bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular orientations and interfacial structure of C60 on Pt(111)
Authors: Liu Cunding , Qin Zhihui , Chen Jian , Guo Qinmin , Yu Yinghui , Cao Gengyu
Published: January 2011

Molecular orientations and assembled structures of C60 molecules on Pt(111) have been characterized by low-temperature scanning tunneling microscopy for coverage between 0.1 ML and 1.5 ML. At room temperature, C60 molecules preferentially decorate the steps and nucleate into single layer islands (SLIs) with hexagonal close-packed structures upon increasing coverage. C60 islands comprise two differently oriented C60/Pt(111)-(√13 × √13) R13.9° phases, in which five types of molecular orientation of C60 carbon cage configurations are clearly identified by the high-resolution scanning tunneling microscopy image. Further annealing treatment leads to more uniform molecular orientation without apparent aggregation of C60 SLIs. As coverage increases above 1 ML, domains corresponding to (2√3 × 2√3) R30° superstructure appear. To explain the above transformation, an interfacial reconstruction model is proposed according to the detailed study of the molecular adsorption structures in different domains.
Rovibrational states of the H2O–H2 complex: An ab initio calculation
Authors: van der Avoird Ad , Nesbitt David J.
Published: January 2011

All bound rovibrational levels of the H2O–H2 dimer are calculated for total angular momentum J = 0–5 on two recent intermolecular potential surfaces reported by Valiron et al. [J. Chem. Phys. 129, 134306 (2008)] and Hodges et al. [J. Chem. Phys. 120, 710 (2004)] obtained through ab initio calculations. The method used handles correctly the large amplitude internal motions in this complex; it involves a discrete variable representation of the intermolecular distance coordinate R and a basis of coupled free rotor wave functions for the hindered internal rotations and the overall rotation of the dimer. The basis is adapted to the permutation symmetry associated with the para/ortho (p/o) nature of both H2O and H2 as well as to inversion symmetry. Dimers containing oH2 are more strongly bound than dimers with pH2, as expected, with dissociation energies \documentclass[12pt]{minimal}\begin{document}$D_0$\end{document}D0 of 33.57, 36.63, 53.60, and 59.04 \documentclass[12pt]{minimal}\begin{document}${\rm cm}^{-1}$\end{document} cm −1for pH2O–pH2, oH2O–pH2, pH2O–oH2, and oH2O–oH2, respectively, on the potential of Valiron et al. that corresponds to a binding energy \documentclass[12pt]{minimal}\begin{document}$D_e$\end{document}De of 235.14 \documentclass[12pt]{minimal}\begin{document}${\rm cm}^{-1}$\end{document} cm −1. Rovibrational wave functions are computed as well and the nature of the bound states in the four different dimer species is discussed. Converged rovibrational levels on both potentials agree well with the high-resolution spectrum reported by Weida and Nesbitt [J. Chem. Phys. 110, 156 (1999)]; the hindered internal rotor model that was used to interpret this spectrum is qualitatively correct.
Bimolecular reaction rates from ring polymer molecular dynamics: Application to H + CH4→ H2 + CH3
Authors: Suleimanov Yury V. , Collepardo-Guevara Rosana , Manolopoulos David E.
Published: January 2011

In a recent paper, we have developed an efficient implementation of the ring polymer molecular dynamics (RPMD) method for calculating bimolecular chemical reaction rates in the gas phase, and illustrated it with applications to some benchmark atom–diatom reactions. In this paper, we show that the same methodology can readily be used to treat more complex polyatomic reactions in their full dimensionality, such as the hydrogen abstraction reaction from methane, H + \documentclass[12pt]{minimal}\begin{document}${\rm CH}_4 \rightarrow$\end{document} CH 4→ \documentclass[12pt]{minimal}\begin{document}${\rm H}_2$\end{document}H2 + \documentclass[12pt]{minimal}\begin{document}${\rm CH}_3$\end{document} CH 3. The present calculations were carried out using a modified and recalibrated version of the Jordan–Gilbert potential energy surface. The thermal rate coefficients obtained between 200 and 2000 K are presented and compared with previous results for the same potential energy surface. Throughout the temperature range that is available for comparison, the RPMD approximation gives better agreement with accurate quantum mechanical (multiconfigurational time-dependent Hartree) calculations than do either the centroid density version of quantum transition state theory (QTST) or the quantum instanton (QI) model. The RPMD rate coefficients are within a factor of 2 of the exact quantum mechanical rate coefficients at temperatures in the deep tunneling regime. These results indicate that our previous assessment of the accuracy of the RPMD approximation for atom–diatom reactions remains valid for more complex polyatomic reactions. They also suggest that the sensitivity of the QTST and QI rate coefficients to the choice of the transition state dividing surface becomes more of an issue as the dimensionality of the reaction increases.
Communication: Free-energy analysis of hydration effect on protein with explicit solvent: Equilibrium fluctuation of cytochrome c
Authors: Karino Yasuhito , Matubayasi Nobuyuki
Published: January 2011

The relationship between the protein conformation and the hydration effect is investigated for the equilibrium fluctuation of cytochrome c. To elucidate the hydration effect with explicit solvent, the solvation free energy of the protein immersed in water was calculated using the molecular dynamics simulation coupled with the method of energy representation. The variations of the protein intramolecular energy and the solvation free energy are found to compensate each other in the course of equilibrium structural fluctuation. The roles of the attractive and repulsive components in the protein–water interaction are further examined for the solvation free energy. The attractive component represented as the average sum of protein–water interaction energy is dominated by the electrostatic effect and is correlated to the solvation free energy through the linear-response-type relationship. No correlation with the (total) solvation free energy is seen, on the other hand, for the repulsive component expressed as the excluded-volume effect.
Are asymmetric stretch Raman spectra by centrosymmetric molecules depolarized?: The 2ν3 overtone of CO2
Authors: Chrysos M. , Verzhbitskiy I. A. , Rachet F. , Kouzov A. P.
Published: January 2011

Molecular vibrations that are not totally symmetrical give rise to depolarized lines [P. Atkins and J. de Paula, Atkins’ Physical Chemistry (Oxford University Press, UK, 2006), p. 464]. But in the case of stretching vibrations in centrosymmetric molecules, the statement has so far not been conclusively verified. It is the purpose of this article to report a rigorous experimental and theoretical analysis of the 2\documentclass[12pt]{minimal}\begin{document}$\nu _3$\end{document}ν3 band of CO2—the first overtone of the asymmetrical stretch vibration. The anisotropic spectrum was extracted and its spectral moment calculated from light-scattering measurements, taken at room temperature and for a wide range of CO2-gas densities. Evidence for a near-entirely depolarized Raman band is provided, with integrated depolarization ratio \documentclass[12pt]{minimal}\begin{document}$\eta _{int}= \frac{6}{7.16}$\end{document}ηint=67.16, closely approaching the upper bound \documentclass[12pt]{minimal}\begin{document}$\eta _{max}=\frac{6}{7}$\end{document}ηmax=67. Agreement with theoretical predictions is found, on the basis of quality ab initio data for polarizability properties, provided that electro-optical and mechanical anharmonicity and intermode coupling effects between symmetric \documentclass[12pt]{minimal}\begin{document}$\nu _1$\end{document}ν1 and antisymmetric \documentclass[12pt]{minimal}\begin{document}$\nu _3$\end{document}ν3 stretching vibrations are incorporated.
Communication: Thermodynamic scaling of the Debye process in primary alcohols
Authors: Pawlus Sebastian , Paluch Marian , Grzybowski Andrzej
Published: January 2011

The molecular dynamics of hydrogen-bonded liquids usually does not satisfy the thermodynamic scaling. However, very recently, two opposite conclusions about validity of thermodynamical scaling in monohydroxy alcohol, 2-ethyl-1-hexanol, were presented by Reiser et al. [J. Chem. Phys. 132, 181101 (2010)] and Fragiadakis et al. [J. Chem. Phys. 132, 144505 (2010)]. In this communication we present new experimental results that can explain this ostensible contradiction.
Adsorption of nitrogen oxides on graphene and graphene oxides: Insights from density functional calculations
Authors: Tang Shaobin , Cao Zexing
Published: January 2011

The interactions of nitrogen oxides NOx (x = 1,2,3) and N2O4 with graphene and graphene oxides (GOs) were studied by the density functional theory. Optimized geometries, binding energies, and electronic structures of the gas molecule-adsorbed graphene and GO were determined on the basis of first-principles calculations. The adsorption of nitrogen oxides on GO is generally stronger than that on graphene due to the presence of the active defect sites, such as the hydroxyl and carbonyl functional groups and the carbon atom near these groups. These active defect sites increase the binding energies and enhance charge transfers from nitrogen oxides to GO, eventually leading to the chemisorption of gas molecules and the doping character transition from acceptor to donor for NO2 and NO. The interaction of nitrogen oxides with GO with various functional groups can result in the formation of hydrogen bonds OH⋅⋅⋅O (N) between –OH and nitrogen oxides and new weak covalent bonds C⋅⋅⋅N and C⋅⋅⋅O, as well as the H abstraction to form nitrous acid- and nitric acidlike moieties. The spin-polarized density of states reveals a strong hybridization of frontier orbitals of NO2 and NO3 with the electronic states around the Fermi level of GO, and gives rise to the strong acceptor doping by these molecules and remarkable charge transfers from molecules to GO, compared to NO and N2O4 adsorptions on GO. The calculated results show good agreement with experimental observations.
Chain stiffness, salt valency, and concentration influences on titration curves of polyelectrolytes: Monte Carlo simulations
Authors: Carnal Fabrice , Stoll Serge
Published: January 2011

Monte Carlo simulations have been used to study two different models of a weak linear polyelectrolyte surrounded by explicit counterions and salt particles: (i) a rigid rod and (ii) a flexible chain. We focused on the influence of the pH, chain stiffness, salt concentration, and valency on the polyelectrolyte titration process and conformational properties. It is shown that chain acid–base properties and conformational properties are strongly modified when multivalent salt concentration variation ranges below the charge equivalence. Increasing chain stiffness allows to minimize intramolecular electrostatic monomer interactions hence improving the deprotonation process. The presence of di and trivalent salt cations clearly promotes the chain degree of ionization but has only a limited effect at very low salt concentration ranges. Moreover, folded structures of fully charged chains are only observed when multivalent salt at a concentration equal or above charge equivalence is considered. Long-range electrostatic potential is found to influence the distribution of charges along and around the polyelectrolyte backbones hence resulting in a higher degree of ionization and a lower attraction of counterions and salt particles at the chain extremities.
Terraced spreading of nanofilms under a nonmonotonic disjoining pressure
Authors: Landman Kerry A. , White Lee R.
Published: January 2011

A thin (∼nanometer) film of a viscous, essentially nonvolatile liquid spreads over a substrate controlled by the disjoining pressure Π(h) exerted by the two interfaces on one another. Such films are commonly used as hard disk lubricants in the magnetic recording industry. Macroscopic nonuniformities in the film caused by a perturbation of the uniformly spread state flow away and the film is “healed” in a time frame governed by the appropriate hydrodynamic equations. Lubrication theory may be used to derive a diffusion equation for the local film height h(x,t) as a function of position and time which shows that an effective height-dependent diffusion coefficient D(h)=−[h3/3μBξ(h)][dΠ(h)/dh] controls the spreading dynamics, where μB is the bulk liquid viscosity and ξ(h) is a function accounting for any variation of local viscosity near the substrate due to molecularity of the liquid. Such an approach is possible due to the very small ratio of the film height to the in-plane length scale of the disturbance. Provided the disjoining pressure is positive and monotonically decreasing with film thickness, the motion of the film is unexceptional, exhibiting the usual smooth profiles associated with diffusive flow with time. However, for nonmonotonic disjoining pressures, the film is experimentally observed to exhibit vertical terraces. These abrupt jumps in height do not disappear with time and they move slowly or are stationary. This phenomenon is investigated here. We demonstrate how a physically consistent “weak” solution of the diffusion equation can be constructed, where only positive values of the diffusion coefficient are sampled. The film heights at the jump discontinuity are determined by an equal area rule for the disjoining pressure. Numerical simulations for a realistic nonmonotonic disjoining pressure exhibit finite termination on the low-side and vertical terraces, thereby matching the behavior observed in experimental systems.
Nonequilibrium molecular transport photoinduced by potential energy fluctuations
Authors: Dekhtyar Marina L. , Rozenbaum Viktor M.
Published: January 2011

The mechanism of directed substrate-parallel motion of molecules caused by photoinduced potential energy fluctuations is investigated. Unlike simplistic models (e.g., an on-off ratchet), the approach suggested implies that the necessary asymmetry of the potential energy can arise not only from the asymmetry of the substrate potential but also from an asymmetric distribution of the fluctuating charge density in the molecule. The thus induced asymmetry of the potential energy governs the direction motion and enables, under certain conditions, its reversal at some frequencies of resonant laser pulses or temperature. These inferences are exemplified by the model charge distributions in the molecule and substrate, and the charge density fluctuations which are obtained by quantum chemical calculations for the realistic molecule of a substituted phenylpyrene compound on a model substrate.
Measurement of the Soret and diffusion coefficients for benchmark binary mixtures by means of digital interferometry
Authors: Mialdun A. , Shevtsova V.
Published: January 2011

We report on the development of the optical digital interferometry (ODI) technique for measuring diffusion and Soret coefficients. The unique feature of this method is that it traces the transient path of the system in the entire two-dimensional cross section of a cell. In this way, it is applicable not only for measurements of Soret coefficients, but also for studying diffusive transport mechanism and convection. Presently, this method is not widely used and, in our view, not because of fundamental limitations but rather due to a lack of properly developed postexperimental procedures of the raw data analysis. Thus, in this paper our attention is focused on the successive analysis of different steps: the fringe analysis, the choice of reference images, the thermal design of the cell, and multiparameter fitting procedure. Using the ODI technique, we have measured the diffusion and the Soret coefficients for three binary mixtures composed of dodecane (\documentclass[12pt]{minimal}\begin{document}${\rm C}_{12}{\rm H}_{26}$\end{document}C12H26), isobutylbenzene, and 1,2,3,4-tetrahydronaphtalene at a mean temperature of \documentclass[12pt]{minimal}\begin{document}$25^{\circ }$\end{document}25∘C and 50 wt. % in each component. These measurements were compared with their benchmark values and show an agreement within less than 3%.
Fourier transform infrared isotopic study of linear MnC3: Identification of the ν1(σ) fundamental
Authors: Bejjani Micheline , Rittby C. M. L. , Graham W. M. R.
Published: January 2011

Linear MnC3 has been detected in the products from the dual laser ablation of carbon and manganese rods trapped in solid Ar at ∼12 K. The ν1(σ) vibrational fundamental, an asymmetric carbon stretching mode, has been identified at 1846.9 cm−1. Fourier transform infrared measurements of 13C isotopic shift are in good agreement with the predictions of density functional theory calculations using the mPW1PW91 functional with 6–311+G(3df) basis set. This is the first optical detection of the linear isomer of MnC3 for which previous photoelectron spectroscopy studies have reported evidence of a cyclic isomer.
Communication: Highest occupied molecular orbital–lowest unoccupied molecular orbital gaps of doped silicon clusters from core level spectroscopy
Authors: Lau J. T. , Vogel M. , Langenberg A. , Hirsch K. , Rittmann J. , Zamudio-Bayer V. , Möller T. , Issendorff B. von
Published: January 2011

A method to determine band gaps of size-selected and isolated nanoparticles by combination of valence band and core-level photoionization spectroscopy is presented. This approach is widely applicable and provides a convenient alternative to current standard techniques for the determination of band gaps by optical or photoelectron spectroscopy. A first application to vanadium doped silicon clusters confirms a striking size-dependence of their highest occupied–lowest unoccupied molecular orbital gaps.
Molecular-orbital-free algorithm for the excited-state force in time-dependent density functional theory
Authors: Liu Jie , Liang Wan Zhen
Published: January 2011

Starting from the equation of motion in the density matrix formulation, we reformulate the analytical gradient of the excited-state energy at the time-dependent density functional theory level in the nonorthogonal Gaussian atom-centered orbital (AO) basis. Analogous to the analytical first derivative in molecular-orbital (MO) basis, a Z-vector equation has been derived with respect to the reduced one-electronic density matrix in AO basis, which provides a potential possibility to exploit quantum locality of the density matrix and avoids the matrix transformation between the AO and the MO basis. Numerical tests are finished for the excited-state geometry optimization and adiabatic excitation energy calculation of a series of small molecules. The results demonstrate the computational efficiency and accuracy of the current AO-based energy gradient expression in comparison with the MO-based scheme.
Modeling gas permeation through membranes by kinetic Monte Carlo: Applications to H2, O2, and N2 in hydrated Nafion®
Authors: Dorenbos Gert , Morohoshi Kei
Published: January 2011

We present a simulation tool in order to predict gas permeation through heterogeneous, microphase separated structures. The method combines dissipative particle dynamics (DPD) with kinetic Monte Carlo (KMC). Morphologies obtained from DPD are mapped onto a high density grid on which gas diffusion takes place. Required input parameters for the KMC calculations are the gas solubility and gas diffusion constant within each of the pure phase components. Our method was tested and validated for permeation of H2, O2, and N2 gasses through hydrated Nafion membranes at various temperatures and water contents. We predict that membranes that contain an equal volume fraction of water, those with the highest ion exchange capacity exhibit the largest N2 and O2 permeation rates. For membranes of the same ion exchange capacity the H2, O2, and N2 and permeability increases approximately linearly with Bragg spacing. We also predict that O2 gas permeation depends much more on bottleneck phenomena within the phase separated morphologies than H2 gas permeation. Overall, the calculated H2 and O2 permeability is found to be slightly lower than experimental values. This is attributed to the robustness of DPD resulting in ∼7% larger Bragg spacing as compared with experiment and/or increased gas solubility within the polymer phase with water uptake.
The effect of particle inertia on triaxial ellipsoids in creeping shear: From drift toward chaos to a single periodic solution
Authors: Lundell Fredrik
Published: January 2011

The motion of inertial, triaxial ellipsoids in creeping shear flow is explained for a wide range of aspect ratios and Stokes numbers (St, quantifying particle inertia). Particle inertia induces a drift toward rotation around the shortest axis, with this axis aligned with the vorticity axis of the flow. For aspect ratio combinations in a certain region, this periodic state is unstable for low St and the particle moves in a chaotic manner. At higher St, the instability is stabilized and one single final periodic motion is well defined also for (in the limit of St=0) unstable aspect ratios.
Tuning the transport properties of a (C60)2 bridge with electron and hole dopings
Authors: Zheng X. H. , Wang X. L. , Dai Z. X. , Zeng Z.
Published: January 2011

The tuning effects of substitutional B and N dopings on the electron transport properties of a C60 dimer bridge [(C60)2] are investigated by nonequilibrium Green's functions in combination with density functional theory. It is found that, unlike C60, the equilibrium conductance of (C60)2 is very small. However, it can be controlled by electron (N) doping or hole (B) doping, which shifts the molecular energy levels so that the LUMOs or HOMOs align well with the Fermi level and results in LUMO-mediated transport or HOMO-mediated transport. The conductance increases accordingly with a certain number of N or B atoms doped in the C60s. Interestingly, when one C60 is doped with N atoms and the other is doped with B atoms, new transport behaviors arise and rectification is achieved due to the special alignment of the energy levels of the individual C60s with the Fermi level. It suggests that cluster or molecule assembling can often realize specific functions which are not available by single molecules and should be taken into consideration in the design of molecular devices.
Coupled vesicle morphogenesis and domain organization
Authors: Huang Changjin , Yuan Hongyan , Zhang Sulin
Published: January 2011

Protein-enriched membrane domains with distinct biophysical properties have been thought as the basic organizing units of cellular membrane. Using particle dynamics simulations, here we study phase separation dynamics and domain formation in binary vesicles. Our simulations clearly show the intimate coupling between domain compositions, lateral domain organization, and vesicle shape transformation. Our simulation results provide insights into the essential role of membrane domains in the coordinated remodeling of cellular membranes and in protein and lipid sorting.
Study and tailoring spin dynamic properties of CoFeB during rapid thermal annealing
Authors: Zhang Yaping , Fan Xin , Wang Weigang , Kou Xiaoming , Cao Rong , Chen Xing , Ni Chaoying , Pan Liqing , Xiao John Q.
Published: January 2011

We studied the real-time evolution of magnetic dynamic and static properties of 20 nm CoFeB thin film during annealing at 380 °C. The ferromagnetic resonance linewidth quickly reduces by 30% within 300 s annealing, and monotonically increases upon longer annealing. The magnetic static coercivity shows similar trend. The underlying physical relation between linewidth and anisotropy can be connected by the two-magnon scattering theory. By doping of Nb into CoFeB films, the damping was maintained at a low value within 2000 s annealing. This method to tailor the dynamic properties of CoFeB may benefit the development of magnetics and spintronics based microwave devices.
InP-based heterojunction bipolar transistors with InGaAs/GaAs strained-layer-superlattice
Authors: Driad R. , Aidam R. , Yang Q. , Maier M. , Güllich H. , Schlechtweg M. , Ambacher O.
Published: January 2011

In this paper, we report the design, fabrication, and characterization of an InP/InGaAs heterojunction bipolar transistor (HBT) employing a lattice-mismatched In0.53Ga0.47As/GaAs strained-layer-superlattice (SLS) base structure. The performance of the SLS-base device is also compared with that of an In0.53Ga0.47As uniform-base structure. The digitally graded-base devices exhibit a slightly lower gain at low bias voltage and a higher current gain at high currents. While the offset voltage remains comparable in the two structures, the graded-base InP/InGaAs HBTs, with built-in fields of ∼66 kV/cm, have typically a maximum dc current gain of 18% larger than that of transistors with uniform base.
Miscible viscous fingering involving viscosity increase by a chemical reaction with moderate Damköhler number
Authors: Nagatsu Yuichiro , Kondo Yusuke , Kato Yoshihito , Tada Yutaka
Published: January 2011

In our previous study, we experimentally studied the effects of increased or decreased viscosity of the more-viscous liquid caused by chemical reactions at a very high Damköhler number, Da (defined as the ratio between a characteristic time of fluid motion and that of a chemical reaction), on miscible viscous fingering [Y. Nagatsu et al., “Experimental study on miscible viscous fingering involving viscosity changes induced by variations in chemical species concentrations due to chemical reactions,” J. Fluid Mech. 571, 475 (2007)]. In another study, we experimentally studied the effects of decreased viscosity caused by chemical reaction at a moderate Da on the fingering [Y. Nagatsu et al., “Effects of moderate Damköhler number on miscible viscous fingering involving viscosity decrease due to a chemical reaction,” J. Fluid Mech. 625, 97 (2009)]. In the present study, we investigated the effects of increased viscosity caused by chemical reaction at a moderate Da on the fingering in a radial Hele-Shaw cell. We observed that the present reaction decreased the area occupied by the fingering pattern around the injection hole. As a result, the fingering pattern became less dense following the reaction. The smaller the Da, the less significant the influence of the reaction on the fingering pattern. The present experimental results provide a coherent link between the results of earlier studies of miscible viscous fingering involving changes in the viscosity caused by chemical reactions.
Socio-seasonal changes in scent-marking habits in the carnivorous marsupial Dasyurus maculatus at communal latrines
Authors: Ruibal Monica , Peakall Rod , Claridge Andrew
Published: January 2011

Scat DNA analyses and monthly monitoring were used to elucidate patterns of latrine use in a free-ranging population of a rare Australian marsupial carnivore, the spotted-tailed quoll (Dasyurus maculatus) Kerr. In all, 132 latrines were identified at large complex outcrops and on bedrock in drainage lines, creeks and rivers at a single woodland site in south-eastern mainland Australia. Annual cyclic variation in scat deposition was found over the two years that latrines were monitored. Peaks in scat deposition on latrines coincided with seasonal social behaviours and differed between sites on outcrops and sites along drainage lines. A marked increase in scat deposition on latrines in drainage lines was recorded during the mating season and at outcrop latrines when females were nursing young. Genetic analyses of scats collected over one breeding season revealed that multiple individuals of both sexes defaecated at latrines. The communal use of latrines during the mating season along with the seasonal patterns of scat deposition demonstrates that latrines are important scent-marking sites that facilitate social communication among individuals of this solitary-living species. The collective evidence indicates that latrines play a major role in aiding reproduction and interindividual spacing.
Rho activation of mDia formins is modulated by an interaction with inverted formin 2 (INF2)
Authors: Sun Hua , Schlondorff Johannes S. , Brown Elizabeth J. , Higgs Henry N. , Pollak Martin R.
Published: January 2011

Inverted formin 2 (INF2) encodes a member of the diaphanous subfamily of formin proteins. Mutations in INF2 cause human kidney disease characterized by focal and segmental glomerulosclerosis. Disease-causing mutations occur only in the diaphanous inhibitory domain (DID), suggesting specific roles for this domain in the pathogenesis of disease. In a yeast two-hybrid screen, we identified the diaphanous autoregulatory domains (DADs) of the mammalian diaphanous-related formins (mDias) mDia1, mDia2, and mDia 3 as INF2_DID-interacting partners. The mDias are Rho family effectors that regulate actin dynamics. We confirmed in vitro INF2_DID/mDia_DAD binding by biochemical assays, confirmed the in vivo interaction of these protein domains by coimmunoprecipitation, and observed colocalization of INF2 and mDias in glomerular podocytes. We investigated the influence of this INF2_DID/mDia_DAD interaction on mDia mediated actin polymerization and on serum response factor (SRF) activation. We find that the interaction of INF2_DID with mDia_DAD inhibited mDia-mediated, Rho-activated actin polymerization, as well as SRF-responsive gene transcriptional changes. Similar assays using the disease-causing E184K and R218Q mutations in INF2_DID showed a decreased effect on SRF activation and gene transcription. The binding of INF2_DID to mDia_DAD may serve as a negative regulatory mechanism for mDias’ function in actin-dependent cell processes. The effects of disease-causing INF2 mutations suggest an important role for this protein and its interaction with other formins in modulating glomerular podocyte phenotype and function.
Allostery in the ferredoxin protein motif does not involve a conformational switch
Authors: Nechushtai Rachel , Lammert Heiko , Michaeli Dorit , Eisenberg-Domovich Yael , Zuris John A. , Luca Maria A. , Capraro Dominique T. , Fish Alex , Shimshon Odelia , Roy Melinda , Schug Alexander , Whitford Paul C. , Livnah Oded , Onuchic José N. , Jennings Patricia A.
Published: January 2011

Regulation of protein function via cracking, or local unfolding and refolding of substructures, is becoming a widely recognized mechanism of functional control. Oftentimes, cracking events are localized to secondary and tertiary structure interactions between domains that control the optimal position for catalysis and/or the formation of protein complexes. Small changes in free energy associated with ligand binding, phosphorylation, etc., can tip the balance and provide a regulatory functional switch. However, understanding the factors controlling function in single-domain proteins is still a significant challenge to structural biologists. We investigated the functional landscape of a single-domain plant-type ferredoxin protein and the effect of a distal loop on the electron-transfer center. We find the global stability and structure are minimally perturbed with mutation, whereas the functional properties are altered. Specifically, truncating the L1,2 loop does not lead to large-scale changes in the structure, determined via X-ray crystallography. Further, the overall thermal stability of the protein is only marginally perturbed by the mutation. However, even though the mutation is distal to the iron–sulfur cluster (∼20 
Å
), it leads to a significant change in the redox potential of the iron–sulfur cluster (57 mV). Structure-based all-atom simulations indicate correlated dynamical changes between the surface-exposed loop and the iron–sulfur cluster-binding region. Our results suggest intrinsic communication channels within the ferredoxin fold, composed of many short-range interactions, lead to the propagation of long-range signals. Accordingly, protein interface interactions that involve L1,2 could potentially signal functional changes in distal regions, similar to what is observed in other allosteric systems.
Nouvelles concordances pour l’enseignement des langues
Authors: Garrigues Mylene
Published: January 2011

The use of concordances in the teaching or learning of foreign languages is a common practice. This has developed into a distinct field of research for language educationalists. This paper shows how the features of the intex system offer new possibilities in this domain.
INTEX pour l’annotation semi-automatique d’un corpus d’anaphores
Authors: Tutin Agnès
Published: January 2011

Anaphors constitute a well-known problem in automatic text generation and natural language understanding. Using corpora to deal with such phenomena could help to develop robust processing techniques. Building such resources is, though, a tedious and time-consuming task and could more easily be accomplished by partial automation.

In this paper, we show how the intex system can be used for this task. We show that in a newspaper corpus (in this case, le Monde Diplomatique), discursive grammatical anaphors can easily be located via associated linguistic features. A series of transducers generating tags for categories and functions can thus be built, and constitutes an efficient pre-processing stage (though manual checking remains necessary). The heuristics, quickly and easily developed, are specific to the task. The study goes on to show, however, that discarding non-anaphoric pronouns is not straightforward in the case of non-referential personal pronouns or indefinite pronouns, and that the tagging of the grammatical function seems limited in the absence of real syntactic processing.
Breeding crops for tolerance to salinity, waterlogging and inundation.
Authors: Mullan D. J. , Barrett-Lennard E. G.
Published: January 2011

During the next century, global climate change is likely to cause substantial increases in the severity with which salinity, waterlogging and inundation affect crop production in many of the world's agricultural regions. In this chapter we address the effects of climate change on these three environmental stresses in terms of their threat to sustainable crop production. The effects of salinity, waterlogging and inundation on crop plants are examined, with a focus also directed towards the exacerbating effects of the complex interactions between these stresses. We identify key plant physiological traits as targets for breeding initiatives. Three possible approaches to the development of crops for saline, waterlogged and inundated soils are considered: (i) selection within crop species; (ii) the development of hybrids between adapted wild species and crop plants; and (iii) the domestication of halophytes. Finally, we detail some of the complex research, development and agricultural issues that need to be addressed by a broad research and development community in order to increase crop production during the foreseeable period of global climate change.
Multi-location testing as a tool to identify plant response to global climate change.
Authors: Braun H. J. , Atlin G. , Payne T.
Published: January 2011

Plant breeding, using the combined potential of conventional, molecular and genetically modified technologies, will provide cultivars with greatly enhanced nutrient and water-use efficiency, enhanced tolerance to heat and drought, resistance to diseases and appropriate end-use and nutritional quality, and, possibly most important, increased ability to cope with the increasing extremes in temperature and precipitation occurring at one location over years. Modern crop cultivars developed by seed companies, international crop research centres and national breeding programmes often exhibit very wide geographical adaptation, as well as broad adaptation to the range of environmental and management conditions that occur within and between a target population of environments, or megaenvironments. To identify such cultivars, multi-location testing done by the International Maize and Wheat Improvement Center (CIMMYT) and the International Rice Research Institute (IRRI) remains the most efficient system. International evaluation networks based on exchange of and free access to germplasm and multi-location testing are therefore a cornerstone in the strategies and efforts to develop wheat, rice and maize germplasm that is adapted to the increasingly variable growing conditions encountered due to global climate change. Information from such trials must be combined with information from managed stress trials. Wide performance adaptation is essential to respond to global climate change, to the vagaries of spatial heterogeneity within farmers' fields and their production input management efficacies, and from unpredictable temporal climatic seasonal variability.
Management of resident soil microbial community structure and function to suppress soilborne disease development.
Authors: Mazzola M.
Published: January 2011

Climate change is likely to alter the distribution and severity of soilborne diseases affecting both intensive and low-input agricultural production systems. Naturally occurring disease suppressive soils have been documented in a variety of cropping systems, and in many instances the biological attributes contributing to suppressiveness have been identified. While these studies have often yielded an understanding of operative mechanisms leading to the suppressive state, significant difficulty has been realized in the transfer of this knowledge into the development of effective field-level disease control practices. Early efforts focused on the inundative application of individual or mixtures of microbial strains recovered from these systems, and known to function in specific soil suppressiveness. However, the introduction of biological agents into non-native soil ecosystems typically fails to yield commercially viable or consistent levels of disease control. Of late, greater emphasis has been placed on manipulation of the cropping system to manage resident beneficial rhizosphere microorganisms as a means to suppress soilborne plant pathogens. One such strategy is the cropping of specific plant species or genotypes, or the application of soil amendments with the goal of selectively enhancing disease suppressive microbial communities. This chapter will briefly review the existence of biologically functional disease suppressive soils, document the research history supporting the potential in managing microbial communities for disease control, describe methods available for the effective manipulation of bioactive populations, and describe specific examples demonstrating the effective application of the approach.
Biotechnology in agriculture.
Authors: Whitford R. , Gilbert M. , Langridge P.
Published: January 2011

Climate change is predicted to result in disruption of many farming systems. The Food and Agriculture Organization (FAO) predicts a 15-20% fall in global agricultural production by 2080. Consequently, adaptation of major crop species to climate change will be the biggest challenge for plant breeders this century. Biotechnology will be important when adapting crops to better tolerate changing stresses. It includes using advanced genetic mapping technologies, like molecular markers, in the breeding and development of new varieties. Molecular markers are used to provide greater focus, accuracy and speed in crop breeding programmes with further advances coming. Genetic modification (GM) techniques are providing access to a diversity of genes, used to develop plant varieties more tolerant to the negative impacts of climate change.
GIS and crop simulation modelling applications in climate change research.
Authors: Hodson D. , White J.
Published: January 2011

The challenges that climate change presents to humanity require an unprecedented ability to predict the responses of crops to environment and management. Geographic information systems (GIS) and crop simulation models are two powerful and highly complementary tools that are increasingly used for such predictive analyses. The role of both technologies in predicting future situations centres around extrapolation. For GIS, extrapolation from the past based on correlation in a very loose sense plays an important role. For crop models, extrapolation based on how known processes respond to factors of interest (i.e. simulation) is a key factor. GIS and crop models can be integrated, providing predictions that combine the spatial perspective of GIS with the stronger representation of temporal processes of simulation models. This chapter reviews the use of these two tools for predicting impacts of climate change and examining options for adaptation. Increasingly, downscaled outputs from a range of global general circulation models under differing future scenarios are used as key inputs for both tools. Examples are given for major food crops and key agricultural zones, with a bias towards tropical and subtropical regions. Consideration is also given to factors limiting efficient application of the tools to climate change research. Both technologies will see increasing use in climate change research and in applications of research in decision making. Credible studies of crop responses to climate involve dealing with large sets of data and potentially millions of simulations, especially if adaptation is considered. While the computational challenges are daunting, the greater challenge is how to devise efficient protocols for selecting the most meaningful scenarios, interpreting the results and summarizing outputs for decision makers.
The concept of pluralism in the Italian public media
Authors: Hanretty Chris
Published: January 2011

In this paper it is argued that the concept of pluralism – the most important value in the Italian media debate – is conceptually confused. The author identifies three mutually incompatible conceptions of pluralism used when discussing the public broadcaster Rai: (1) structural pluralism, satisfied when the public broadcaster is divided into autonomous channels or programme groups; (2) summative pluralism, satisfied when output is divided between political actors according to some ideal distribution; and (3) pluralism ‘lottizzato’, satisfied when a number of different political positions are ‘represented’ by journalists within the broadcaster.
Age-of-Acquisition Effects in Pure Alexia
Authors: Cushman Chelsie L. , Johnson Rebecca L.
Published: January 2011

Pure alexia is an acquired reading disorder in which previously literate adults adopt a letter-by-letter processing strategy. Though these individuals display impaired reading, research shows that they are still able to use certain lexical information in order to facilitate visual word processing. The current experiment investigates the role that a word's age of acquisition (AoA) plays in the reading processes of an individual with pure alexia (G.J.) when other lexical variables have been controlled. Results from a sentence reading task in which eye movement patterns were recorded indicated that G.J. shows a strong effect of AoA, where late-acquired words are more difficult to process than early-acquired words. Furthermore, it was observed that the AoA effect is much greater for G.J. than for age-matched control participants. This indicates that patients with pure alexia rely heavily on intact top-down information, supporting the interactive activation model of reading.
Co-publication with Journal of Physics: Conference Series
Authors: Takahashi M , Saito H
Published: January 2011

Invited papers from ISAMMA 2010 (Sendai, Japan, 12–16 July 2010)

A selection of papers, invited by the conference organisers and peer reviewed by the journal, are published here in a special issue of Journal of Physics D: Applied Physics.

The bulk of the papers presented at the conference, after peer review, are published separately in

Journal of Physics: Conference Series.
Current status and recent topics of rare-earth permanent magnets
Authors: Sugimoto S
Published: January 2011

After the development of Nd–Fe–B magnets, rare-earth magnets are now essential components in many fields of technology, because of their ability to provide a strong magnetic flux. There are two, well-established techniques for the manufacture of rare earth magnets: powder metallurgy is used to obtain high-performance, anisotropic, fully dense magnet bodies; and the melt-spinning or HDDR (hydrogenation, disproportionation, desorption and recombination) process is widely used to produce magnet powders for bonded magnets. In the industry of sintered Nd–Fe–B magnets, the total amount of production has increased and their dominant application has been changed to motors. In particular, their use for motors in hybrid cars is one of the most attractive applications. Bonded magnets have also been used for small motors, and the studies of nanocomposite and Sm–Fe–N magnets have become widespread. This paper reviews the current status and future trend in the research of permanent magnets.
Coercivity distributions in Nd–Fe–B sintered magnets produced by the grain boundary diffusion process
Authors: Nakamura H , Hirota K , Ohashi T , Minowa T
Published: January 2011

The grain boundary diffusion (GBD) process is an effective process for enhancing the coercivity of Nd–Fe–B sintered magnets. When the GBD process is applied to a thick magnet, the magnet exhibits a coercivity distribution. Partial coercivity at the centre is the same as that of the original magnet, but the partial coercivity increases on going towards the magnet surface. In this paper, the effects of conditions of the GBD process on the characteristics of coercivity distributions were investigated. Surface coercivities increase with increasing amount of coatings, while diffusion depths are almost the same. The diffusion treatment temperature varied from 800 to 900 °C, and does not affect the coercivity distributions. A long-time diffusion treatment is effective in enhancing the inner coercivities, but a very long treatment causes a significant reduction in surface coercivity.
Ferromagnetic resonance of epitaxial Fe nanodots grown on MgO measured using coplanar waveguides
Authors: Mizuguchi M , Takanashi K
Published: January 2011

Ferromagnetic resonance measurements of Fe nanodots epitaxially grown on a MgO layer were carried out using a coplanar waveguide to investigate the dynamic behaviours of spins in a magnetic dot assembly. The resonant peaks of Fe nanodots with an average diameter of 10 nm were successfully observed, and a strong magnetic anisotropy was found in the peak frequency shift depending on the magnetic field applied in the film plane. A difference was clearly seen in the peak shift behaviour between Fe nanodots and continuous Fe thin films. The Gilbert damping parameter of the Fe nanodots (nominal thickness: 3 nm) was estimated to be 0.008 12 from the width of the resonant peaks, substantially larger than that of a continuous Fe thin film with a thickness of 8 nm. This difference in damping is attributed to the distribution of the effective field in each nanodot due to size dispersion. Ferromagnetic resonance studies using coplanar waveguides thus enable clarification of the spin dynamics of magnetic dot arrays and the fundamental spin dynamics of a single nanodot.
Control of magnetic domain wall displacement using spin current in small in-plane magnetic field in Permalloy nanowires
Authors: Togawa Yoshihiko , Kimura Takashi , Harada Ken , Tonomura Akira , Otani Yoshichika
Published: January 2011

We microscopically investigate the magnetic domain wall motion induced by current pulse application in a small in-plane magnetic field in U-shaped Permalloy wires by means of Lorentz microscopy together with simultaneous transport measurement. An in-plane magnetic field less than 7 Oe parallel to the wire direction in U-shaped geometry effectively works to impede bidirectional motion of the domain wall induced by current pulse application, i.e. to suppress the stochastic nature of the domain wall displacement. The present finding will provide practical and reliable ways of controlling and manipulating the domain wall dynamics, which are widely applicable in spintronic devices, especially when stochastic nature causes serious problems in device operation. Reliable manipulation of the magnetic state is discussed using the current-driven domain wall motion and domain nucleation in the magnetic wire device.