bluuebunny/crossref_metadata_2025 huggingface dataset:
A charge-transfer surface enhanced Raman scattering model from time-dependent density functional theory calculations on a Ag10-pyridine complex
Authors: Birke Ronald L. , Znamenskiy Vasiliy , Lombardi John R.
Published: June 2010

Vibrational frequency calculations were made for a Ag10-pyridine vertex complex with density functional theory (DFT) for static simulated spectra and with time-dependent DFT (TD-DFT) for preresonance and resonance simulated spectra using both B3LYP/LANL2DZ and BP86/TZP methodologies. In addition, 40 excited states of the complex were calculated and assigned symmetry based on a C2v symmetry of the optimized complex found with B3LYP/LANL2DZ. Molecular orbital isosurfaces show that the excited states involve both Ag10 intercluster excitations and charge-transfer (CT) excitations between the Ag nanocluster and the pyridine molecule. An excitation around 500 nm involving CT from the Ag cluster to pyridine was found in both calculations. For free pyridine, the relative average deviations between unscaled calculated and experimental results were 1.5 cm−1 for BP86 and 3.1 cm−1 for the B3LYP calculations. For the complex, simulated spectra at a variety of excitation wavelengths were calculated. In the case of 514 nm excitation, the simulated Raman cross section from the TD-DFT calculations (near the CT resonance) was plotted versus Raman shift frequency and compared with an experimental surface enhanced Raman scattering (SERS) spectrum obtained on an oxidation-reduction cycle, ORC roughened Ag electrode. The BP86 TD-DFT calculation with finite damping term showed a better fit to experimental spectrum with respect to both relative intensities and frequencies. The average deviation of the unscaled BP86 calculations for 16 bands in the experimental spectrum was 13.0 cm−1. The calculated spectrum in both cases shows many contributions from nontotally symmetric as well as totally symmetric modes, indicating the contribution of Herzberg–Teller (HT) scattering. The simulated intensities of the Raman modes of different symmetry from Ag10-pyridine can be correlated with HT intensity borrowing from excited states of given symmetry and decent oscillator strength. These results explain the appearance of the a2 mode at 388 cm−1 and the moderately strong b2 mode at 1573 cm−1 found in the SERS experimental spectrum. The good agreement between experimental and simulated results indicates that a small Ag nanocluster-pyridine vertex complex can be used to simulate spectra with good relative intensities, if not absolute intensities, and accurate frequencies for most of the SERS bands for adsorbed pyridine on roughened bulk Ag.
Temperature dependence of boundary conditions in phonon hydrodynamics of smooth and rough nanowires
Authors: Sellitto A. , Alvarez F. X. , Jou D.
Published: June 2010

In the analysis of nanosystems, the phonon–wall interaction must be incorporated to the usual description of phonon hydrodynamics, as surface effects become comparable to bulk effects in these systems. In the present paper, we analyze the temperature dependence of two phenomenological coefficients describing the specular and diffusive collisions, on one side, and backscattering collisions, on the other side, in silicon nanowires. Furthermore, we also propose for them a qualitative microscopic interpretation. This dependence is important because it strongly influences the temperature dependence of the effective thermal conductivity of nanosystems.
On the measurement of vortex filament lifetime statistics in turbulence
Authors: Biferale Luca , Scagliarini Andrea , Toschi Federico ,   International Collaboration for Turbulence Research
Published: June 2010

A numerical study of turbulence seeded with light particles is presented. We analyze the statistical properties of coherent, small-scale structures by looking at the trapping events of light particles inside vortex filaments. We study the properties of particles attracting set, measuring its fractal dimension and the probability that the separation between two particles remains within the dissipative scale, even for time lapses as long as the large-scale correlation time, TL. We show how to estimate the vortex lifetime by studying the moment of inertia of bunches of particles, showing the presence of an exponential lifetime distribution, with events up to TL.
Analysis of the excited-state absorption spectral bandshape of oligofluorenes
Authors: Hayes Sophia C. , Silva Carlos
Published: June 2010

We present ultrafast transient absorption spectra of two oligofluorene derivatives in dilute solution. These spectra display a photoinduced absorption band with clear vibronic structure, which we analyze rigorously using a time-dependent formalism of absorption to extract the principal excited-state vibrational normal-mode frequencies that couple to the electronic transition, the configurational displacement of the higher-lying excited state, and the reorganization energies. We can model the excited-state absorption spectrum using two totally symmetric vibrational modes with frequencies 450 (dimer) or 400 cm−1 (trimer), and 1666 cm−1. The reorganization energy of the ground-state absorption is rather insensitive to the oligomer length at 230 meV. However, that of the excited-state absorption evolves from 58 to 166 meV between the oligofluorene dimer and trimer. Based on previous theoretical work [A. Shukla et al., Phys. Rev. B 67, 245203 (2003)], we assign the absorption spectra to a transition from the 1Bu excited state to a higher-lying mAg state, and find that the energy of the excited-state transition with respect to the ground-state transition energy is in excellent agreement with the theoretical predictions for both oligomers studied here. These results and analysis permit profound understanding of the nature of excited-state absorption in π-conjugated polymers, which are the subject of general interest as organic semiconductors in the solid state.
Intramolecular charge ordering in the multi molecular orbital system (TTM-TTP)I3
Authors: Bonnet Marie-Laure , Robert Vincent , Tsuchiizu Masahisa , Omori Yukiko , Suzumura Yoshikazu
Published: June 2010

Starting from the structure of the (TTM-TTP)I3 molecular-based material, we examine the characteristics of frontier molecular orbitals using ab initio (CASSCF/CASPT2) configurations interaction calculations. It is shown that the singly occupied and second-highest-occupied molecular orbitals are close to each other, i.e., this compound should be regarded as a two-orbital system. By dividing virtually the [TTM-TTP] molecule into three fragments, an effective model is constructed to rationalize the origin of this picture. In order to investigate the low-temperature, symmetry breaking experimentally observed in the crystal, the electronic distribution in a pair of [TTM-TTP] molecules is analyzed from CASPT2 calculations. Our inspection supports and explains the speculated intramolecular charge ordering which is likely to give rise to low-energy magnetic properties.
Measurement of ac conductivity of gold nanofilms at microwave frequencies
Authors: Poo Yin , Wu Rui-xin , Fan Xin , Xiao John Q.
Published: June 2010

We proposed an application of the open-terminal method to measure the alternating current (ac) conductivity of metallic nanometer thick films at microwave frequencies. An explicit expression of the conductivity as a function of reflection has been derived. Using the application, we experimentally measured the complex conductivity of gold nanometer films in microwave X band. The results are in good agreement with those obtained by other techniques. We find that the film’s surface morphology affects not only the magnitude but also the frequency dependence of the ac conductivity. In some cases, the direct current conductivity can be lower than the ac conductivity deviating from the Drude model, which can be well qualitatively explained by a circuit model for the granular films.
The role of diffusion of excitons in organic photorefractive materials
Authors: Samiullah Mohammad
Published: June 2010

A theory of photorefractive (PR) effect in organic PR materials based on exciton formation, diffusion, and dissociation in organic polymer semiconductors is presented. The exact numerical and approximate analytical solutions of the model indicate that an increase in the exciton diffusion constant reduces the amplitude of the resulting space-charge electric field. The model also shows that a space-charge field is produced even in the absence of traps, and particular combinations of the detrapping rates and the trap depths could be used to enhance the space-charge field. It is suggested that an organic semiconductor with a smaller exciton diffusivity and traps with optimal detrapping rates would be a better candidate for photorefractivity.
Thermal effects on the magnetization reversal process and its interpretation in perpendicular magnetic recording media
Authors: Srinivasan Kumar , Acharya B. Ramamurthy , Bertero Gerardo
Published: June 2010

We have studied the time-scale and temperature dependence of the magnetization reversal in perpendicular magnetic recording media. One of the under-reported phenomena associated with this reversal is the thermal dependence of the squareness of the magnetic hysteresis loop. Understanding this phenomenon is important because the coercive squareness parameter S∗ is often used to evaluate the strength of the magnetic exchange-coupling interactions between the grains. In this work, we demonstrate that S∗ is a dynamic quantity which depends on the thermal agitation of the magnetization, and it is imperative to take this dependence into account in interpreting magnetic and microstructural effects. Based on the Sharrock model for the dynamic coercivity, we built an expression for the time-scale and temperature dependence of S∗ in highly oriented perpendicular magnetic recording media. Fits of experimental data to the resulting expression were then used to extract the intrinsic squareness parameter Sint∗ which originates in the thermal-independent demagnetization and exchange-interaction effects. Sint∗ was estimated for two sets of perpendicular recording media samples. For the first set of media samples showing progressively smaller grain sizes, the values of S∗ measured at the normal magnetometry time-scales of milliseconds to seconds indicated progressively smaller values. In contrast, the values of the thermal-independent Sint∗ determined from applying the above model were progressively larger. This discrepancy can only be explained on the basis of progressively stronger intergranular exchange coupling, which is offset by strong thermal effects at small grain sizes. For the second set of media samples with increasingly larger segregant oxide content, progressively smaller values of both S∗ and thermal-independent Sint∗ were observed, thus verifying the strong intergranular segregation effects due to greater nonmagnetic grain boundary phase. The phenomenological model for thermal-independent Sint∗ will be helpful in interpreting the microstructural and magnetic properties of perpendicular magnetic recording media, especially as thermal effects become important in the approach to areal densities of 1 Tbits/in2.
Prevention of surface reconstruction at the Au(110)/electrolyte interface by the adsorption of cytosine
Authors: Mansley C. P. , Smith C. I. , Bowfield A. , Fernig D. G. , Edwards C. , Weightman P.
Published: June 2010

It is shown that the adsorption of cytosine at the Au(110)/liquid interface at a potential of 0.0 V “freezes” the Au(110) surface in the (1×1) structure and that the molecule does not change its orientation on the surface as the potential is varied. In contrast the adsorption of adenine does not freeze the Au(110) surface even though both molecules adopt a base stacking structure with individual molecules oriented in a plane vertical to the Au(110) surface with their long axes along [11¯0] rows. It is suggested that cytosine bonds to three Au atoms through the NH2 group, the N(3) and O(8) sites, and that this arrangement stabilizes the Au(110) surface and prevents its reconstruction to the more open (1×2) and (1×3) structures as the applied voltage is varied. The weaker bonding of the adenine molecule with the gold surface is unable to prevent the voltage induced reconstruction of the Au(110) surface.
Crystallization of ion amorphized Ge2Sb2Te5 thin films in presence of cubic or hexagonal phase
Authors: De Bastiani R. , Carria E. , Gibilisco S. , Mio A. , Bongiorno C. , Piccinelli F. , Bettinelli M. , Pennisi A. R. , Grimaldi M. G. , Rimini E.
Published: June 2010

The crystallization kinetics of amorphous Ge2Sb2Te5 (GST) thin films, generated by ion implantation, on top of crystalline GST, either in the cubic or hexagonal phase, was investigated by means of time resolved reflectivity measurements, x-ray diffraction, in situ transmission electron microscopy, and Raman analyses. The crystallization occurred at a lower temperature with respect to a fully amorphous film and in both cases the crystalline phase started growing at the underlying amorphous-crystalline (a-c) interface. However, it was not a solid phase epitaxial growth since cubic GST was always obtained, independent of the phase of the underlying crystal. We speculate that the a-c interface behaves as a continuous region of potential nucleation sites in the crystallization making the crystallization process more efficient.
Communications: Tin cluster anions (Snn−, n=18, 20, 23, and 25) comprise dimers of stable subunits
Authors: Lechtken Anne , Drebov Nedko , Ahlrichs Reinhart , Kappes Manfred M. , Schooss Detlef
Published: June 2010

The gas phase structures of tin cluster anions Snn− have been studied by a combination of trapped ion electron diffraction and density functional theory calculations. In the size range of n=18–25 these clusters comprise dimers of stable subunits. In particular Sn18− and Sn20− are homodimers of Sn9 and Sn10 subunits, respectively. In Sn23− two Sn10 units are linked by three additional bridging atoms and Sn25− is a heterodimer of Sn10 and Sn15 subunits. This rather unexpected growth mode is rationalized by the extraordinary stability of the building blocks Sn9, Sn10, and Sn15.
Contactless measurements of charge migration within single molecules
Authors: Nagaya Kiyonobu , Iwayama Hiroshi , Sugishima Akinori , Ohmasa Yoshinori , Yao Makoto
Published: June 2010

Contactless measurements of charge migration were carried out for three π-conjugated molecules in each of which a bromine atom and an oxygen atom are located on the opposite sides of the aromatic ring. A core hole was generated selectively in the Br atom by x-ray absorption, followed by the Auger cascade, and the subsequent charge migration within the molecule was examined by detecting an O+ ion by means of the coincidence momentum imaging measurements.
Emission color control from blue to red with nanocolumn diameter of InGaN/GaN nanocolumn arrays grown on same substrate
Authors: Sekiguchi Hiroto , Kishino Katsumi , Kikuchi Akihiko
Published: June 2010

A novel technology for controlling the In composition of InGaN quantum wells on the same wafer was developed, which paved the way for the monolithic integration of three-primary-color nano-light-emitting diodes. In the experiment, InGaN/GaN multiple quantum well nanocolumn arrays with nanocolumn diameters from 137 to 270 nm were prepared on the same substrate with the Ti-mask selective area growth by rf-plasma-assisted molecular beam epitaxy. The emission color changed from blue to red (from 479 to 632 nm in wavelength) with increasing nanocolumn diameter. The emission color change mechanism was clearly explained by the beam shadow effect of the neighboring nanocolumns.
Phase field model of dielectric and magnetic composites
Authors: Wang Yu U.
Published: June 2010

Phase field model is developed to calculate heterogeneous distributions of polarization, charge, local field, and effective susceptibility of dielectric and magnetic composites with arbitrary multicomponent microstructures. It solves electrostatic and magnetostatic equations in terms of polarization vector field in reciprocal Fourier space, with interphase boundary conditions automatically satisfied without explicitly tracking interphase interfaces. This advantage allows the model to effectively treat arbitrarily complex multicomponent composites and seamlessly incorporate evolving microstructures from composite fabrication simulations. Evolution of internal field distributions and effective properties in composites during self-assembly fabrication process is presented to demonstrate the model’s capability and potential.
Modeling of flexoelectric effect on capacitor-voltage and memory window of metal-ferroelectric-insulator-silicon capacitor
Authors: Chen Y. Q. , Zheng X. J. , Li W.
Published: June 2010

The flexoelectric effect on electrical behaviors of metal-ferroelectric-insulator-silicon (MFIS) capacitor was investigated by considering stress gradient in Landau–Khalatnikov theory. In the presence of flexoelectric coupling, the compressive stress shifts capacitor-voltage (C-V) loop of MFIS capacitor to the negative voltage axis and enlarges memory window, however, the tensile stress shifts C-V loop to the positive voltage axis and compresses memory window. The magnitudes of stress, flexoelectric coefficient, and characteristic length of stress distribution have a significant influence on C-V characteristic and memory window of MFIS capacitor. The results show stress gradient should be avoided to prevent failure of MFIS capacitor.
High-performance quantum ring detector for the 1–3 terahertz range
Authors: Bhowmick S. , Huang G. , Guo W. , Lee C. S. , Bhattacharya P. , Ariyawansa G. , Perera A. G. U.
Published: June 2010

Molecular beam epitaxy of InAs/GaAs quantum dots and their subsequent transformation to quantum rings by postepitaxy thermal annealing have been investigated. Photoconductive detectors with multiple quantum ring layers in the active region exhibit dark current density ∼10−8 A/cm2 at a bias of 2 V at 4.2 K. The rings have a single bound state, and emission of photoexcited carriers gives rise to a spectral response peaking at 1.82 THz (165 μm) at 5.2 K. Peak responsivity of 25 A/W, specific detectivity, D∗, of 1×1016 Jones and a total quantum efficiency of 19% are measured with 1 V bias at 5.2 K. At 10 K and 1 V, D∗∼3×1015 Jones is measured.
Nanoscale structural variation observed on the vicinal SrTiO3(001) surface
Authors: Shiraki Susumu , Nantoh Masashi , Katano Satoshi , Kawai Maki
Published: June 2010

The vicinal (001) surface of a Nb-doped SrTiO3 single crystal has been investigated by scanning tunneling microscopy and low energy electron diffraction. The stepped surface prepared by annealing in ultrahigh vacuum at 250 °C exhibits a complex atomic structure composed of four types of reconstructions, which shows short-range variation within nanoscale regions. SrO layers show a c(6×2) structure being stable up to 1000 °C, while √13×√13-R33.7°, c(√13×√13)-R33.7°, and c(√2×√18)-R45° structures are formed on TiO2 layers, which disappear at 450–750 °C followed by the formation of 2×2 and √5×√5-R26.6° structures. These results indicate instability of the reconstructions on the TiO2 terminated surface due to the variation in Sr adatom density caused by multikinetic processes, in contrast to the thermodynamically stable SrO terminated surface.
Tunable optical features from self-organized rhodium nanostructures
Authors: Sathe Bhaskar R. , Balan Beena K. , Pillai Vijayamohanan K.
Published: June 2010

Manipulating the surface to tune plasmonic emission is an exciting fundamental challenge and here we report on the development of unique morphology-dependant optical features of Rh nanostructures prepared by an equilibrium procedure. The emergence of surface plasmon peaks at 375 nm and 474 nm, respectively, is ascribed to truncated and smooth surface of nanospheres in contrast to the absence of surface plasmon for bulk Rh(0) in the visible range. Smaller sized, high surface area domains with well developed, faceted organization are responsible for the promising characteristics of these Rh nanospheres which might be especially useful for potential catalytic, field emission and magnetic applications.
Ni endohedral-doped C60 with duality of magnetic moments
Authors: Li J. L. , Yang G. W.
Published: June 2010

We have performed the magnetic properties of Ni endohedral-doped C60 (Ni@C60) by the spin-polarized density functional calculations, and showed that there are three stable configurations depending on different sites of the doped Ni atoms. Due to the high hybridization and confinement effects, the magnetic moment of the Ni-encapsulated metallofullerenes has duality, i.e., altering between 2.02μB and zero, by positioning the Ni atom in the hollow cage of C60. These findings of the alternative magnetic moments of the Ni-encapsulated C60 implied that Ni@C60 could be expected to be promising as a single molecular magnetic switch.
Enhanced photoluminescence from self-organized rubrene single crystal surface structures
Authors: Stöhr R. J. , Beirne G. J. , Michler P. , Scholz R. , Wrachtrup J. , Pflaum J.
Published: June 2010

We report on crystalline pyramidal structures grown via self-organization on the rubrene (001) surface. The analysis of their spectral response by means of photoluminescence with micrometer lateral resolution reveals an intensity enhancement on-top of the surface structures. As we demonstrate this intensity increase can be related to the excitation processes at the molecular level in combination with exciton confinement within the pyramids.
Generation of gigawatt level beat waves
Authors: Li Guolin , Shu Ting , Zhang Jun , Yang Jianhua , Yuan Chengwei
Published: June 2010

The initial experimental results of generating gigawatt level beat waves with two microwave sources are presented. The detailed measures for enhancing the power handling capacities of the applied devices are explained. In the experiments, the operation frequencies of the microwave sources are 9.41 GHz and 9.59 GHz, respectively. The microwave sources are driven by a single accelerator capable of producing dual electron beams to make sure that they are operating simultaneously. The beat frequencies, measured by the oscilloscope directly, are about 180 MHz, and the peak powers of the pulsed beat waves are about 4.3 GW with durations of about 40 ns.
Low efficiency droop in blue-green m-plane InGaN/GaN light emitting diodes
Authors: Ling Shih-Chun , Lu Tien-Chang , Chang Shih-Pang , Chen Jun-Rong , Kuo Hao-Chung , Wang Shing-Chung
Published: June 2010

We investigated the electroluminescence and relatively external quantum efficiency (EQE) of m-plane InGaN/GaN light emitting diodes (LEDs) emitting at 480 nm to elucidate the droop behaviors in nitride-based LEDs. With increasing the injection current density to 100 A/cm2, the m-plane LEDs exhibit only 13% efficiency droop, whereas conventional c-plane LEDs suffer from efficiency droop at very low injection current density and the EQE of c-plane LEDs decrease to as little as 50% of its maximum value. Our simulation models show that in m-plane LEDs the absence of polarization fields manifest not only the hole distribution more uniform among the wells but also the reduction in electron overflow out of electron blocking layer. These results suggest that the nonuniform distribution of holes and electron leakage current due to strong polarization fields are responsible for the relatively significant efficiency droop of conventional c-plane LEDs.
The Disilicides of Tungsten, Molybdenum, Tantalum, Titanium, Cobalt, and Nickel, and Platinum Monosilicide: A Survey of Their Thermodynamic Properties
Authors: Chandrasekharaiah M. S. , Margrave J. L. , O’Hare P. A. G.
Published: June 2010

A critical evaluation is presented of the thermodynamic properties of six disilicides and one monosilicide that are important in the manufacture of very large scale integrated circuits. Values of the standard molar enthalpies of formation ΔfHm○ at T=298.15 K and p°=0.1 MPa are recommended as follows: WSi2, −(79±5) kJ⋅mol−1; MoSi2, −(137±4) kJ⋅mol−1; TiSi2, −(171±11) kJ⋅mol−1; CoSi2, −(103±15) kJ⋅mol−1; NiSi2, −(88±12) kJ⋅mol−1; TaSi2, −(120±20) kJ⋅mol−1; and PtSi, −(119±7) kJ⋅mol−1. Equations are given for the molar enthalpy increments of some of the silicides along with a few evaluated standard Gibbs free energies of formation. Brief descriptions of methods of synthesis and limited structural information have also been included.
Thermodynamic Properties of Synthetic Sapphire (α-Al2O3), Standard Reference Material 720 and the Effect of Temperature-Scale Differences on Thermodynamic Properties
Authors: Archer Donald G.
Published: June 2010

Comparison of the National Institute of Standards and Technology’s Standard Reference Material 720 certificate values for heat capacity with those obtained from recent experimental determinations indicated the possibility of a systematic error in the certificate values. Selected experimental determinations of enthalpy increments and heat capacities were fitted in order to obtain a representation of the thermodynamic properties of α-Al2O3, a sample of which is the standard reference material (SRM-720) for calibration of some types of calorimeters. The fitted equation and calculated values of the heat capacity, the relative enthalpy, and the entropy are given. The new values are more accurate and result from a better representation of the experimental values than did the 1982 SRM-720 certificate values. Additionally, the general problem of the effect of changes in practical temperature scales on thermodynamic properties is briefly discussed, using the results for α-Al2O3. A recent report from the I.U.P.A.C. Commission on Thermodynamics gave a method for the conversion of thermodynamic properties for changes in practical temperature scale. The I.U.P.A.C. method is shown to be not generally correct. A better method for estimation of these changes is given.
Thermodynamic Properties of Gaseous Silicon Monotelluride and the Bond Dissociation Enthalpy D°m(SiTe) at T→0
Authors: O’Hare P. A. G.
Published: June 2010

Statistical-thermodynamic calculations have been combined with the results of high-temperature Knudsen-effusion studies of the vaporization of Si2Te3 to calculate the thermodynamic properties of SiTe(g) from T→0 to T=2000 K. The dissociation enthalpy D○m(SiTe, T→0) is (448±8) kJ⋅mol−1; its value is discussed vis-a-vis the other silicon monochalcogenides.
The Viscosity of Ammonia
Authors: Fenghour A. , Wakeham William A. , Vesovic V. , Watson J. T. R. , Millat J. , Vogel E.
Published: June 2010

A new representation of the viscosity of ammonia is presented. The representative equations are based on a set of experimental data selected as a result of a critical assessment of the available information. The validity of the representation extends from 196 K to the critical temperature for both liquid and vapor phases. In the supercritical region the temperature range extends to 680 K for pressures at or below ambient and to 600 K for pressures up to 50 MPa. The accuracy of the representation varies from 0.5% for the viscosity of the dilute gas phase at moderate temperatures to about 5% for the viscosity at high pressures and temperatures. Tables of the viscosity generated by the correlating equation at selected temperatures and pressures and along the saturation line are presented to provide easy reference as well as for the validation of computer codes.
Thermodynamic Properties of the Aqueous Ions (2+ and 3+) of Iron and the Key Compounds of Iron
Authors: Parker V. B. , Khodakovskii I. L.
Published: June 2010

Recommended thermochemical property values, ΔfH°, ΔfG°, and S° for the aqueous ions of iron, Fe2+ and Fe3+, are given at 298.15 K in SI units. They are consistent with the CODATA Key Values for Thermodynamics. The values are: ΔfH°=−90.0±0.5 kJ⋅mol−1, ΔfG°=−90.53±1.0 kJ⋅mol−1, S°=−101.6±3.7 J⋅mol−1⋅K−1 for Fe2+(ao) and ΔfH°=−49.0±1.5 kJ⋅mol−1, ΔfG°=−16.28±1.1 kJ⋅mol−1, S° =−278.4±7.7 J⋅mol−1⋅K−1 for Fe3+(ao). The evaluation involves the analysis of the enthalpy changes, Gibbs energy changes, and the entropy measurements for all key substances in the key network. A consistent set of thermochemical property values is given for FeOOH(cr, Goethite), FeCl2(cr), FeCl3(cr), FeBr2(cr), FeBr3(cr), FeI2(cr), and FeSO4⋅7H2O(cr), as well as ‘‘reconstituted’’ recommended process values with uncertainties involving these substances. All recommended values are also given for a standard state of p°=1 atm. A computer based reaction catalog of measurements accompanies the text analysis.
Critical Review of Rate Constants for Reactions of Transients from Metal Ions and Metal Complexes in Aqueous Solution
Authors: Buxton George V. , Mulazzani Quinto G. , Ross Alberta B.
Published: June 2010

Kinetic data for transient metal species in aqueous solution have been critically reviewed. The compilation covers over 2000 measurements of rate constants involving 660 metal ions and metal complexes from Groups 4-15; lanthanides and actinides are not included. Most of the data have been obtained by the methods of pulse radiolysis or flash photolysis. Data have been collected from 500 publications through 1993.
Energy Levels of Zinc, Zn I through Zn X
X
X
Authors: Sugar Jack , Musgrove Arlene
Published: June 2010

Atomic energy levels of zinc have been compiled for all stages of ionization for which experimental data are available. No data have yet been published for Zn IX, Zn X, Zn XXVI, and Zn XXVIII, and only several resonance lines of Zn XXIX and Zn XXX. Very accurate calculated values are compiled for Zn XXIX and Zn XXX. Experimental g-factors and leading percentages from calculated eigenvectors are given. A value for the ionization energy, either experimental when available or theoretical, is included for the neutral atom and each ion. A review of the published literature is given.
Thermodynamic Properties of the Aqueous Ba2+ Ion and the Key Compounds of Barium
Authors: Parker V. B.
Published: June 2010

Recommended thermochemical property values, Δf H°, Δf G° and S° for the aqueous ion of barium, Ba2+, are given at 298.15 K in SI units. The values are: Δf H°=534.64±1.80 kJ⋅mol−1, Δf G°=−557.60±1.81 kJ⋅mol−1 and S°=8.80±0.50 J⋅K−1 mol−1. They are consistent with the CODATA Key Values for Thermodynamics. The evaluation involves the analysis of the enthalpy changes, Gibbs energy changes, and the entropy measurements for all key substances in the key network. A consistent set of thermochemical property values is given for BaO(cr), BaH2(cr), BaCl2(cr), BaCl2⋅2H2O(cr), Ba(NO3)2(cr), and BaCO3(cr,witherite), as well as reconstituted recommended process values with uncertainties for reactions involving these substances.
A Database for the Static Dielectric Constant of Water and Steam
Authors: Fernández D. P. , Mulev Y. , Goodwin A. R. H. , Sengers J. M. H. Levelt
Published: June 2010

All reliable sources of data for the static dielectric constant or relative permittivity of water and steam, many of them unpublished or inaccessible, have been collected, evaluated, corrected when required, and converted to the ITS-90 temperature scale. The data extend over a temperature range from 238 to 873 K and over a pressure range from 0.1 MPa up to 1189 MPa. The evaluative part of this work includes a review of the different types of measurement techniques, and the corrections for frequency dependence due to the impedance of circuit components, and to electrode polarization. It also includes a detailed assessment of the uncertainty of each particular data source, as compared to other sources in the same range of pressure and temperature. Both the raw and the corrected data have been tabulated, and are also available on diskette. A comprehensive list of references to the literature is included.
Morphological change in continental West Germanic
Authors: De Vogelaer Gunther
Published: June 2010

In Dutch, Frisian and German dialects, bewildering morphological variation is found in the person-marking system (e.g., the Syntactic Atlas of Dutch Dialects for Dutch and Frisian, and Goossens 1994, Weiss 2005 and Fuss 2005 for German). One type of variation concerns the formation of subject clitics in clauses with inverted word order, i.e. with the subject following the verb. These elements are subsequently extended to other syntactic positions through analogy, via a pathway described by Kathol (2001): originally enclitic elements spread first to the position enclitic to the complementiser, then to verbs in sentences with regular word order, and finally, in a rare number of cases, to verbs in the sentence-final position in subclauses. This paper shows that Kathol’s proposed pathway actually comprises two similar but not identical pathways, i.e. one for specifically enclitic elements, and one for elements occurring both pro- and enclitically. This implies that developments must be modelled as an ‘analogical map’ rather than a pathway, which will be illustrated extensively with data from Dutch, Frisian and German dialects. The map will be shown to apply to more data than Kathol’s original pathway: it not only captures the extension of clitics, but also the spread of many innovative agreement markers and pronouns, and, hence, a range of person marking phenomena, including complementiser agreement (e.g., Carstens 2003, Weiss 2005), clitic doubling (e.g., Fuss 2005) and double agreement (e.g., Zwart 1997). Finally, following Hill (2007), some of the motivations underlying the change and the factors determining their direction are discussed.
Markov dynamic models for long-timescale protein motion
Authors: Chiang Tsung-Han , Hsu David , Latombe Jean-Claude
Published: June 2010

Molecular dynamics (MD) simulation is a well-established method for studying protein motion at the atomic scale. However, it is computationally intensive and generates massive amounts of data. One way of addressing the dual challenges of computation efficiency and data analysis is to construct simplified models of long-timescale protein motion from MD simulation data. In this direction, we propose to use Markov models with hidden states, in which the Markovian states represent potentially overlapping probabilistic distributions over protein conformations. We also propose a principled criterion for evaluating the quality of a model by its ability to predict long-timescale protein motions. Our method was tested on 2D synthetic energy landscapes and two extensively studied peptides, alanine dipeptide and the villin headpiece subdomain (HP-35 NleNle). One interesting finding is that although a widely accepted model of alanine dipeptide contains six states, a simpler model with only three states is equally good for predicting long-timescale motions. We also used the constructed Markov models to estimate important kinetic and dynamic quantities for protein folding, in particular, mean first-passage time. The results are consistent with available experimental measurements.

Contact:  chiangts@comp.nus.edu.sg
Sparse multitask regression for identifying common mechanism of response to therapeutic targets
Authors: Zhang Kai , Gray Joe W. , Parvin Bahram
Published: June 2010

Motivation: Molecular association of phenotypic responses is an important step in hypothesis generation and for initiating design of new experiments. Current practices for associating gene expression data with multidimensional phenotypic data are typically (i) performed one-to-one, i.e. each gene is examined independently with a phenotypic index and (ii) tested with one stress condition at a time, i.e. different perturbations are analyzed separately. As a result, the complex coordination among the genes responsible for a phenotypic profile is potentially lost. More importantly, univariate analysis can potentially hide new insights into common mechanism of response.

Results: In this article, we propose a sparse, multitask regression model together with co-clustering analysis to explore the intrinsic grouping in associating the gene expression with phenotypic signatures. The global structure of association is captured by learning an intrinsic template that is shared among experimental conditions, with local perturbations introduced to integrate effects of therapeutic agents. We demonstrate the performance of our approach on both synthetic and experimental data. Synthetic data reveal that the multi-task regression has a superior reduction in the regression error when compared with traditional L1-and L2-regularized regression. On the other hand, experiments with cell cycle inhibitors over a panel of 14 breast cancer cell lines demonstrate the relevance of the computed molecular predictors with the cell cycle machinery, as well as the identification of hidden variables that are not captured by the baseline regression analysis. Accordingly, the system has identified CLCA2 as a hidden transcript and as a common mechanism of response for two therapeutic agents of CI-1040 and Iressa, which are currently in clinical use.

Contact:  b_parvin@lbl.gov
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM
Authors: Vaske Charles J. , Benz Stephen C. , Sanborn J. Zachary , Earl Dent , Szeto Christopher , Zhu Jingchun , Haussler David , Stuart Joshua M.
Published: June 2010

Motivation: High-throughput data is providing a comprehensive view of the molecular changes in cancer tissues. New technologies allow for the simultaneous genome-wide assay of the state of genome copy number variation, gene expression, DNA methylation and epigenetics of tumor samples and cancer cell lines.

Analyses of current data sets find that genetic alterations between patients can differ but often involve common pathways. It is therefore critical to identify relevant pathways involved in cancer progression and detect how they are altered in different patients.

Results: We present a novel method for inferring patient-specific genetic activities incorporating curated pathway interactions among genes. A gene is modeled by a factor graph as a set of interconnected variables encoding the expression and known activity of a gene and its products, allowing the incorporation of many types of omic data as evidence. The method predicts the degree to which a pathway's activities (e.g. internal gene states, interactions or high-level ‘outputs’) are altered in the patient using probabilistic inference.

Compared with a competing pathway activity inference approach called SPIA, our method identifies altered activities in cancer-related pathways with fewer false-positives in both a glioblastoma multiform (GBM) and a breast cancer dataset. PARADIGM identified consistent pathway-level activities for subsets of the GBM patients that are overlooked when genes are considered in isolation. Further, grouping GBM patients based on their significant pathway perturbations divides them into clinically-relevant subgroups having significantly different survival outcomes. These findings suggest that therapeutics might be chosen that target genes at critical points in the commonly perturbed pathway(s) of a group of patients.

Availability:Source code available at http://sbenz.github.com/Paradigm

Contact:  jstuart@soe.ucsc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model
Authors: Yizhak Keren , Benyamini Tomer , Liebermeister Wolfram , Ruppin Eytan , Shlomi Tomer
Published: June 2010

Motivation: The availability of modern sequencing techniques has led to a rapid increase in the amount of reconstructed metabolic networks. Using these models as a platform for the analysis of high throughput transcriptomic, proteomic and metabolomic data can provide valuable insight into conditional changes in the metabolic activity of an organism. While transcriptomics and proteomics provide important insights into the hierarchical regulation of metabolic flux, metabolomics shed light on the actual enzyme activity through metabolic regulation and mass action effects. Here we introduce a new method, termed integrative omics-metabolic analysis (IOMA) that quantitatively integrates proteomic and metabolomic data with genome-scale metabolic models, to more accurately predict metabolic flux distributions. The method is formulated as a quadratic programming (QP) problem that seeks a steady-state flux distribution in which flux through reactions with measured proteomic and metabolomic data, is as consistent as possible with kinetically derived flux estimations.

Results: IOMA is shown to successfully predict the metabolic state of human erythrocytes (compared to kinetic model simulations), showing a significant advantage over the commonly used methods flux balance analysis and minimization of metabolic adjustment. Thereafter, IOMA is shown to correctly predict metabolic fluxes in Escherichia coli under different gene knockouts for which both metabolomic and proteomic data is available, achieving higher prediction accuracy over the extant methods. Considering the lack of high-throughput flux measurements, while high-throughput metabolomic and proteomic data are becoming readily available, we expect IOMA to significantly contribute to future research of cellular metabolism.

Contacts:  kerenyiz@post.tau.ac.il; tomersh@cs.technion.ac.il
Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate
Authors: Ye Ding , Fu Yan , Sun Rui-Xiang , Wang Hai-Peng , Yuan Zuo-Fei , Chi Hao , He Si-Min
Published: June 2010

Motivation: Identification of post-translationally modified proteins has become one of the central issues of current proteomics. Spectral library search is a new and promising computational approach to mass spectrometry-based protein identification. However, its potential in identification of unanticipated post-translational modifications has rarely been explored. The existing spectral library search tools are designed to match the query spectrum to the reference library spectra with the same peptide mass. Thus, spectra of peptides with unanticipated modifications cannot be identified.

Results: In this article, we present an open spectral library search tool, named pMatch. It extends the existing library search algorithms in at least three aspects to support the identification of unanticipated modifications. First, the spectra in library are optimized with the full peptide sequence information to better tolerate the peptide fragmentation pattern variations caused by some modification(s). Second, a new scoring system is devised, which uses charge-dependent mass shifts for peak matching and combines a probability-based model with the general spectral dot-product for scoring. Third, a target-decoy strategy is used for false discovery rate control. To demonstrate the effectiveness of pMatch, a library search experiment was conducted on a public dataset with over 40 000 spectra in comparison with SpectraST, the most popular library search engine. Additional validations were done on four published datasets including over 150 000 spectra. The results showed that pMatch can effectively identify unanticipated modifications and significantly increase spectral identification rate.

Availability:  http://pfind.ict.ac.cn/pmatch/

Contact:  yfu@ict.ac.cn; rxsun@ict.ac.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Semi-automated ontology generation within OBO-Edit
Authors: Wächter Thomas , Schroeder Michael
Published: June 2010

Motivation: Ontologies and taxonomies have proven highly beneficial for biocuration. The Open Biomedical Ontology (OBO) Foundry alone lists over 90 ontologies mainly built with OBO-Edit. Creating and maintaining such ontologies is a labour-intensive, difficult, manual process. Automating parts of it is of great importance for the further development of ontologies and for biocuration.

Results: We have developed the Dresden Ontology Generator for Directed Acyclic Graphs (DOG4DAG), a system which supports the creation and extension of OBO ontologies by semi-automatically generating terms, definitions and parent–child relations from text in PubMed, the web and PDF repositories. DOG4DAG is seamlessly integrated into OBO-Edit. It generates terms by identifying statistically significant noun phrases in text. For definitions and parent–child relations it employs pattern-based web searches. We systematically evaluate each generation step using manually validated benchmarks. The term generation leads to high-quality terms also found in manually created ontologies. Up to 78% of definitions are valid and up to 54% of child–ancestor relations can be retrieved. There is no other validated system that achieves comparable results.

By combining the prediction of high-quality terms, definitions and parent–child relations with the ontology editor OBO-Edit we contribute a thoroughly validated tool for all OBO ontology engineers.

Availability: DOG4DAG is available within OBO-Edit 2.1 at http://www.oboedit.org

Contact:  thomas.waechter@biotec.tu-dresden.de;

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation
Authors: Yang Rendong , Su Zhen
Published: June 2010

Motivation: Circadian rhythms are prevalent in most organisms. Identification of circadian-regulated genes is a crucial step in discovering underlying pathways and processes that are clock-controlled. Such genes are largely detected by searching periodic patterns in microarray data. However, temporal gene expression profiles usually have a short time-series with low sampling frequency and high levels of noise. This makes circadian rhythmic analysis of temporal microarray data very challenging.

Results: We propose an algorithm named ARSER, which combines time domain and frequency domain analysis for extracting and characterizing rhythmic expression profiles from temporal microarray data. ARSER employs autoregressive spectral estimation to predict an expression profile's periodicity from the frequency spectrum and then models the rhythmic patterns by using a harmonic regression model to fit the time-series. ARSER describes the rhythmic patterns by four parameters: period, phase, amplitude and mean level, and measures the multiple testing significance by false discovery rate q-value. When tested on well defined periodic and non-periodic short time-series data, ARSER was superior to two existing and widely-used methods, COSOPT and Fisher's G-test, during identification of sinusoidal and non-sinusoidal periodic patterns in short, noisy and non-stationary time-series. Finally, analysis of Arabidopsis microarray data using ARSER led to identification of a novel set of previously undetected non-sinusoidal periodic transcripts, which may lead to new insights into molecular mechanisms of circadian rhythms.

Availability: ARSER is implemented by Python and R. All source codes are available from http://bioinformatics.cau.edu.cn/ARSER

Contact:  zhensu@cau.edu.cn