bluuebunny/crossref_metadata_2025 huggingface dataset:
Vibrational and rotational structure and excited-state dynamics of pyrene
Authors: Baba Masaaki , Saitoh Motohisa , Kowaka Yasuyuki , Taguma Kunio , Yoshida Kazuto , Semba Yosuke , Kasahara Shunji , Yamanaka Takaya , Ohshima Yasuhiro , Hsu Yen-Chu , Lin Sheng Hsien
Published: December 2009

Vibrational level structure in the S0 A1g and S1 B13u states of pyrene was investigated through analysis of fluorescence excitation spectra and dispersed fluorescence spectra for single vibronic level excitation in a supersonic jet and through referring to the results of ab initio theoretical calculation. The vibrational energies are very similar in the both states. We found broad spectral feature in the dispersed fluorescence spectrum for single vibronic level excitation with an excess energy of 730 cm−1. This indicates that intramolecular vibrational redistribution efficiently occurs at small amounts of excess energy in the S1 B13u state of pyrene. We have also observed a rotationally resolved ultrahigh-resolution spectrum of the 000 band. Rotational constants have been determined and it has been shown that the pyrene molecule is planar in both the S0 and S1 states, and that its geometrical structure does not change significantly upon electronic excitation. Broadening of rotational lines with the magnetic field by the Zeeman splitting of MJ levels was very small, indicating that intersystem crossing to the triplet state is minimal. The long fluorescence lifetime indicates that internal conversion to the S0 state is also slow. We conclude that the similarity of pyrene’s molecular structure and potential energy curve in its S0 and S1 states is the main cause of the slow radiationless transitions.
Bidentate ligation of magnesium by 1,2-dimethoxyethane in the gas phase
Authors: Soorkia S. , Collier M. , Soep B. , Mestdagh J.-M.
Published: December 2009

The 1:1 Mg⋯1,2-dimethoxyethane (Mg-DXE) complexes are studied experimentally and theoretically. They are generated by a laser ablation source in a supersonic expansion. They are studied spectroscopically by resonance two-photon ionization. Density functional theory/Becke three-dimensional Lee, Yang, and Parr and ab initio calculations using the MOLPRO quantum chemistry package are performed to document their ground and excited states in a series of geometry ranging from monodentate to bidentate ligation of Mg by the O atoms of DXE. An absorption band is observed in the 27 800–30 500 cm−1 range, which, thanks to the calculations, is attributed to the bidentate complex. The structure of the band is discussed in terms of the excitation of electronic states of the complex correlating adiabatically to the 3s3p P1 and 3s4s S1 states of Mg at large separation between Mg and DXE.
Numerical simulations of rubber networks at moderate to high tensile strains using a purely enthalpic force extension curve for individual chains
Authors: Hanson David E.
Published: December 2009

We report the results of numerical simulations of random, three-dimensional, periodic, tetrafunctional networks in response to a volume-preserving tensile strain. For the intranode force, we use a polynomial fit to a purely enthalpic ab initio force extension curve for extended polyisoprene. The simulation includes a relaxation procedure to minimize the node forces and enforces chain rupture when the extension of a network chain reaches the ab initio rupture strain. For the reasonable assumption that the distribution of network chain lengths is Gaussian, we find that the calculated snap-back velocity, temperature increase due to chain ruptures and predicted tensile stress versus strain curve are consistent with experimental data in the moderate to high extension regime. Our results show that a perfect tetrafunctional polyisoprene network is extremely robust, capable of supporting tensile stresses at least a factor of 10 greater than what is observed experimentally.
Interferometric polarization pulse shaper stabilized by an external laser diode for arbitrary vector field shaping
Authors: Sato Masaaki , Suzuki Takayuki , Misawa Kazuhiko
Published: December 2009

We achieved reliable and stable generation of pulses with all possible polarization states by a Mach–Zehnder pulse shaper. This was realized by incorporating a stabilization mechanism using an external laser diode in the interferometric pulse shaper. This stabilization mechanism has overcome an inherent instability in the Mach–Zehnder interferometer, which caused serious distortion of shaped pulses. For a demonstration of polarization shaping, we generated and measured chiral pulses with a rotating major axis of polarizing orientations at arbitrary frequencies. We expect these chiral pulses enables us to study on new chirality-related light-matter interactions.
Deposition of transparent, conductive tin oxide films on glass using a radio-frequency induction heater
Authors: Solano I. , Schwoebel P. R.
Published: December 2009

Tin oxide films are often used as transparent, conductive coatings on glass in the scientific research setting. The standard approach of depositing these films in an oven leads to poor visibility of the substrate and thus inhibits the ready formation of uniform, low resistivity films. In this note we describe a simple tin oxide film deposition technique using a radio-frequency induction heater that allows for in situ visualization of the deposition process and resulting film. Uniform films having resistivities as low as 2 mΩ cm with transmittances of approximately 85% in the visible light spectrum were readily deposited.
Collinear laser spectroscopy of francium using online rubidium vapor neutralization and amplitude modulated lasers
Authors: Sell J. F. , Gulyuz K. , Sprouse G. D.
Published: December 2009

Performing collinear laser spectroscopy on low intensity radioactive beams requires sensitive detection techniques. We explain our apparatus to detect atomic resonances in neutralized F208–210r ion beams at beam energies of 5 keV and intensities of 105 s−1. Efficient neutralization (≥80%) is accomplished by passing the beam through a dense Rb vapor. Increased detection efficiency is achieved by amplitude modulating the exciting laser to decrease the scattered light background, allowing fluorescence detection only when the laser is near its minimum in the modulation cycle. Using this technique in a collinear geometry we achieve a background reduction by a factor of 180 and a signal-to-noise increase of 2.2, with the lifetime of the atomic state playing a role in the efficiency of this process. Such laser modulation will also produce sidebands on the atomic spectra which we illustrate.
Trajectory surface-hopping study of methane photodissociation dynamics
Authors: Lodriguito Maricris D. , Lendvay György , Schatz George C.
Published: December 2009

We use the fewest switches nonadiabatic trajectory surface hopping approach to study the photodissociation of methane on its lowest singlet excited state potential surface (1 T12) at 122 nm, with emphasis on product state branching and energy partitioning. The trajectories and couplings are based on CASSCF(8,9) calculations with an aug-cc-pvdz basis set. We demonstrate that nonadiabatic dynamics is important to describe the dissociation processes. We find that CH3(X̃ A22″)+H and CH2(ã A11)+H2 are the major dissociation channels, as have been observed experimentally. CH3+H is mostly formed by direct dissociation that is accompanied by hopping to the ground state. CH2+H2 can either be formed by hopping to the ground state to give CH2(ã A11)+H2 or by adiabatic dissociation to CH2(b̃ B11)+H2. In the latter case, the CH2(b̃ B11) can then undergo internal conversion to the ground singlet state by Renner–Teller induced hopping. Less important dissociation mechanisms lead to CH2+H+H and to CH+H2+H. Intersystem crossing effects, which are not included, do not seem essential to describe the experimentally observed branching behavior. About 5% of trajectories involve a roaming atom mechanism which can eventually lead to formation of products in any of the dissociation channels. Branching fractions to give H and H2 are in good agreement with experiment, and the H atom translational energy distribution shows bimodal character which also matches observations.
Blue electroluminescence from ZnO based heterojunction diodes with CdZnO active layers
Authors: Li L. , Yang Z. , Kong J. Y. , Liu J. L.
Published: December 2009

p -ZnO / i -CdZnO / n -ZnO was grown on n-type Si substrates by plasma-assisted molecular-beam epitaxy. Rectifying I-V curves show typical diode characteristics. Blue electroluminescence emissions at around 459 nm were observed when the diodes were forward-biased at room temperature. The emission intensity increases with the increase of the injection current. Temperature dependent electroluminescence measurements suggest that the peak positions of blue emissions represent the band gap of the CdZnO active layer, which changes with the temperature.
Sculpting nanometer-sized light landscape with plasmonic nanocolumns
Authors: Marty Renaud , Arbouet Arnaud , Girard Christian , Margueritat Jérémie , Gonzalo José , Afonso Carmen N.
Published: December 2009

Plasmonic structures are commonly used to both confine and enhance surface electromagnetic fields. In the past ten years, their peculiar optical properties have given rise to many promising applications ranging from high density data storage to surface optical trapping. In this context, we investigated both far-field and near-field optical response of a collection of densely packed silver nanocolumns embedded in amorphous aluminum oxide using the discrete dipole approximation. In the far field, a good fit of the calculated to the experimental absorption spectra can only be achieved when in addition to interaction between neighboring nanocolumns, a nanorod shape with periodic shrinks mimicking the experimental morphology of the nanocolumns is used. In the near field, modulated field intensities following the nanocolumns distribution and tunable with the incident wavelength are predicted outside the region occupied by the nanocolumns. This plasmonic image transfer has a resolution of approximately 1.8D where D is the diameter of the nanocolumns that in our case is 2.4 nm.
One-dimensional description of diffusion in a tube of abruptly changing diameter: Boundary homogenization based approach
Authors: Berezhkovskii Alexander M. , Barzykin Alexander V. , Zitserman Vladimir Yu.
Published: December 2009

Reduction of three-dimensional (3D) description of diffusion in a tube of variable cross section to an approximate one-dimensional (1D) description has been studied in detail previously only in tubes of slowly varying diameter. Here we discuss an effective 1D description in the opposite limiting case when the tube diameter changes abruptly, i.e., in a tube composed of any number of cylindrical sections of different diameters. The key step of our approach is an approximate description of the particle transitions between the wide and narrow parts of the tube as trapping by partially absorbing boundaries with appropriately chosen trapping rates. Boundary homogenization is used to determine the trapping rate for transitions from the wide part of the tube to the narrow one. This trapping rate is then used in combination with the condition of detailed balance to find the trapping rate for transitions in the opposite direction, from the narrow part of the tube to the wide one. Comparison with numerical solution of the 3D diffusion equation allows us to test the approximate 1D description and to establish the conditions of its applicability. We find that suggested 1D description works quite well when the wide part of the tube is not too short, whereas the length of the narrow part can be arbitrary. Taking advantage of this description in the problem of escape of diffusing particle from a cylindrical cavity through a cylindrical tunnel we can lift restricting assumptions accepted in earlier theories: We can consider the particle motion in the tunnel and in the cavity on an equal footing, i.e., we can relax the assumption of fast intracavity relaxation used in all earlier theories. As a consequence, the dependence of the escape kinetics on the particle initial position in the system can be analyzed. Moreover, using the 1D description we can analyze the escape kinetics at an arbitrary tunnel radius, whereas all earlier theories are based on the assumption that the tunnel is narrow.
Electric breakdown in ultrathin MgO tunnel barrier junctions for spin-transfer torque switching
Authors: Schäfers M. , Drewello V. , Reiss G. , Thomas A. , Thiel K. , Eilers G. , Münzenberg M. , Schuhmann H. , Seibt M.
Published: December 2009

Magnetic tunnel junctions for spin-transfer torque (STT) switching are prepared to investigate the dielectric breakdown. Intact and broken tunnel junctions are characterized by transport measurements prior to transmission electron microscopy analysis. The comparison to our previous model for thicker MgO tunnel barriers reveals a different breakdown mechanism arising from the high current densities in a STT device: instead of local pinhole formation at a constant rate, massive electromigration and heating leads to displacement of the junction material and voids are appearing. This is determined by element resolved energy dispersive x-ray spectroscopy and three dimensional tomographic reconstruction.
The cationic energy landscape in alkali silicate glasses: Properties and relevance
Authors: Lammert Heiko , Banhatti Radha D. , Heuer Andreas
Published: December 2009

Individual cationic site energies are explicitly determined from molecular dynamics simulations of alkali silicate glasses, and the properties and relevance of this local energetics to ion transport are studied. The absence of relaxations on the time scale of ion transport proves the validity of a static description of the energy landscape, as it is generally used in hopping models. The Coulomb interaction among the cations turns out to be essential to obtain an average energy landscape in agreement with typical simplified hopping models. Strong correlations exist both between neighboring sites and between different energetic contributions at one site, and they shape essential characteristics of the energy landscape. A model energy landscape with a single vacancy is used to demonstrate why average site energies, including the full Coulomb interaction, are still insufficient to describe the site population of ions, or their dynamics. This model explains how the relationship between energetics and ion dynamics is weakened, and thus establishes conclusively that a hopping picture with static energies fails to capture all the relevant information. It is therefore suggested that alternative simplified models of ion conduction are needed.
On the origin of ultrafast nonradiative transitions in nitro-polycyclic aromatic hydrocarbons: Excited-state dynamics in 1-nitronaphthalene
Authors: Reichardt Christian , Vogt R. Aaron , Crespo-Hernández Carlos E.
Published: December 2009

The electronic energy relaxation of 1-nitronaphthalene was studied in nonpolar, aprotic, and protic solvents in the time window from femtoseconds to microseconds. Excitation at 340 or 360 nm populates the Franck–Condon S1(ππ∗) state, which is proposed to bifurcate into two essentially barrierless nonradiative decay channels with sub-200 fs lifetimes. The first main decay channel connects the S1 state with a receiver Tn state that has considerable nπ∗ character. The receiver Tn state undergoes internal conversion to populate the vibrationally excited T1(ππ∗) state in 2–4 ps. It is shown that vibrational cooling dynamics in the T1 state depends on the solvent used, with average lifetimes in the range from 6 to 12 ps. Furthermore, solvation dynamics competes effectively with vibrational cooling in the triplet manifold in primary alcohols. The relaxed T1 state undergoes intersystem crossing back to the ground state within a few microseconds in N2-saturated solutions in all the solvents studied. The second minor channel involves conformational relaxation of the bright S1 state (primarily rotation of the NO2-group) to populate a dissociative singlet state with significant charge-transfer character and negligible oscillator strength. This dissociative channel is proposed to be responsible for the observed photochemistry in 1-nitronaphthalene. Ground- and excited-state calculations at the density functional level of theory that include bulk and explicit solvent effects lend support to the proposed mechanism where the fluorescent S1 state decays rapidly and irreversibly to dark excited states. A four-state kinetic model is proposed that satisfactorily explains the origin of the nonradiative electronic relaxation pathways in 1-nitronaphthalene.
Observation of metal precipitates at prebreakdown sites in multicrystalline silicon solar cells
Authors: Kwapil Wolfram , Gundel Paul , Schubert Martin C. , Heinz Friedemann D. , Warta Wilhelm , Weber Eicke R. , Goetzberger Adolf , Martinez-Criado Gema
Published: December 2009

The local prebreakdown behavior of a damage etched multicrystalline silicon solar cell produced from virgin grade feedstock was characterized. At the position of micrometer-scaled prebreakdown sites, which correlate with recombination active defects found along grain boundaries, micro-x-ray fluorescence mappings revealed the presence of Fe precipitate colonies. These measurements represent direct evidence that transition metal clusters lead to decreased breakdown voltage and cause soft diode breakdown.
Approximate inclusion of quantum effects in transition path sampling
Authors: Antoniou Dimitri , Schwartz Steven D.
Published: December 2009

We propose a method for incorporating nuclear quantum effects in transition path sampling studies of systems that consist of a few degrees of freedom that must be treated quantum mechanically, while the rest are classical-like. We used the normal mode centroid method to describe the quantum subsystem, which is a method that is not CPU intensive but still reasonably accurate. We applied this mixed centroid/classical transition path sampling method to a model system that has nontrivial quantum behavior, and showed that it can capture the correct quantum dynamical features.
Influence of film composition in Co2MnSi electrodes on tunnel magnetoresistance characteristics of Co2MnSi/MgO/Co2MnSi magnetic tunnel junctions
Authors: Ishikawa Takayuki , Liu Hong-xi , Taira Tomoyuki , Matsuda Ken-ichi , Uemura Tetsuya , Yamamoto Masafumi
Published: December 2009

Fully epitaxial Co2MnSi (CMS)/MgO/CMS magnetic tunnel junctions (MTJs) with various values of Mn composition α in Co2MnαSi electrodes were fabricated and the influence of α on the tunnel magnetoresistance (TMR) characteristics of these MTJs was investigated. MTJs with Mn-rich CMS electrodes showed TMR ratios, up to 1135% at 4.2 K and 236% at room temperature for α=1.29, exceeding those of MTJs with CMS electrodes having an almost stoichiometric composition. A possible origin of the higher TMR ratios for α beyond 1.0 is a decreased density of gap states existing around the Fermi level in the half-metal gap caused by the suppression of CoMn antisites, where a Mn site is replaced by a Co atom, for Mn-rich CMS electrodes.
Improving the coherence time of superconducting coplanar resonators
Authors: Wang H. , Hofheinz M. , Wenner J. , Ansmann M. , Bialczak R. C. , Lenander M. , Lucero Erik , Neeley M. , O’Connell A. D. , Sank D. , Weides M. , Cleland A. N. , Martinis John M.
Published: December 2009

The quality factor and energy decay time of superconducting resonators have been measured as a function of material, geometry, and magnetic field. Once the dissipation of trapped magnetic vortices is minimized, we identify a power-dependent decay mechanism that is consistent with the surface two-level state model. A wide gap between the center conductor and the ground plane, as well as use of the superconductor Re instead of Al, are shown to decrease loss. We also demonstrate that classical measurements of resonator quality factor at low excitation power are consistent with single-photon decay time measured using qubit-resonator swap experiments.
Mechanism of oxidative stress generation in cells by localized near-infrared femtosecond laser excitation
Authors: He Hao , Chan Kam Tai , Kong Siu Kai , Lee Rebecca Kit Ying
Published: December 2009

We examined the effect of femtosecond (fs) and continuous wave (CW) lasers at near-infrared range on the creation of reactive oxygen species in a human liver cancer cell line. By controlling the mitochondria electron transport chain (ETC), it was found that a major part of the oxidative stress was generated by the laser induced thermal effect on the mitochondria while the remaining part was created by direct free electron liberation by the fs pulses, which could be observed after breaking the ETC. The study helps clarify the major effects produced on animal cells when excited by fs lasers.
Resonant tunneling and negative transconductance in single barrier bilayer graphene structure
Authors: Nguyen V. Hung , Bournel A. , Nguyen V. Lien , Dollfus P.
Published: December 2009

Using the nonequilibrium Green’s function method, the electronic transport in a gate-induced barrier bilayer graphene structure is investigated. Strong resonant effects are shown to result in high amplitude oscillation of conductance as a function of Fermi energy and barrier height. Beyond a small effect of negative differential conductance (with peak to valley ratio less than 2), strong oscillations of transconductance are achieved. The amplitude of such oscillations between positive and negative values may exceed 5 mS/μm. This effect might be helpful for further development of graphene-based nanoelectronics.
Strong-field terahertz optical sideband generation for wavelength conversion in asymmetric double quantum wells
Authors: Zhang J.-Z. , Allsopp D.
Published: December 2009

Terahertz (THz) optical sideband generation in asymmetric double quantum wells in strong THz fields is studied theoretically. Both monotonic THz-power dependence and saturation of the first-order sideband intensity can occur, depending on the near infrared (NIR) and THz photon energies. In both respects the calculated sideband intensity behavior agrees with experimental findings [Appl. Phys. Lett. 75, 2728 (1999); Phys. Rev. B 70, 115312 (2004)]. The nonmonotonic THz-power dependence and saturation of the sideband intensity are due to the excitonic Stark splitting. While the sideband saturation imposes limitations on the wavelength conversion efficiency, the simultaneous broadening of sideband resonances benefits wavelength conversion by increasing the number of NIR frequencies available for wavelength conversion.
Large magnetostrain in polycrystalline Ni–Mn–In–Co
Authors: Liu Jian , Aksoy Seda , Scheerbaum Nils , Acet Mehmet , Gutfleisch Oliver
Published: December 2009

This letter reports the magnetic shape memory effect in a polycrystalline Ni45.2Mn36.7In13Co5.1 alloy having the martensitic transformation around 310 K. An application of magnetic field shifts the transformation to lower temperatures by 6.7 K/T. Originating from the magnetically induced martensite-austenite transformation, a large magnetostrain of 0.25% at 310 K was observed in a textured polycrystalline Ni45.2Mn36.7In13Co5.1 sample. Temperature, anisotropy, and cycling effects on the magnetostrain are discussed.
Nanomechanically induced molecular conductance switch
Authors: Li Xiao-Fei , Wang Lingling , Chen Ke-Qiu , Luo Yi
Published: December 2009

A mechanical single molecular switch using specific metallic broken carbon nanotubes (BCNTs) as electrodes is designed. It can operate by simply pressing one of the electrodes mechanically with robust performance. The device has been modeled by combining molecular dynamics simulations and first principles calculations. With the help of molecular dynamic simulations, a realistic description of the broken ends of the BCNT is obtained, while high ON/OFF conductance ratio has been obtained from nonequilibrium Green’s function calculations. A microscopic mechanism is suggested for the switch behavior.
Modeling of dynamic wetting far from equilibrium
Authors: Carlson Andreas , Do-Quang Minh , Amberg Gustav
Published: December 2009

In this paper we present simulations of dynamic wetting far from equilibrium based on phase field theory. In direct simulations of recent experiments [J. C. Bird, S. Mandre, and H. A. Stone, Phys. Rev. Lett. 100, 234501 (2008)], we show that in order to correctly capture the dynamics of rapid wetting, it is crucial to account for nonequilibrium at the contact line, where the gas, liquid, and solid meet. A term in the boundary condition at the solid surface that naturally arises in the phase field theory is interpreted as allowing for the establishment of a local structure in the immediate vicinity of the contact line. A direct qualitative and quantitative match with experimental data of spontaneously wetting liquid droplets is shown.
2-Dimensional soil and vadose-zone representation using an EM38 and EM34 and a laterally constrained inversion model
Authors: Triantafilis J. , Santos F. A. Monteiro
Published: December 2009

The network of prior streams and palaeochannels common across the Riverine Plains of the Murray–Darling Basin act as conduits for the redistribution of water and soluble salts beneath the root-zone. To improve scientific understanding of these hydrological processes there is the need to better represent and map the connectivity and spatial extent of these physiographic and stratigraphic features. Groundbased electromagnetic (EM) instruments, which measure bulk soil electrical conductivity (σa), have been used widely to map their areal distribution across the landscape. However, methods to resolve their location with depth have rarely been attempted. In this paper we employ a 1-D inversion algorithm with 2-D smoothness constraints to predict the true electrical conductivity (σ) at discrete depth increments using EM data. The EM data we use include the root-zone measuring EM38 and the deeper sensing EM34. We collected EM38 data in the vertical (EM38v) and horizontal (EM38h) dipole modes and EM34 data in the horizontal mode and coil spacing of 10, 20, and 40 m (respectively, EM34-10, EM34-20, and EM34-40). In order to compare and contrast the value of the various EM data we carried out multiple inversions using different combinations, which include: independent inversions of (i) EM38 (root-zone) and (ii) EM34 data (vadose-zone), and in combination using (iii) EM38v, EM38h, and EM34-10 (near-surface), and (iv) all 5 EM datasets (regolith) available. The general patterns of σ are shown to compare favourably with the known pedoderms, physiographic, and stratigraphic features and soil particle size fractions collected from calibration cores drilled across the lower Macquarie Valley study area. In general we find that the EM38 assists in resolving root-zone variability, specifically duplex soil profiles and physiographic features such as prior streams, while the use of the EM34 assists in resolving the stratigraphic nature of the vadose-zone and specifically the likely location of palaeochannels and subsurface anomalies that may indicate the location of good quality groundwater and/or clay aquitards. In this case, our potential to use σ to predict clay content is limited by the non-linearity of the cumulative functions. In order to improve on the non-linearity of our inversion we need to develop a full solution of the forward problem.
Scaling analysis of soil water retention parameters and physical properties of a Chinese agricultural soil
Authors: Wang Zhenying , Shu Qiaosheng , Liu Zuoxin , Si Bingcheng
Published: December 2009

Measurement scale of soil water retention parameters is often different from the application scale. Knowledge of scaling property of soil hydraulic parameters is important because scaling allows information to be transferred from one scale to another. The objective of this study is to examine whether these parameters have fractal scaling properties in a cultivated agricultural soil in China. Undisturbed soil samples (128) were collected from a 640-m transect at Fuxin, China. Soil water retention curve and soil physical properties were measured from each sample, and residual water content (θr), saturated soil water content (θs), and parameters αvG and n of the van Genuchten water retention function were determined by curve-fitting. In addition, multiple scale variability was evaluated through multifractal analyses.
Mass probability distribution of all properties was related to the support scale in a power law manner. Some properties such as sand content, silt content, θs, and n had mono-fractal scaling behaviour, indicating that, whether for high or low data values, they can be upscaled from small-scale measurements to large-scale applications using the measured data. The spatial distribution of organic carbon content had typically multifractal scaling property, and other properties – clay content, θr, and αvG – showed a weakly multifractal distribution. The upscaling or downscaling of multifractal distribution was more complex than that of monofractal distribution. It also suggested that distinguishing mono-fractals and multifractals is important for understanding the underlying processes, for simulation and for spatial interpolation of soil water retention characteristics and physical properties.
Two-component protein-engineered physical hydrogels for cell encapsulation
Authors: Wong Po Foo Cheryl T. S. , Lee Ji Seok , Mulyasasmita Widya , Parisi-Amon Andreina , Heilshorn Sarah C.
Published: December 2009

Current protocols to encapsulate cells within physical hydrogels require substantial changes in environmental conditions (pH, temperature, or ionic strength) to initiate gelation. These conditions can be detrimental to cells and are often difficult to reproduce, therefore complicating their use in clinical settings. We report the development of a two-component, molecular-recognition gelation strategy that enables cell encapsulation without environmental triggers. Instead, the two components, which contain multiple repeats of WW and proline-rich peptide domains, undergo a sol–gel phase transition upon simple mixing and hetero-assembly of the peptide domains. We term these materials mixing-induced, two-component hydrogels. Our results demonstrate use of the WW and proline-rich domains in protein-engineered materials and expand the library of peptides successfully designed into engineered proteins. Because both of these association domains are normally found intracellularly, their molecular recognition is not disrupted by the presence of additional biomolecules in the extracellular milieu, thereby enabling reproducible encapsulation of multiple cell types, including PC-12 neuronal-like cells, human umbilical vein endothelial cells, and murine adult neural stem cells. Precise variations in the molecular-level design of the two components including (
i
) the frequency of repeated association domains per chain and (
ii
) the association energy between domains enable tailoring of the hydrogel viscoelasticity to achieve plateau shear moduli ranging from ≈9 to 50 Pa. Because of the transient physical crosslinks that form between association domains, these hydrogels are shear-thinning, injectable, and self-healing. Neural stem cells encapsulated in the hydrogels form stable three-dimensional cultures that continue to self-renew, differentiate, and sprout extended neurites.
Specific apoptosis induction by the dual PI3K/mTor inhibitor NVP-BEZ235 in HER2 amplified and PIK3CA mutant breast cancer cells
Authors: Brachmann Saskia M. , Hofmann Irmgard , Schnell Christian , Fritsch Christine , Wee Susan , Lane Heidi , Wang Shaowen , Garcia-Echeverria Carlos , Maira Sauveur-Michel
Published: December 2009

NVP-BEZ235 is a dual PI3K/mTOR inhibitor currently in phase I clinical trials. We profiled this compound against a panel of breast tumor cell lines to identify the patient populations that would benefit from such treatment. In this setting, NVP-BEZ235 selectively induced cell death in cell lines presenting either HER2 amplification and/or PIK3CA mutation, but not in cell lines with PTEN loss of function or KRAS mutations, for which resistance could be attributed, in part to ERK pathway activity. An in depth analysis of death markers revealed that the cell death observed upon NVP-BEZ235 treatment could be recapitulated with other PI3K inhibitors and that this event is linked to active PARP cleavage indicative of an apoptotic process. Moreover, the effect seemed to be partly independent of the caspase-9 executioner and mitochondrial activated caspases, suggesting an alternate route for apoptosis induction by PI3K inhibitors. Overall, this study will provide guidance for patient stratification for forthcoming breast cancer phase II trials for NVP-BEZ235.
The DM domain protein DMRT1 is a dose-sensitive regulator of fetal germ cell proliferation and pluripotency
Authors: Krentz Anthony D. , Murphy Mark W. , Kim Shinseog , Cook Matthew S. , Capel Blanche , Zhu Rui , Matin Angabin , Sarver Aaron L. , Parker Keith L. , Griswold Michael D. , Looijenga Leendert H. J. , Bardwell Vivian J. , Zarkower David
Published: December 2009

Dmrt1
(
doublesex
and
mab-3
related transcription factor 1) is a conserved transcriptional regulator of male differentiation required for testicular development in vertebrates. Here, we show that in mice of the 129Sv strain, loss of
Dmrt1
causes a high incidence of teratomas, whereas these tumors do not form in
Dmrt1
mutant C57BL/6J mice. Conditional gene targeting indicates that
Dmrt1
is required in fetal germ cells but not in Sertoli cells to prevent teratoma formation. Mutant 129Sv germ cells undergo apparently normal differentiation up to embryonic day 13.5 (E13.5), but some cells fail to arrest mitosis and ectopically express pluripotency markers. Expression analysis and chromatin immunoprecipitation identified DMRT1 target genes, whose missexpression may underlie teratoma formation. DMRT1 indirectly activates the GDNF coreceptor
Ret
, and it directly represses the pluripotency regulator
Sox2
. Analysis of human germ cell tumors reveals similar gene expression changes correlated to
DMRT1
levels.
Dmrt1
behaves genetically as a dose-sensitive tumor suppressor gene in 129Sv mice, and natural variation in
Dmrt1
activity can confer teratoma susceptibility. This work reveals a genetic link between testicular dysgenesis, pluripotency regulation, and teratoma susceptibility that is highly sensitive to genetic background and to gene dosage.
Cross-modal cueing of attention alters appearance and early cortical processing of visual stimuli
Authors: Störmer Viola S. , McDonald John J. , Hillyard Steven A.
Published: December 2009

The question of whether attention makes sensory impressions appear more intense has been a matter of debate for over a century. Recent psychophysical studies have reported that attention increases apparent contrast of visual stimuli, but the issue continues to be debated. We obtained converging neurophysiological evidence from human observers as they judged the relative contrast of visual stimuli presented to the left and right visual fields following a lateralized auditory cue. Cross-modal cueing of attention boosted the apparent contrast of the visual target in association with an enlarged neural response in the contralateral visual cortex that began within 100 ms after target onset. The magnitude of the enhanced neural response was positively correlated with perceptual reports of the cued target being higher in contrast. The results suggest that attention increases the perceived contrast of visual stimuli by boosting early sensory processing in the visual cortex.
A backward progression of attentional effects in the ventral stream
Authors: Buffalo Elizabeth A. , Fries Pascal , Landman Rogier , Liang Hualou , Desimone Robert
Published: December 2009

The visual processing of behaviorally relevant stimuli is enhanced through top-down attentional feedback. One possibility is that feedback targets early visual areas first and the attentional enhancement builds up at progressively later stages of the visual hierarchy. An alternative possibility is that the feedback targets the higher-order areas first and the attentional effects are communicated “backward” to early visual areas. Here, we compared the magnitude and latency of attentional enhancement of firing rates in V1, V2, and V4 in the same animals performing the same task. We found a reverse order of attentional effects, such that attentional enhancement was larger and earlier in V4 and smaller and later in V1, with intermediate results in V2. These results suggest that attentional mechanisms operate via feedback from higher-order areas to lower-order ones.
miR319a targeting of
TCP4
is critical for petal growth and development in
Arabidopsis
Authors: Nag Anwesha , King Stacey , Jack Thomas
Published: December 2009

In a genetic screen in a
drnl-2
background, we isolated a loss-of-function allele in
miR319a
(

miR319a
129

). Previously,
miR319a
has been postulated to play a role in leaf development based on the dramatic curled-leaf phenotype of plants that ectopically express
miR319a
(
jaw-D
).

miR319a
129

mutants exhibit defects in petal and stamen development; petals are narrow and short, and stamens exhibit defects in anther development. The

miR319a
129

loss-of-function allele contains a single-base change in the middle of the encoded miRNA, which reduces the ability of
miR319a
to recognize targets. Analysis of the expression patterns of the three members of the miR319 gene family (
miR319a
,
miR319b
, and
miR319c
) indicates that these genes have largely non-overlapping expression patterns suggesting that these genes have distinct developmental functions.
miR319a
functions by regulating the TCP transcription factors
TCP2
,
TCP3
,
TCP4
,
TCP10
, and
TCP24
; the level of RNA expression of these TCP genes is down-regulated in
jaw-D
and elevated in

miR319a
129

. Several lines of evidence demonstrate that
TCP4
is a key target of
miR319a
. First, the

tcp4
soj6

mutant, which contains a mutation in the
TCP4
miRNA-binding site complementary to the

miR319a
129

mutation, suppresses the flower phenotype of

miR319a
129

. Second, expression of wild-type
TCP4
in petals and stamens (i.e., AP3:TCP4) has no effect on flower development; by contrast, a miRNA-resistant version of
TCP4
, when expressed in petals and stamens (i.e., pAP3:mTCP4) causes these organs not to develop. Surprisingly, when AP3:TCP4 is present in a

miR319a
129

background, petal and stamen development is severely disrupted, suggesting that proper regulation by
miR319a
of
TCP4
is critical in these floral organs.
Absence of geochemical evidence for an impact event at the Bølling–Allerød/Younger Dryas transition
Authors: Paquay François S. , Goderis Steven , Ravizza Greg , Vanhaeck Frank , Boyd Matthew , Surovell Todd A. , Holliday Vance T. , Haynes C. Vance , Claeys Philippe
Published: December 2009

High concentrations of iridium have been reported in terrestrial sediments dated at 12.9 ka and are interpreted to support an extraterrestrial impact event as the cause of the observed extinction in the Rancholabrean fauna, changes in the Paleoindian cultures, and the onset of the Younger Dryas cooling [Firestone RB, et al. (2007)Proc Natl Acad Sci USA104:16016–16021]. Here, we report platinum group element (PGE: Os, Ir, Ru, Rh, Pt, Pd), gold (Au) concentrations, and187Os/188Os ratios in time-equivalent terrestrial, lacustrine, and marine sections to seek robust evidence of an extraterrestrial contribution. First, our results do not reproduce the previously reported elevated Ir concentrations. Second,187Os/188Os isotopic ratios in the sediment layers investigated are similar to average crustal values, indicating the absence of a significant meteoritic Os contribution to these sediments. Third, no PGE anomalies distinct from crustal signatures are present in the marine record in either the Gulf of California (DSDP 480, Guaymas Basin) or the Cariaco Basin (ODP 1002C). Our data show no evidence of an extraterrestrial (ET)-PGE enrichment anomaly in any of the investigated depositional settings investigated across North America and in one section in Belgium. The lack of a clear ET-PGE signature in this sample suite is inconsistent with the impact of a large chondritic projectile at the Bølling–Allerød/Younger Dryas transition.
Magnesium-aspartate-based crystallization switch inspired from shell molt of crustacean
Authors: Tao Jinhui , Zhou Dongming , Zhang Zhisen , Xu Xurong , Tang Ruikang
Published: December 2009

Many animals such as crustacean periodically undergo cyclic molt of the exoskeleton. During this process, amorphous calcium mineral phases are biologically stabilized by magnesium and are reserved for the subsequent rapid formation of new shell tissue. However, it is a mystery how living organisms can regulate the transition of the precursor phases precisely. We reveal that the shell mineralization from the magnesium stabilized precursors is associated with the presence of Asp-rich proteins. It is suggested that a cooperative effect of magnesium and Asp-rich compound can result into a crystallization switch in biomineralization. Our in vitro experiments confirm that magnesium increases the lifetime of amorphous calcium carbonate and calcium phosphate in solution so that the crystallization can be temporarily switched off. Although Asp monomer alone inhibits the crystallization of pure amorphous calcium minerals, it actually reduces the stability of the magnesium-stabilized precursors to switch on the transformation from the amorphous to crystallized phases. These modification effects on crystallization kinetics can be understood by an Asp-enhanced magnesium desolvation model. The interesting magnesium-Asp-based switch is a biologically inspired lesson from nature, which can be developed into an advanced strategy to control material fabrications.
Error-prone translesion replication of damaged DNA suppresses skin carcinogenesis by controlling inflammatory hyperplasia
Authors: Tsaalbi-Shtylik Anastasia , Verspuy Johan W. A. , Jansen Jacob G. , Rebel Heggert , Carlée Leone M. , van der Valk Martin A. , Jonkers Jos , de Gruijl Frank R. , de Wind Niels
Published: December 2009

The induction of skin cancer involves both mutagenic and proliferative responses of the epidermis to ultraviolet (UV) light. It is believed that tumor initiation requires the mutagenic replication of damaged DNA by translesion synthesis (TLS) pathways. The mechanistic basis for the induction of proliferation, providing tumor promotion, is poorly understood. Here, we have investigated the role of TLS in the initiation and promotion of skin carcinogenesis, using a sensitive nucleotide excision repair-deficient mouse model that carries a hypomorphic allele of the error-prone TLS geneRev1. Despite a defect in UV-induced mutagenesis, skin carcinogenesis was accelerated in these mice. This paradoxical phenotype was caused by the induction of inflammatory hyperplasia of the mutant skin that provides strong tumor promotion. The induction of hyperplasia was associated with mild and transient replicational stress of the UV-damaged genome, triggering DNA damage signaling and senescence. The concomitant expression of Interleukin-6 (IL-6) is in agreement with an executive role for IL-6 and possibly other cytokines in the autocrine induction of senescence and the paracrine induction of inflammatory hyperplasia. In conclusion, error-prone TLS suppresses tumor-promoting activities of UV light, thereby controlling skin carcinogenesis.
A designer ligand specific for Kv1.3 channels from a scorpion neurotoxin-based library
Authors: Takacs Zoltan , Toups Megan , Kollewe Astrid , Johnson Erik , Cuello Luis G. , Driessens Gregory , Biancalana Matthew , Koide Akiko , Ponte Cristiano G. , Perozo Eduardo , Gajewski Thomas F. , Suarez-Kurtz Guilherme , Koide Shohei , Goldstein Steve A. N.
Published: December 2009

Venomous animals immobilize prey using protein toxins that act on ion channels and other targets of biological importance. Broad use of toxins for biomedical research, diagnosis, and therapy has been limited by inadequate target discrimination, for example, among ion channel subtypes. Here, a synthetic toxin is produced by a new strategy to be specific for human Kv1.3 channels, critical regulators of immune T cells. A phage display library of 11,200 de novo proteins is designed using the α-KTx scaffold of 31 scorpion toxin sequences known or predicted to bind to potassium channels. Mokatoxin-1 (moka1) is isolated by affinity selection on purified target. Moka1 blocks Kv1.3 at nanomolar levels that do not inhibit Kv1.1, Kv1.2, or KCa1.1. As a result, moka1 suppresses CD3/28-induced cytokine secretion by T cells without cross-reactive gastrointestinal hyperactivity. The 3D structure of moka1 rationalizes its specificity and validates the engineering approach, revealing a unique interaction surface supported on an α-KTx scaffold. This scaffold-based/target-biased strategy overcomes many obstacles to production of selective toxins.
The atomic structure of baculovirus polyhedra reveals the independent emergence of infectious crystals in DNA and RNA viruses
Authors: Coulibaly Fasséli , Chiu Elaine , Gutmann Sascha , Rajendran Chitra , Haebel Peter W. , Ikeda Keiko , Mori Hajime , Ward Vernon K. , Schulze-Briese Clemens , Metcalf Peter
Published: December 2009

Baculoviruses are ubiquitous insect viruses well known for their use as bioinsecticides, gene therapy vectors, and protein expression systems. Overexpression of recombinant proteins in insect cell culture utilizes the strong promoter of the polyhedrin gene. In infected larvae, the polyhedrin protein forms robust intracellular crystals called polyhedra, which protect encased virions for prolonged periods in the environment. Polyhedra are produced by two unrelated families of insect viruses, baculoviruses and cypoviruses. The atomic structure of cypovirus polyhedra revealed an intricate packing of trimers, which are interconnected by a projecting N-terminal helical arm of the polyhedrin molecule. Baculovirus and cypovirus polyhedra share nearly identical lattices, and the N-terminal region of the otherwise unrelated baculovirus polyhedrin protein sequence is also predicted to be α-helical. These results suggest homology between the proteins and a common structural basis for viral polyhedra. Here, we present the 2.2-Å structure of baculovirus polyhedra determined by x-ray crystallography from microcrystals produced in vivo. We show that the underlying molecular organization is, in fact, very different. Although both polyhedra have nearly identical unit cell dimensions and share I23 symmetry, the polyhedrin molecules are structurally unrelated and pack differently in the crystals. In particular, disulfide bonds and domain-swapped N-terminal domains stabilize the building blocks of baculovirus polyhedra and interlocking C-terminal arms join unit cells together. We show that the N-terminal projecting helical arms have different structural roles in baculovirus and cypovirus polyhedra and conclude that there is no structural evidence for a common evolutionary origin for both classes of polyhedra.