality, we performed feature selection by first removing redundant features and then applying sequential forward selection using the wrapper approach. To evaluate the predictive performance, we performed 10-fold cross validation with 1000 random splits of the data and calculated the area under the ROC curve (AUC). Results: Feature selection identified 2 texture features (homogeneity and/or wavelet decompositions) for NB and LR, while for LDA SUVmax and one texture feature (correlation) were identified. All 3 classifiers achieved statistically significant improvements over conventional PET imaging metrics such as tumor volume (AUC = 0.668) and SUVmax (AUC = 0.737). Overall, NB achieved the best predictive performance (AUC = 0.806). This also compares favorably with MTV using the best threshold at an SUV of 11.6 (AUC = 0.746). At a sensitivity of 80%, NB achieved 69% specificity, while SUVmax and tumor volume only had 36% and 47% specificity. Conclusion: Through a systematic analysis of advanced PET imaging features, we are able to build models with improved predictive value over conventional imaging metrics. If validated in a large independent cohort, the proposed techniques could potentially aid in identifying patients who might benefit from adjuvant therapy.« less

Metabolomic fingerprinting employing DART-TOFMS for authentication of tomatoes and peppers from organic and conventional farming.

PubMed

Novotná, H; Kmiecik, O; Gałązka, M; Krtková, V; Hurajová, A; Schulzová, V; Hallmann, E; Rembiałkowska, E; Hajšlová, J

2012-01-01

The rapidly growing demand for organic food requires the availability of analytical tools enabling their authentication. Recently, metabolomic fingerprinting/profiling has been demonstrated as a challenging option for a comprehensive characterisation of small molecules occurring in plants, since their pattern may reflect the impact of various external factors. In a two-year pilot study, concerned with the classification of organic versus conventional crops, ambient mass spectrometry consisting of a direct analysis in real time (DART) ion source and a time-of-flight mass spectrometer (TOFMS) was employed. This novel methodology was tested on 40 tomato and 24 pepper samples grown under specified conditions. To calculate statistical models, the obtained data (mass spectra) were processed by the principal component analysis (PCA) followed by linear discriminant analysis (LDA). The results from the positive ionisation mode enabled better differentiation between organic and conventional samples than the results from the negative mode. In this case, the recognition ability obtained by LDA was 97.5% for tomato and 100% for pepper samples and the prediction abilities were above 80% for both sample sets. The results suggest that the year of production had stronger influence on the metabolomic fingerprints compared with the type of farming (organic versus conventional). In any case, DART-TOFMS is a promising tool for rapid screening of samples. Establishing comprehensive (multi-sample) long-term databases may further help to improve the quality of statistical classification models.

Structural and functional outcomes of a therapeutic strategy targeting low disease activity in patients with elderly-onset rheumatoid arthritis: a prospective cohort study (CRANE).

PubMed

Sugihara, Takahiko; Ishizaki, Tatsuro; Hosoya, Tadashi; Iga, Shoko; Yokoyama, Waka; Hirano, Fumio; Miyasaka, Nobuyuki; Harigai, Masayoshi

2015-05-01

The aim of this study was to evaluate structural damage and physical disability in patients with elderly-onset RA (EORA) who were treated in clinical practice with a therapeutic strategy targeting low disease activity (LDA). Data from 151 MTX-naive patients (mean age 74.9 years) with EORA from a prospective, monocentric registry were analysed. Treatment was adjusted every 3 months targeting LDA [28-joint DAS using ESR (DAS28-ESR) <3.2]. Treatment was initiated with non-biologic DMARDs (nbDMARDs), followed by TNF inhibitors (TNFis) or tocilizumab. The primary outcome was change from week 0 to week 52 in the modified total Sharp score (ΔmTSS). Secondary outcomes were derived from the HAQ Disability Index (HAQ-DI) and DAS28 at week 52. Predictors of clinically relevant radiographic progression [CRRP; ΔmTSS/year more than the smallest detectable change (2.1 points)] were examined using multivariate logistic regression models. Adherence to the treat-to-target strategy was observed in 83.4% of the 151 patients at week 24 and in 75.5% at week 52. At week 52, 67.6% of the patients were receiving a nbDMARD alone, 31.0% a TNFi with or without MTX and 1.4% tocilizumab. At week 52, structural remission (ΔmTSS/yr ≤0.5) was achieved in 49.7% of the patients, functional remission (HAQ-DI ≤0.5) in 63.4% and LDA in 51.0%. Clinical responses at weeks 12 and 24 were significant independent predictors of CRRP. Cumulative disease activity during the first 12 weeks predicted CRRP with a C-statistic of 0.888. Achieving structural remission, functional remission and LDA in clinical practice in EORA patients are realistic goals. Our results indicate significant benefits for a therapeutic strategy targeting LDA for EORA patients in clinical practice. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

[Vis-NIR spectroscopic pattern recognition combined with SG smoothing applied to breed screening of transgenic sugarcane].

PubMed

Liu, Gui-Song; Guo, Hao-Song; Pan, Tao; Wang, Ji-Hua; Cao, Gan

2014-10-01

Based on Savitzky-Golay (SG) smoothing screening, principal component analysis (PCA) combined with separately supervised linear discriminant analysis (LDA) and unsupervised hierarchical clustering analysis (HCA) were used for non-destructive visible and near-infrared (Vis-NIR) detection for breed screening of transgenic sugarcane. A random and stability-dependent framework of calibration, prediction, and validation was proposed. A total of 456 samples of sugarcane leaves planting in the elongating stage were collected from the field, which was composed of 306 transgenic (positive) samples containing Bt and Bar gene and 150 non-transgenic (negative) samples. A total of 156 samples (negative 50 and positive 106) were randomly selected as the validation set; the remaining samples (negative 100 and positive 200, a total of 300 samples) were used as the modeling set, and then the modeling set was subdivided into calibration (negative 50 and positive 100, a total of 150 samples) and prediction sets (negative 50 and positive 100, a total of 150 samples) for 50 times. The number of SG smoothing points was ex- panded, while some modes of higher derivative were removed because of small absolute value, and a total of 264 smoothing modes were used for screening. The pairwise combinations of first three principal components were used, and then the optimal combination of principal components was selected according to the model effect. Based on all divisions of calibration and prediction sets and all SG smoothing modes, the SG-PCA-LDA and SG-PCA-HCA models were established, the model parameters were optimized based on the average prediction effect for all divisions to produce modeling stability. Finally, the model validation was performed by validation set. With SG smoothing, the modeling accuracy and stability of PCA-LDA, PCA-HCA were signif- icantly improved. For the optimal SG-PCA-LDA model, the recognition rate of positive and negative validation samples were 94.3%, 96.0%; and were 92.5%, 98.0% for the optimal SG-PCA-LDA model, respectively. Vis-NIR spectro- scopic pattern recognition combined with SG smoothing could be used for accurate recognition of transgenic sugarcane leaves, and provided a convenient screening method for transgenic sugarcane breeding.

Application of FT-IR spectroscopy on breast cancer serum analysis

NASA Astrophysics Data System (ADS)

Elmi, Fatemeh; Movaghar, Afshin Fayyaz; Elmi, Maryam Mitra; Alinezhad, Heshmatollah; Nikbakhsh, Novin

2017-12-01

Breast cancer is regarded as the most malignant tumor among women throughout the world. Therefore, early detection and proper diagnostic methods have been known to help save women's lives. Fourier Transform Infrared (FT-IR) spectroscopy, coupled with PCA-LDA analysis, is a new technique to investigate the characteristics of serum in breast cancer. In this study, 43 breast cancer and 43 healthy serum samples were collected, and the FT-IR spectra were recorded for each one. Then, PCA analysis and linear discriminant analysis (LDA) were used to analyze the spectral data. The results showed that there were differences between the spectra of the two groups. Discriminating wavenumbers were associated with several spectral differences over the 950-1200 cm- 1(sugar), 1190-1350 cm- 1 (collagen), 1475-1710 cm- 1 (protein), 1710-1760 cm- 1 (ester), 2800-3000 cm- 1 (stretching motions of -CH2 & -CH3), and 3090-3700 cm- 1 (NH stretching) regions. PCA-LDA performance on serum IR could recognize changes between the control and the breast cancer cases. The diagnostic accuracy, sensitivity, and specificity of PCA-LDA analysis for 3000-3600 cm- 1 (NH stretching) were found to be 83%, 84%, 74% for the control and 80%, 76%, 72% for the breast cancer cases, respectively. The results showed that the major spectral differences between the two groups were related to the differences in protein conformation in serum samples. It can be concluded that FT-IR spectroscopy, together with multivariate data analysis, is able to discriminate between breast cancer and healthy serum samples.

PPIs Prevent Aspirin-Induced Gastrointestinal Bleeding Better than H2RAs. A Systematic Review and Meta-analysis.

PubMed

Szabó, Imre L; Mátics, Robert; Hegyi, Peter; Garami, Andras; Illés, Anita; Sarlós, Patricia; Bajor, Judit; Szűcs, Akos; Mosztbacher, Dora; Márta, Katalin; Szemes, Kata; Csekő, Kata; Kővári, Balint; Rumbus, Zoltan; Vincze, Áron

2017-12-01

Aspirin is one of the most widely used medication for its analgesic and anti-platelet properties and thus a major cause for gastrointestinal (GI) bleeding. This study compared the preventive effect of histamine-2 receptor antagonists (H2RAs) and proton-pump inhibitors (PPIs) against chronic low-dose aspirin (LDA)-related GI bleeding and ulcer formation. Electronic databases of Pubmed, Embase and Cochrane Central Register of Controlled Trials were searched for human observations (randomised controlled trials and observational studies) comparing the long term effects of PPIs and H2RAs treatment in the prevention of GI bleeding or ulcer formation in patients on chronic LDA treatment listed up till September 30, 2016. Two independent authors searched databases using PICO questions (aspirin, H2RA, PPI, GI bleeding or ulcer), and reviewed abstracts and articles for comprehensive studies keeping adequate study quality. Data of weighted odds ratios were statistically evaluated using Comprehensive Metaanalysis (Biostat, Inc., Engelwood, MJ, USA), potential bias was checked. Nine studies for GI bleeding and eight studies for ulcer formation were found meeting inclusion criteria, altogether 1,879 patients were included into review. The H2RAs prevented less effectively LDA-related GI bleeding (OR= 2.102, 95% CI: 1.008-4.385, p<0.048) and ulcer formation (OR= 2.257, 95% CI: 1.277-3.989, p<0.005) than PPIs. The meta-analysis showed that H2RAs were less effective in the prevention of LDA-related GI bleeding and ulcer formation suggesting the preferable usage of PPIs in case of tolerance.

Serum amyloid A and haptoglobin concentrations and liver fat percentage in lactating dairy cows with abomasal displacement.

PubMed

Guzelbektes, H; Sen, I; Ok, M; Constable, P D; Boydak, M; Coskun, A

2010-01-01

There has been increased interest in measuring the serum concentration of acute phase reactants such as serum amyloid A [SAA] and haptoglobin [haptoglobin] in periparturient cattle in order to provide a method for detecting the presence of inflammation or bacterial infection. To determine whether [SAA] and [haptoglobin] are increased in cows with displaced abomasum as compared with healthy dairy cows. Fifty-four adult dairy cows in early lactation that had left displaced abomasum (LDA, n = 34), right displaced abomasum or abomasal volvulus (RDA/AV, n = 11), or were healthy on physical examination (control, n = 9). Inflammatory diseases or bacterial infections such as mastitis, metritis, or pneumonia were not clinically apparent in any animal. Jugular venous blood was obtained from all cows and analyzed. Liver samples were obtained by biopsy in cattle with abomasal displacement. [SAA] and [haptoglobin] concentrations were increased in cows with LDA or RDA/AV as compared with healthy controls. Cows with displaced abomasum had mild to moderate hepatic lipidosis, based on liver fat percentages of 9.3 +/- 5.3% (mean +/- SD, LDA) and 10.8 +/- 7.7% (RDA/AV). [SAA] and [haptoglobin] were most strongly associated with liver fat percentage, r(s) = +0.55 (P < .0001) and r(s) = +0.42 (P = .0041), respectively. An increase in [SAA] or [haptoglobin] in postparturient dairy cows with LDA or RDA/AV is not specific for inflammation or bacterial infection. An increase in [SAA] or [haptoglobin] may indicate the presence of hepatic lipidosis in cattle with abomasal displacement.

Population differences in the postcrania of modern South Africans and the implications for ancestry estimation.

PubMed

Liebenberg, Leandi; L'Abbé, Ericka N; Stull, Kyra E

2015-12-01

The cranium is widely recognized as the most important skeletal element to use when evaluating population differences and estimating ancestry. However, the cranium is not always intact or available for analysis, which emphasizes the need for postcranial alternatives. The purpose of this study was to quantify postcraniometric differences among South Africans that can be used to estimate ancestry. Thirty-nine standard measurements from 11 postcranial bones were collected from 360 modern black, white and coloured South Africans; the sex and ancestry distribution were equal. Group differences were explored with analysis of variance (ANOVA) and Tukey's honestly significant difference (HSD) test. Linear and flexible discriminant analysis (LDA and FDA, respectively) were conducted with bone models as well as numerous multivariate subsets to identify the model and method that yielded the highest correct classifications. Leave-one-out (LDA) and k-fold (k=10; FDA) cross-validation with equal priors were used for all models. ANOVA and Tukey's HSD results reveal statistically significant differences between at least two of the three groups for the majority of the variables, with varying degrees of group overlap. Bone models, which consisted of all measurements per bone, resulted in low accuracies that ranged from 46% to 63% (LDA) and 41% to 66% (FDA). In contrast, the multivariate subsets, which consisted of different variable combinations from all elements, achieved accuracies as high as 85% (LDA) and 87% (FDA). Thus, when using a multivariate approach, the postcranial skeleton can distinguish among three modern South African groups with high accuracy. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Differentiation of cumin seeds using a metal-oxide based gas sensor array in tandem with chemometric tools.

PubMed

Ghasemi-Varnamkhasti, Mahdi; Amiri, Zahra Safari; Tohidi, Mojtaba; Dowlati, Majid; Mohtasebi, Seyed Saeid; Silva, Adenilton C; Fernandes, David D S; Araujo, Mário C U

2018-01-01

Cumin is a plant of the Apiaceae family (umbelliferae) which has been used since ancient times as a medicinal plant and as a spice. The difference in the percentage of aromatic compounds in cumin obtained from different locations has led to differentiation of some species of cumin from other species. The quality and price of cumin vary according to the specie and may be an incentive for the adulteration of high value samples with low quality cultivars. An electronic nose simulates the human olfactory sense by using an array of sensors to distinguish complex smells. This makes it an alternative for the identification and classification of cumin species. The data, however, may have a complex structure, difficult to interpret. Given this, chemometric tools can be used to manipulate data with two-dimensional structure (sensor responses in time) obtained by using electronic nose sensors. In this study, an electronic nose based on eight metal oxide semiconductor sensors (MOS) and 2D-LDA (two-dimensional linear discriminant analysis), U-PLS-DA (Partial least square discriminant analysis applied to the unfolded data) and PARAFAC-LDA (Parallel factor analysis with linear discriminant analysis) algorithms were used in order to identify and classify different varieties of both cultivated and wild black caraway and cumin. The proposed methodology presented a correct classification rate of 87.1% for PARAFAC-LDA and 100% for 2D-LDA and U-PLS-DA, indicating a promising strategy for the classification different varieties of cumin, caraway and other seeds. Copyright © 2017 Elsevier B.V. All rights reserved.

Volatile-Compound Fingerprinting by Headspace-Gas-Chromatography Ion-Mobility Spectrometry (HS-GC-IMS) as a Benchtop Alternative to 1H NMR Profiling for Assessment of the Authenticity of Honey.

PubMed

Gerhardt, Natalie; Birkenmeier, Markus; Schwolow, Sebastian; Rohn, Sascha; Weller, Philipp

2018-02-06

This work describes a simple approach for the untargeted profiling of volatile compounds for the authentication of the botanical origins of honey based on resolution-optimized HS-GC-IMS combined with optimized chemometric techniques, namely PCA, LDA, and kNN. A direct comparison of the PCA-LDA models between the HS-GC-IMS and 1 H NMR data demonstrated that HS-GC-IMS profiling could be used as a complementary tool to NMR-based profiling of honey samples. Whereas NMR profiling still requires comparatively precise sample preparation, pH adjustment in particular, HS-GC-IMS fingerprinting may be considered an alternative approach for a truly fully automatable, cost-efficient, and in particular highly sensitive method. It was demonstrated that all tested honey samples could be distinguished on the basis of their botanical origins. Loading plots revealed the volatile compounds responsible for the differences among the monofloral honeys. The HS-GC-IMS-based PCA-LDA model was composed of two linear functions of discrimination and 10 selected PCs that discriminated canola, acacia, and honeydew honeys with a predictive accuracy of 98.6%. Application of the LDA model to an external test set of 10 authentic honeys clearly proved the high predictive ability of the model by correctly classifying them into three variety groups with 100% correct classifications. The constructed model presents a simple and efficient method of analysis and may serve as a basis for the authentication of other food types.

Ethnicity identification from face images

NASA Astrophysics Data System (ADS)

Lu, Xiaoguang; Jain, Anil K.

2004-08-01

Human facial images provide the demographic information, such as ethnicity and gender. Conversely, ethnicity and gender also play an important role in face-related applications. Image-based ethnicity identification problem is addressed in a machine learning framework. The Linear Discriminant Analysis (LDA) based scheme is presented for the two-class (Asian vs. non-Asian) ethnicity classification task. Multiscale analysis is applied to the input facial images. An ensemble framework, which integrates the LDA analysis for the input face images at different scales, is proposed to further improve the classification performance. The product rule is used as the combination strategy in the ensemble. Experimental results based on a face database containing 263 subjects (2,630 face images, with equal balance between the two classes) are promising, indicating that LDA and the proposed ensemble framework have sufficient discriminative power for the ethnicity classification problem. The normalized ethnicity classification scores can be helpful in the facial identity recognition. Useful as a "soft" biometric, face matching scores can be updated based on the output of ethnicity classification module. In other words, ethnicity classifier does not have to be perfect to be useful in practice.

Mining Adverse Events of Dietary Supplements from Product Labels by Topic Modeling.

PubMed

Wang, Yefeng; Gunashekar, Divya R; Adam, Terrence J; Zhang, Rui

2017-01-01

The adverse events of the dietary supplements should be subject to scrutiny due to their growing clinical application and consumption among U.S. adults. An effective method for mining and grouping the adverse events of the dietary supplements is to evaluate product labeling for the rapidly increasing number of new products available in the market. In this study, the adverse events information was extracted from the product labels stored in the Dietary Supplement Label Data-base (DSLD) and analyzed by topic modeling techniques, specifically Latent Dirichlet Allocation (LDA). Among the 50 topics generated by LDA, eight topics were manually evaluated, with topic relatedness ranging from 58.8% to 100% on the product level, and 57.1% to 100% on the ingredient level. Five out of these eight topics were coherent groupings of the dietary supplements based on their adverse events. The results demonstrated that LDA is able to group supplements with similar adverse events based on the dietary supplement labels. Such information can be potentially used by consumers to more safely use dietary supplements.

Protein Sub-Nuclear Localization Based on Effective Fusion Representations and Dimension Reduction Algorithm LDA.

PubMed

Wang, Shunfang; Liu, Shuhui

2015-12-19

An effective representation of a protein sequence plays a crucial role in protein sub-nuclear localization. The existing representations, such as dipeptide composition (DipC), pseudo-amino acid composition (PseAAC) and position specific scoring matrix (PSSM), are insufficient to represent protein sequence due to their single perspectives. Thus, this paper proposes two fusion feature representations of DipPSSM and PseAAPSSM to integrate PSSM with DipC and PseAAC, respectively. When constructing each fusion representation, we introduce the balance factors to value the importance of its components. The optimal values of the balance factors are sought by genetic algorithm. Due to the high dimensionality of the proposed representations, linear discriminant analysis (LDA) is used to find its important low dimensional structure, which is essential for classification and location prediction. The numerical experiments on two public datasets with KNN classifier and cross-validation tests showed that in terms of the common indexes of sensitivity, specificity, accuracy and MCC, the proposed fusing representations outperform the traditional representations in protein sub-nuclear localization, and the representation treated by LDA outperforms the untreated one.

Decoding magnetoencephalographic rhythmic activity using spectrospatial information.

PubMed

Kauppi, Jukka-Pekka; Parkkonen, Lauri; Hari, Riitta; Hyvärinen, Aapo

2013-12-01

We propose a new data-driven decoding method called Spectral Linear Discriminant Analysis (Spectral LDA) for the analysis of magnetoencephalography (MEG). The method allows investigation of changes in rhythmic neural activity as a result of different stimuli and tasks. The introduced classification model only assumes that each "brain state" can be characterized as a combination of neural sources, each of which shows rhythmic activity at one or several frequency bands. Furthermore, the model allows the oscillation frequencies to be different for each such state. We present decoding results from 9 subjects in a four-category classification problem defined by an experiment involving randomly alternating epochs of auditory, visual and tactile stimuli interspersed with rest periods. The performance of Spectral LDA was very competitive compared with four alternative classifiers based on different assumptions concerning the organization of rhythmic brain activity. In addition, the spectral and spatial patterns extracted automatically on the basis of trained classifiers showed that Spectral LDA offers a novel and interesting way of analyzing spectrospatial oscillatory neural activity across the brain. All the presented classification methods and visualization tools are freely available as a Matlab toolbox. © 2013.

Detection of nasopharyngeal cancer using confocal Raman spectroscopy and genetic algorithm technique

NASA Astrophysics Data System (ADS)

Li, Shao-Xin; Chen, Qiu-Yan; Zhang, Yan-Jiao; Liu, Zhi-Ming; Xiong, Hong-Lian; Guo, Zhou-Yi; Mai, Hai-Qiang; Liu, Song-Hao

2012-12-01

Raman spectroscopy (RS) and a genetic algorithm (GA) were applied to distinguish nasopharyngeal cancer (NPC) from normal nasopharyngeal tissue. A total of 225 Raman spectra are acquired from 120 tissue sites of 63 nasopharyngeal patients, 56 Raman spectra from normal tissue and 169 Raman spectra from NPC tissue. The GA integrated with linear discriminant analysis (LDA) is developed to differentiate NPC and normal tissue according to spectral variables in the selected regions of 792-805, 867-880, 996-1009, 1086-1099, 1288-1304, 1663-1670, and 1742-1752 cm-1 related to proteins, nucleic acids and lipids of tissue. The GA-LDA algorithms with the leave-one-out cross-validation method provide a sensitivity of 69.2% and specificity of 100%. The results are better than that of principal component analysis which is applied to the same Raman dataset of nasopharyngeal tissue with a sensitivity of 63.3% and specificity of 94.6%. This demonstrates that Raman spectroscopy associated with GA-LDA diagnostic algorithm has enormous potential to detect and diagnose nasopharyngeal cancer.

Mining Adverse Events of Dietary Supplements from Product Labels by Topic Modeling

PubMed Central

Wang, Yefeng; Gunashekar, Divya R.; Adam, Terrence J.; Zhang, Rui

2018-01-01

The adverse events of the dietary supplements should be subject to scrutiny due to their growing clinical application and consumption among U.S. adults. An effective method for mining and grouping the adverse events of the dietary supplements is to evaluate product labeling for the rapidly increasing number of new products available in the market. In this study, the adverse events information was extracted from the product labels stored in the Dietary Supplement Label Database (DSLD) and analyzed by topic modeling techniques, specifically Latent Dirichlet Allocation (LDA). Among the 50 topics generated by LDA, eight topics were manually evaluated, with topic relatedness ranging from 58.8% to 100% on the product level, and 57.1% to 100% on the ingredient level. Five out of these eight topics were coherent groupings of the dietary supplements based on their adverse events. The results demonstrated that LDA is able to group supplements with similar adverse events based on the dietary supplement labels. Such information can be potentially used by consumers to more safely use dietary supplements. PMID:29295169

Pattern Recognition Approaches for Breast Cancer DCE-MRI Classification: A Systematic Review.

PubMed

Fusco, Roberta; Sansone, Mario; Filice, Salvatore; Carone, Guglielmo; Amato, Daniela Maria; Sansone, Carlo; Petrillo, Antonella

2016-01-01

We performed a systematic review of several pattern analysis approaches for classifying breast lesions using dynamic, morphological, and textural features in dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). Several machine learning approaches, namely artificial neural networks (ANN), support vector machines (SVM), linear discriminant analysis (LDA), tree-based classifiers (TC), and Bayesian classifiers (BC), and features used for classification are described. The findings of a systematic review of 26 studies are presented. The sensitivity and specificity are respectively 91 and 83 % for ANN, 85 and 82 % for SVM, 96 and 85 % for LDA, 92 and 87 % for TC, and 82 and 85 % for BC. The sensitivity and specificity are respectively 82 and 74 % for dynamic features, 93 and 60 % for morphological features, 88 and 81 % for textural features, 95 and 86 % for a combination of dynamic and morphological features, and 88 and 84 % for a combination of dynamic, morphological, and other features. LDA and TC have the best performance. A combination of dynamic and morphological features gives the best performance.

Pressure-induced transformations in amorphous silicon: A computational study

NASA Astrophysics Data System (ADS)

Garcez, K. M. S.; Antonelli, A.

2014-02-01

We study the transformations between amorphous phases of Si through molecular simulations using the environment dependent interatomic potential (EDIP) for Si. Our results show that upon pressure, the material undergoes a transformation from the low density amorphous (LDA) Si to the high density amorphous (HDA) Si. This transformation can be reversed by decompressing the material. This process, however, exhibits clear hysteresis, suggesting that the transformation LDA ↔ HDA is first-order like. The HDA phase is predominantly five-fold coordinated, whereas the LDA phase is the normal tetrahedrally bonded amorphous Si. The HDA phase at 400 K and 20 GPa was submitted to an isobaric annealing up to 800 K, resulting in a denser amorphous phase, which is structurally distinct from the HDA phase. Our results also show that the atomic volume and structure of this new amorphous phase are identical to those of the glass obtained by an isobaric quenching of the liquid in equilibrium at 2000 K and 20 GPa down to 400 K. The similarities between our results and those for amorphous ices suggest that this new phase is the very high density amorphous Si.

Discrimination and characterization of strawberry juice based on electronic nose and tongue: comparison of different juice processing approaches by LDA, PLSR, RF, and SVM.

PubMed

Qiu, Shanshan; Wang, Jun; Gao, Liping

2014-07-09

An electronic nose (E-nose) and an electronic tongue (E-tongue) have been used to characterize five types of strawberry juices based on processing approaches (i.e., microwave pasteurization, steam blanching, high temperature short time pasteurization, frozen-thawed, and freshly squeezed). Juice quality parameters (vitamin C, pH, total soluble solid, total acid, and sugar/acid ratio) were detected by traditional measuring methods. Multivariate statistical methods (linear discriminant analysis (LDA) and partial least squares regression (PLSR)) and neural networks (Random Forest (RF) and Support Vector Machines) were employed to qualitative classification and quantitative regression. E-tongue system reached higher accuracy rates than E-nose did, and the simultaneous utilization did have an advantage in LDA classification and PLSR regression. According to cross-validation, RF has shown outstanding and indisputable performances in the qualitative and quantitative analysis. This work indicates that the simultaneous utilization of E-nose and E-tongue can discriminate processed fruit juices and predict quality parameters successfully for the beverage industry.

Screening analysis of biodiesel feedstock using UV-vis, NIR and synchronous fluorescence spectrometries and the successive projections algorithm.

PubMed

Insausti, Matías; Gomes, Adriano A; Cruz, Fernanda V; Pistonesi, Marcelo F; Araujo, Mario C U; Galvão, Roberto K H; Pereira, Claudete F; Band, Beatriz S F

2012-08-15

This paper investigates the use of UV-vis, near infrared (NIR) and synchronous fluorescence (SF) spectrometries coupled with multivariate classification methods to discriminate biodiesel samples with respect to the base oil employed in their production. More specifically, the present work extends previous studies by investigating the discrimination of corn-based biodiesel from two other biodiesel types (sunflower and soybean). Two classification methods are compared, namely full-spectrum SIMCA (soft independent modelling of class analogies) and SPA-LDA (linear discriminant analysis with variables selected by the successive projections algorithm). Regardless of the spectrometric technique employed, full-spectrum SIMCA did not provide an appropriate discrimination of the three biodiesel types. In contrast, all samples were correctly classified on the basis of a reduced number of wavelengths selected by SPA-LDA. It can be concluded that UV-vis, NIR and SF spectrometries can be successfully employed to discriminate corn-based biodiesel from the two other biodiesel types, but wavelength selection by SPA-LDA is key to the proper separation of the classes. Copyright © 2012 Elsevier B.V. All rights reserved.

Protein Sub-Nuclear Localization Based on Effective Fusion Representations and Dimension Reduction Algorithm LDA

PubMed Central

Wang, Shunfang; Liu, Shuhui

2015-01-01

An effective representation of a protein sequence plays a crucial role in protein sub-nuclear localization. The existing representations, such as dipeptide composition (DipC), pseudo-amino acid composition (PseAAC) and position specific scoring matrix (PSSM), are insufficient to represent protein sequence due to their single perspectives. Thus, this paper proposes two fusion feature representations of DipPSSM and PseAAPSSM to integrate PSSM with DipC and PseAAC, respectively. When constructing each fusion representation, we introduce the balance factors to value the importance of its components. The optimal values of the balance factors are sought by genetic algorithm. Due to the high dimensionality of the proposed representations, linear discriminant analysis (LDA) is used to find its important low dimensional structure, which is essential for classification and location prediction. The numerical experiments on two public datasets with KNN classifier and cross-validation tests showed that in terms of the common indexes of sensitivity, specificity, accuracy and MCC, the proposed fusing representations outperform the traditional representations in protein sub-nuclear localization, and the representation treated by LDA outperforms the untreated one. PMID:26703574

Esophageal cancer detection based on tissue surface-enhanced Raman spectroscopy and multivariate analysis

NASA Astrophysics Data System (ADS)

Feng, Shangyuan; Lin, Juqiang; Huang, Zufang; Chen, Guannan; Chen, Weisheng; Wang, Yue; Chen, Rong; Zeng, Haishan

2013-01-01

The capability of using silver nanoparticle based near-infrared surface enhanced Raman scattering (SERS) spectroscopy combined with principal component analysis (PCA) and linear discriminate analysis (LDA) to differentiate esophageal cancer tissue from normal tissue was presented. Significant differences in Raman intensities of prominent SERS bands were observed between normal and cancer tissues. PCA-LDA multivariate analysis of the measured tissue SERS spectra achieved diagnostic sensitivity of 90.9% and specificity of 97.8%. This exploratory study demonstrated great potential for developing label-free tissue SERS analysis into a clinical tool for esophageal cancer detection.

Spectral discrimination of serum from liver cancer and liver cirrhosis using Raman spectroscopy

NASA Astrophysics Data System (ADS)

Yang, Tianyue; Li, Xiaozhou; Yu, Ting; Sun, Ruomin; Li, Siqi

2011-07-01

In this paper, Raman spectra of human serum were measured using Raman spectroscopy, then the spectra was analyzed by multivariate statistical methods of principal component analysis (PCA). Then linear discriminant analysis (LDA) was utilized to differentiate the loading score of different diseases as the diagnosing algorithm. Artificial neural network (ANN) was used for cross-validation. The diagnosis sensitivity and specificity by PCA-LDA are 88% and 79%, while that of the PCA-ANN are 89% and 95%. It can be seen that modern analyzing method is a useful tool for the analysis of serum spectra for diagnosing diseases.

Observation of polyamorphism in the phase change alloy Ge1Sb2Te4

NASA Astrophysics Data System (ADS)

Kalkan, B.; Sen, S.; Cho, J.-Y.; Joo, Y.-C.; Clark, S. M.

2012-10-01

A high-pressure synchrotron x-ray diffraction study of the phase change alloy Ge1Sb2Te4 demonstrates the existence of a polyamorphic phase transition between the "as deposited" low density amorphous (LDA) phase and a high density amorphous (HDA) phase at ˜10 GPa. The entropy of the HDA phase is expected to be higher than that of the LDA phase resulting in a negative Clapeyron slope for this transition. These phase relations may enable the polyamorphic transition to play a role in the memory and data storage applications.

Ultra-slow dynamics in low density amorphous ice revealed by deuteron NMR: indication of a glass transition.

PubMed

Löw, Florian; Amann-Winkel, Katrin; Loerting, Thomas; Fujara, Franz; Geil, Burkhard

2013-06-21

The postulated glass-liquid transition of low density amorphous ice (LDA) is investigated with deuteron NMR stimulated echo experiments. Such experiments give access to ultra-slow reorientations of water molecules on time scales expected for structural relaxation of glass formers close to the glass-liquid transition temperature. An involved data analysis is necessary to account for signal contributions originating from a gradual crystallization to cubic ice. Even if some ambiguities remain, our findings support the view that pressure amorphized LDA ices are of glassy nature and undergo a glass-liquid transition before crystallization.

Effect of finite sample size on feature selection and classification: a simulation study.

PubMed

Way, Ted W; Sahiner, Berkman; Hadjiiski, Lubomir M; Chan, Heang-Ping

2010-02-01

The small number of samples available for training and testing is often the limiting factor in finding the most effective features and designing an optimal computer-aided diagnosis (CAD) system. Training on a limited set of samples introduces bias and variance in the performance of a CAD system relative to that trained with an infinite sample size. In this work, the authors conducted a simulation study to evaluate the performances of various combinations of classifiers and feature selection techniques and their dependence on the class distribution, dimensionality, and the training sample size. The understanding of these relationships will facilitate development of effective CAD systems under the constraint of limited available samples. Three feature selection techniques, the stepwise feature selection (SFS), sequential floating forward search (SFFS), and principal component analysis (PCA), and two commonly used classifiers, Fisher's linear discriminant analysis (LDA) and support vector machine (SVM), were investigated. Samples were drawn from multidimensional feature spaces of multivariate Gaussian distributions with equal or unequal covariance matrices and unequal means, and with equal covariance matrices and unequal means estimated from a clinical data set. Classifier performance was quantified by the area under the receiver operating characteristic curve Az. The mean Az values obtained by resubstitution and hold-out methods were evaluated for training sample sizes ranging from 15 to 100 per class. The number of simulated features available for selection was chosen to be 50, 100, and 200. It was found that the relative performance of the different combinations of classifier and feature selection method depends on the feature space distributions, the dimensionality, and the available training sample sizes. The LDA and SVM with radial kernel performed similarly for most of the conditions evaluated in this study, although the SVM classifier showed a slightly higher hold-out performance than LDA for some conditions and vice versa for other conditions. PCA was comparable to or better than SFS and SFFS for LDA at small samples sizes, but inferior for SVM with polynomial kernel. For the class distributions simulated from clinical data, PCA did not show advantages over the other two feature selection methods. Under this condition, the SVM with radial kernel performed better than the LDA when few training samples were available, while LDA performed better when a large number of training samples were available. None of the investigated feature selection-classifier combinations provided consistently superior performance under the studied conditions for different sample sizes and feature space distributions. In general, the SFFS method was comparable to the SFS method while PCA may have an advantage for Gaussian feature spaces with unequal covariance matrices. The performance of the SVM with radial kernel was better than, or comparable to, that of the SVM with polynomial kernel under most conditions studied.

Non-equilibrium thermodynamics theory of econometric source discovery for large data analysis

NASA Astrophysics Data System (ADS)

van Bergem, Rutger; Jenkins, Jeffrey; Benachenhou, Dalila; Szu, Harold

2014-05-01

Almost all consumer and firm transactions are achieved using computers and as a result gives rise to increasingly large amounts of data available for analysts. The gold standard in Economic data manipulation techniques matured during a period of limited data access, and the new Large Data Analysis (LDA) paradigm we all face may quickly obfuscate most tools used by Economists. When coupled with an increased availability of numerous unstructured, multi-modal data sets, the impending 'data tsunami' could have serious detrimental effects for Economic forecasting, analysis, and research in general. Given this reality we propose a decision-aid framework for Augmented-LDA (A-LDA) - a synergistic approach to LDA which combines traditional supervised, rule-based Machine Learning (ML) strategies to iteratively uncover hidden sources in large data, the artificial neural network (ANN) Unsupervised Learning (USL) at the minimum Helmholtz free energy for isothermal dynamic equilibrium strategies, and the Economic intuitions required to handle problems encountered when interpreting large amounts of Financial or Economic data. To make the ANN USL framework applicable to economics we define the temperature, entropy, and energy concepts in Economics from non-equilibrium molecular thermodynamics of Boltzmann viewpoint, as well as defining an information geometry, on which the ANN can operate using USL to reduce information saturation. An exemplar of such a system representation is given for firm industry equilibrium. We demonstrate the traditional ML methodology in the economics context and leverage firm financial data to explore a frontier concept known as behavioral heterogeneity. Behavioral heterogeneity on the firm level can be imagined as a firm's interactions with different types of Economic entities over time. These interactions could impose varying degrees of institutional constraints on a firm's business behavior. We specifically look at behavioral heterogeneity for firms that are operating with the label of `Going-Concern' and firms labeled according to institutional influence they may be experiencing, such as constraints on firm hiring/spending while in a Bankruptcy or a Merger procedure. Uncovering invariant features, or behavioral data metrics from observable firm data in an economy can greatly benefit the FED, World Bank, etc. We find that the ML/LDA communities can benefit from Economic intuitions just as much as Economists can benefit from generic data exploration tools. The future of successful Economic data understanding, modeling, simulation, and visualization can be amplified by new A-LDA models and approaches for new and analogous models of Economic system dynamics. The potential benefits of improved economic data analysis and real time decision aid tools are numerous for researchers, analysts, and federal agencies who all deal with increasingly large amounts of complex data to support their decision making.

Proposing an adaptive mutation to improve XCSF performance to classify ADHD and BMD patients

NASA Astrophysics Data System (ADS)

Sadatnezhad, Khadijeh; Boostani, Reza; Ghanizadeh, Ahmad

2010-12-01

There is extensive overlap of clinical symptoms observed among children with bipolar mood disorder (BMD) and those with attention deficit hyperactivity disorder (ADHD). Thus, diagnosis according to clinical symptoms cannot be very accurate. It is therefore desirable to develop quantitative criteria for automatic discrimination between these disorders. This study is aimed at designing an efficient decision maker to accurately classify ADHD and BMD patients by analyzing their electroencephalogram (EEG) signals. In this study, 22 channels of EEGs have been recorded from 21 subjects with ADHD and 22 individuals with BMD. Several informative features, such as fractal dimension, band power and autoregressive coefficients, were extracted from the recorded signals. Considering the multimodal overlapping distribution of the obtained features, linear discriminant analysis (LDA) was used to reduce the input dimension in a more separable space to make it more appropriate for the proposed classifier. A piecewise linear classifier based on the extended classifier system for function approximation (XCSF) was modified by developing an adaptive mutation rate, which was proportional to the genotypic content of best individuals and their fitness in each generation. The proposed operator controlled the trade-off between exploration and exploitation while maintaining the diversity in the classifier's population to avoid premature convergence. To assess the effectiveness of the proposed scheme, the extracted features were applied to support vector machine, LDA, nearest neighbor and XCSF classifiers. To evaluate the method, a noisy environment was simulated with different noise amplitudes. It is shown that the results of the proposed technique are more robust as compared to conventional classifiers. Statistical tests demonstrate that the proposed classifier is a promising method for discriminating between ADHD and BMD patients.

Proposing an adaptive mutation to improve XCSF performance to classify ADHD and BMD patients.

PubMed

Sadatnezhad, Khadijeh; Boostani, Reza; Ghanizadeh, Ahmad

2010-12-01

There is extensive overlap of clinical symptoms observed among children with bipolar mood disorder (BMD) and those with attention deficit hyperactivity disorder (ADHD). Thus, diagnosis according to clinical symptoms cannot be very accurate. It is therefore desirable to develop quantitative criteria for automatic discrimination between these disorders. This study is aimed at designing an efficient decision maker to accurately classify ADHD and BMD patients by analyzing their electroencephalogram (EEG) signals. In this study, 22 channels of EEGs have been recorded from 21 subjects with ADHD and 22 individuals with BMD. Several informative features, such as fractal dimension, band power and autoregressive coefficients, were extracted from the recorded signals. Considering the multimodal overlapping distribution of the obtained features, linear discriminant analysis (LDA) was used to reduce the input dimension in a more separable space to make it more appropriate for the proposed classifier. A piecewise linear classifier based on the extended classifier system for function approximation (XCSF) was modified by developing an adaptive mutation rate, which was proportional to the genotypic content of best individuals and their fitness in each generation. The proposed operator controlled the trade-off between exploration and exploitation while maintaining the diversity in the classifier's population to avoid premature convergence. To assess the effectiveness of the proposed scheme, the extracted features were applied to support vector machine, LDA, nearest neighbor and XCSF classifiers. To evaluate the method, a noisy environment was simulated with different noise amplitudes. It is shown that the results of the proposed technique are more robust as compared to conventional classifiers. Statistical tests demonstrate that the proposed classifier is a promising method for discriminating between ADHD and BMD patients.

Pure spin current injection in hydrogenated graphene structures

NASA Astrophysics Data System (ADS)

Zapata-Peña, Reinaldo; Mendoza, Bernardo S.; Shkrebtii, Anatoli I.

2017-11-01

We present a theoretical study of spin-velocity injection (SVI) of a pure spin current (PSC) induced by linearly polarized light that impinges normally on the surface of two 50% hydrogenated noncentrosymmetric two-dimensional (2D) graphene structures. The first structure, labeled Up and also known as graphone, is hydrogenated only on one side, and the second, labeled Alt, is 25% hydrogenated at both sides. The hydrogenation opens an energy gap on both structures. The PSC formalism has been developed in the length gauge perturbing Hamiltonian, and includes, through the single-particle density matrix, the excited coherent superposition of the spin-split conduction bands inherent to the noncentrosymmetric nature of the structures considered in this work. We analyze two possibilities: in the first, the spin is fixed along a chosen direction, and the resulting SVI is calculated; in the second, we choose the SVI direction along the surface plane, and calculate the resulting spin orientation. This is done by changing the energy ℏ ω and polarization angle α of the incoming light. The results are calculated within a full electronic band structure scheme using the density functional theory (DFT) in the local density approximation (LDA). The maxima of the spin velocities are reached when ℏ ω =0.084 eV and α =35∘ for the Up structure, and ℏ ω =0.720 eV and α =150∘ for the Alt geometry. We find a speed of 668 and 645 km/s for the Up and the Alt structures, respectively, when the spin points perpendicularly to the surface. Also, the response is maximized by fixing the spin-velocity direction along a high-symmetry axis, obtaining a speed of 688 km/s with the spin pointing at 13∘ from the surface normal, for the Up, and 906 km/s and the spin pointing at 60∘ from the surface normal, for the Alt system. These speed values are orders of magnitude larger than those of bulk semiconductors, such as CdSe and GaAs, thus making the hydrogenated graphene structures excellent candidates for spintronics applications.

Automatic Detection of Lung and Liver Lesions in 3-D Positron Emission Tomography Images: A Pilot Study

NASA Astrophysics Data System (ADS)

Lartizien, Carole; Marache-Francisco, Simon; Prost, Rémy

2012-02-01

Positron emission tomography (PET) using fluorine-18 deoxyglucose (18F-FDG) has become an increasingly recommended tool in clinical whole-body oncology imaging for the detection, diagnosis, and follow-up of many cancers. One way to improve the diagnostic utility of PET oncology imaging is to assist physicians facing difficult cases of residual or low-contrast lesions. This study aimed at evaluating different schemes of computer-aided detection (CADe) systems for the guided detection and localization of small and low-contrast lesions in PET. These systems are based on two supervised classifiers, linear discriminant analysis (LDA) and the nonlinear support vector machine (SVM). The image feature sets that serve as input data consisted of the coefficients of an undecimated wavelet transform. An optimization study was conducted to select the best combination of parameters for both the SVM and the LDA. Different false-positive reduction (FPR) methods were evaluated to reduce the number of false-positive detections per image (FPI). This includes the removal of small detected clusters and the combination of the LDA and SVM detection maps. The different CAD schemes were trained and evaluated based on a simulated whole-body PET image database containing 250 abnormal cases with 1230 lesions and 250 normal cases with no lesion. The detection performance was measured on a separate series of 25 testing images with 131 lesions. The combination of the LDA and SVM score maps was shown to produce very encouraging detection performance for both the lung lesions, with 91% sensitivity and 18 FPIs, and the liver lesions, with 94% sensitivity and 10 FPIs. Comparison with human performance indicated that the different CAD schemes significantly outperformed human detection sensitivities, especially regarding the low-contrast lesions.

Application of class-modelling techniques to infrared spectra for analysis of pork adulteration in beef jerkys.

PubMed

Kuswandi, Bambang; Putri, Fitra Karima; Gani, Agus Abdul; Ahmad, Musa

2015-12-01

The use of chemometrics to analyse infrared spectra to predict pork adulteration in the beef jerky (dendeng) was explored. In the first step, the analysis of pork in the beef jerky formulation was conducted by blending the beef jerky with pork at 5-80 % levels. Then, they were powdered and classified into training set and test set. The second step, the spectra of the two sets was recorded by Fourier Transform Infrared (FTIR) spectroscopy using atenuated total reflection (ATR) cell on the basis of spectral data at frequency region 4000-700 cm(-1). The spectra was categorised into four data sets, i.e. (a) spectra in the whole region as data set 1; (b) spectra in the fingerprint region (1500-600 cm(-1)) as data set 2; (c) spectra in the whole region with treatment as data set 3; and (d) spectra in the fingerprint region with treatment as data set 4. The third step, the chemometric analysis were employed using three class-modelling techniques (i.e. LDA, SIMCA, and SVM) toward the data sets. Finally, the best result of the models towards the data sets on the adulteration analysis of the samples were selected and the best model was compared with the ELISA method. From the chemometric results, the LDA model on the data set 1 was found to be the best model, since it could classify and predict 100 % accuracy of the sample tested. The LDA model was applied toward the real samples of the beef jerky marketed in Jember, and the results showed that the LDA model developed was in good agreement with the ELISA method.

Ring-mold craters in lineated valley fill and lobate debris aprons on Mars: Evidence for subsurface glacial ice

NASA Astrophysics Data System (ADS)

Kress, Ailish M.; Head, James W.

2008-12-01

Ring-mold craters (RMCs), concentric crater forms shaped like a truncated torus and named for their similarity to the cooking implement, are abundant in lobate debris aprons (LDA) and lineated valley fill (LVF) in the northern mid-latitudes on Mars, but are not seen in surrounding terrain. LDA and LVF have been interpreted to form by flow of debris, but uncertainty remains concerning the mechanism of flow, with hypotheses ranging from pore-ice-assisted creep of talus to debris-covered glaciers. RMCs average less than a few hundred meters in diameter and occur in association with normal bowl-shaped impact craters whose average diameters are commonly less than RMCs. On the basis of their morphologic similarities to laboratory impact craters formed in ice and the physics of impact cratering into layered material, we interpret the unusual morphology of RMCs to be the result of impact into a relatively pure ice substrate below a thin regolith, with strength-contrast properties, spallation, viscous flow and sublimation being factors in the development of the ring-mold shape. Associated smaller bowl-shaped craters are interpreted to have formed within a layer of regolith-like sublimation till overlying the ice substrate. Estimates of crater depths of excavation between populations of bowl-shaped and ring-mold craters suggest that the debris layer is relatively thin. These results support the hypothesis that LDA and LVF formed as debris-covered glaciers and predict that many hundreds of meters of ice remain today in LDA and LVF deposits, beneath a veneer of sublimation till. RMCs can be used in other parts of Mars to predict and assess the presence of ancient ice-related deposits.

Detection of a gravitropism phenotype in glutamate receptor-like 3.3 mutants of Arabidopsis thaliana using machine vision and computation.

PubMed

Miller, Nathan D; Durham Brooks, Tessa L; Assadi, Amir H; Spalding, Edgar P

2010-10-01

Gene disruption frequently produces no phenotype in the model plant Arabidopsis thaliana, complicating studies of gene function. Functional redundancy between gene family members is one common explanation but inadequate detection methods could also be responsible. Here, newly developed methods for automated capture and processing of time series of images, followed by computational analysis employing modified linear discriminant analysis (LDA) and wavelet-based differentiation, were employed in a study of mutants lacking the Glutamate Receptor-Like 3.3 gene. Root gravitropism was selected as the process to study with high spatiotemporal resolution because the ligand-gated Ca(2+)-permeable channel encoded by GLR3.3 may contribute to the ion fluxes associated with gravity signal transduction in roots. Time series of root tip angles were collected from wild type and two different glr3.3 mutants across a grid of seed-size and seedling-age conditions previously found to be important to gravitropism. Statistical tests of average responses detected no significant difference between populations, but LDA separated both mutant alleles from the wild type. After projecting the data onto LDA solution vectors, glr3.3 mutants displayed greater population variance than the wild type in all four conditions. In three conditions the projection means also differed significantly between mutant and wild type. Wavelet analysis of the raw response curves showed that the LDA-detected phenotypes related to an early deceleration and subsequent slower-bending phase in glr3.3 mutants. These statistically significant, heritable, computation-based phenotypes generated insight into functions of GLR3.3 in gravitropism. The methods could be generally applicable to the study of phenotypes and therefore gene function.

Detection of a Gravitropism Phenotype in glutamate receptor-like 3.3 Mutants of Arabidopsis thaliana Using Machine Vision and Computation

PubMed Central

Miller, Nathan D.; Durham Brooks, Tessa L.; Assadi, Amir H.; Spalding, Edgar P.

2010-01-01

Gene disruption frequently produces no phenotype in the model plant Arabidopsis thaliana, complicating studies of gene function. Functional redundancy between gene family members is one common explanation but inadequate detection methods could also be responsible. Here, newly developed methods for automated capture and processing of time series of images, followed by computational analysis employing modified linear discriminant analysis (LDA) and wavelet-based differentiation, were employed in a study of mutants lacking the Glutamate Receptor-Like 3.3 gene. Root gravitropism was selected as the process to study with high spatiotemporal resolution because the ligand-gated Ca2+-permeable channel encoded by GLR3.3 may contribute to the ion fluxes associated with gravity signal transduction in roots. Time series of root tip angles were collected from wild type and two different glr3.3 mutants across a grid of seed-size and seedling-age conditions previously found to be important to gravitropism. Statistical tests of average responses detected no significant difference between populations, but LDA separated both mutant alleles from the wild type. After projecting the data onto LDA solution vectors, glr3.3 mutants displayed greater population variance than the wild type in all four conditions. In three conditions the projection means also differed significantly between mutant and wild type. Wavelet analysis of the raw response curves showed that the LDA-detected phenotypes related to an early deceleration and subsequent slower-bending phase in glr3.3 mutants. These statistically significant, heritable, computation-based phenotypes generated insight into functions of GLR3.3 in gravitropism. The methods could be generally applicable to the study of phenotypes and therefore gene function. PMID:20647506

Escape from Lethal Bacterial Competition through Coupled Activation of Antibiotic Resistance and a Mobilized Subpopulation

PubMed Central

Stubbendieck, Reed M.; Straight, Paul D.

2015-01-01

Bacteria have diverse mechanisms for competition that include biosynthesis of extracellular enzymes and antibiotic metabolites, as well as changes in community physiology, such as biofilm formation or motility. Considered collectively, networks of competitive functions for any organism determine success or failure in competition. How bacteria integrate different mechanisms to optimize competitive fitness is not well studied. Here we study a model competitive interaction between two soil bacteria: Bacillus subtilis and Streptomyces sp. Mg1 (S. Mg1). On an agar surface, colonies of B. subtilis suffer cellular lysis and progressive degradation caused by S. Mg1 cultured at a distance. We identify the lytic and degradative activity (LDA) as linearmycins, which are produced by S. Mg1 and are sufficient to cause lysis of B. subtilis. We obtained B. subtilis mutants spontaneously resistant to LDA (LDAR) that have visibly distinctive morphology and spread across the agar surface. Every LDAR mutant identified had a missense mutation in yfiJK, which encodes a previously uncharacterized two-component signaling system. We confirmed that gain-of-function alleles in yfiJK cause a combination of LDAR, changes in colony morphology, and motility. Downstream of yfiJK are the yfiLMN genes, which encode an ATP-binding cassette transporter. We show that yfiLMN genes are necessary for LDA resistance. The developmental phenotypes of LDAR mutants are genetically separable from LDA resistance, suggesting that the two competitive functions are distinct, but regulated by a single two-component system. Our findings suggest that a subpopulation of B. subtilis activate an array of defensive responses to counter lytic stress imposed by competition. Coordinated regulation of development and antibiotic resistance is a streamlined mechanism to promote competitive fitness of bacteria. PMID:26647299