bluuebunny/crossref_metadata_2025 huggingface dataset:
Theoretical analysis on changes in thermodynamic quantities upon protein folding: Essential role of hydration
Authors: Imai Takashi , Harano Yuichi , Kinoshita Masahiro , Kovalenko Andriy , Hirata Fumio
Published: June 2007

The free energy change associated with the coil-to-native structural transition of protein G in aqueous solution is calculated by using the molecular theory of solvation, also known as the three-dimensional reference interaction site model theory, to uncover the molecular mechanism of protein folding. The free energy is decomposed into the protein intramolecular energy, the hydration energy, and the hydration entropy. The folding is accompanied with a large gain in the protein intramolecular energy. However, it is almost canceled by the correspondingly large loss in the hydration energy due to the dehydration, resulting in the total energy gain about an order of magnitude smaller than might occur in vacuum. The hydration entropy gain is found to be a substantial driving force in protein folding. It is comparable with or even larger than the total energy gain. The total energy gain coupled with the hydration entropy gain is capable of suppressing the conformational entropy loss in the folding. Based on careful analysis of the theoretical results, the authors present a challenging physical picture of protein folding where the overall folding process is driven by the water entropy effect.
Mid-infrared AlxIn1−xSb light-emitting diodes
Authors: Haigh M. K. , Nash G. R. , Smith S. J. , Buckle L. , Emeny M. T. , Ashley T.
Published: June 2007

The properties of AlxIn1−xSb light-emitting diodes (LEDs) have been investigated as a function of aluminum concentrations between 0% and 8.8%. By varying the aluminum concentration it is possible to tailor the peak emission wavelength to match the characteristic absorption of CO2, CO, CH4, NO, and NO2, making these diodes suitable for use in infrared gas sensing applications. The total emitted power and internal quantum efficiency were found to have maxima of 27mW∕cm2 and 4.2%, respectively, at a composition of 2.5%, where the peak emission was found to be 5.3μm, making LEDs of this composition particularly suited to the detection of NO.
Monte Carlo simulations of equilibrium solubilities and structure of water in n-alkanes and polyethylene
Authors: Johansson E. , Bolton K. , Theodorou D. N. , Ahlström P.
Published: June 2007

Gibbs ensemble Monte Carlo methods based on a force field that combines the simple point charge [Berendsen et al., in Intermolecular Forces, edited by Pullman (Reidel, Dordrecht, 1981), p. 331] and transferable potentials for phase equilibria [Martin and Siepmann, J. Phys. Chem. B 102, 2659 (1998)] models were used to study the equilibrium properties of binary systems consisting of water and n-alkanes with chain lengths from hexane to hexadecane. In addition, systems where extended linear alkane chains (up to 300 carbon units long) were used to represent amorphous polyethylene were simulated in the presence of water using a connectivity altering osmotic Gibbs ensemble. In these simulations the equilibrium between a liquid water phase and a polymer phase into which water was inserted was studied. The predicted solubilities, which were determined between 350 and 550K, are in good agreement with experiment, where experimental results are available, and the density of water molecules in the hydrocarbons is approximately 63% as high as in saturated water vapor under the same conditions. At the lower temperatures most of the water exists as monomers; increasing the temperature leads to an increase in the density of water in the alkane phase and hence in the fraction of molecules that participate in clusters. Dimers are the most prevalent clusters in all hydrocarbons and at all temperatures studied, and the fraction of clusters of given size decrease with increasing cluster size. A large fraction of trimers, tetramers, and pentamers, which are the cluster sizes for which topologies have been studied, are cyclic at low temperatures, but at higher temperatures linear structures predominate. The same properties are observed for pure water vapor clusters in equilibrium with the liquid phase, showing that the cluster topologies are not significantly affected by the surrounding hydrocarbon.
Real or artifactual symmetry breaking in the BNB radical: A multireference coupled cluster viewpoint
Authors: Li Xiangzhu , Paldus Josef
Published: June 2007

The ground state of the linear BNB radical has been examined via the recently developed reduced multireference coupled cluster method with singles and doubles that is perturbatively corrected for triples [RMR CCSD(T)] using the correlation consistent basis sets (cc-pVXZ, X=D, T, and Q). Similar to earlier results that were based on the single reference CCSD(T) and BD(T) approaches, the RMR CCSD(T) method also predicts an asymmetric structure with two BN bonds of unequal length, even though the MR effects significantly reduce the barrier height. The computed frequencies for the symmetric and antisymmetric stretching modes agree reasonably well with the experimental data.
Band gap energy modifications observed in trivalent In substituted nanocrystalline SnO2
Authors: Drake C. , Seal S.
Published: June 2007

The effect of In doping concentration on the optical band gap of nano-SnO2 is investigated as a function of calcination temperature. Changes in the band gap explain the room temperature H2 gas sensing of doped nano-SnO2. The band gap was found to be lower than those reported for SnO2 (3.6eV) from 2.55to3.43eV and may be explained by the presence of nonequilibrium oxygen vacancies in the oxide lattice and band bending effects at the nanoscale.
Scanning gate microscopy of InAs nanowires
Authors: Zhou X. , Dayeh S. A. , Wang D. , Yu E. T.
Published: June 2007

Scanning gate microscopy, in which a conductive probe tip in an atomic force microscope is employed as a local, nanoscale top gate contact, has been used to characterize local carrier and current modulation effects in a 45nm diameter InAs semiconductor nanowire grown by metal organic chemical vapor deposition. Measurement of current flow in the nanowire as a function of tip position reveals that for both positive and negative tip bias voltages, carrier and current modulation is strongest when the probe tip is near the source and drain nanowire contacts, reaching a global maximum approximately 100–200nm distant from the source contact and a secondary maximum a similar distance from the drain contact and decreasing at greater tip-contact distances. This effect is explained, with verification by numerical simulation, as a consequence of the capacitance between the tip and the source and drain contacts as a function of tip location. Measurement of transconductance as a function of tip position reveals that the transconductance is approximately 80%–90% greater near the source contact than at the center of the nanowire.
Temperature dependencies of annealing behaviors of GaInNAsSb∕GaNAs quantum wells for long wavelength dilute-nitride lasers
Authors: Bae Hopil P. , Bank Seth R. , Yuen Homan B. , Sarmiento Tomas , Pickett Evan R. , Wistey Mark A. , Harris James S.
Published: June 2007

The photoluminescence (PL) spectra of GaInNAs(Sb)∕GaNAs quantum well samples emitting around 1.5μm, annealed at different temperatures and for different durations, were compared. Two distinct processes with widely different temperature dependencies are identified: PL intensity improvement at the beginning of annealing and PL intensity degradation when overannealed. The degradation process has a much steeper temperature dependence than the improvement process, so lower-temperature, longer-duration annealings result in both a higher photoluminescence intensity and a broader process window than higher-temperature, shorter-duration annealings. The lowest threshold of 1.55 GaInNAs(Sb) lasers up to now was obtained exclusively with short, hot annealings, this finding offers another method of further improving dilute-nitride laser performance. Similar trends are found for different compositions and thicknesses of GaInNAs(Sb).
Sensitive detection of nanoparticles using metallic nanoslit arrays
Authors: Lee Kuang-Li , Lee Chia-Wei , Wei Pei-Kuen
Published: June 2007

The detection sensitivity of small nanoparticles was studied using surface plasmons in a metallic nanoslit array. When 13nm gold nanoparticles were immobilized on the array, the resonant wavelength and intensity of surface plasmons are substantially changed. Spectroscopic measurements and finite-difference time-domain calculations identified that the surface plasmons in the slit gap had a greater sensitivity than those on the outside surface. Using a nanoslit array with a gap of 50nm, a thickness of 150nm, and a period of 600nm, the authors achieved a detection sensitivity of 1nanoparticle∕μm2 for a 0.2% intensity change.
Near bulk-limited R0A of long-wavelength infrared type-II InAs∕GaSb superlattice photodiodes with polyimide surface passivation
Authors: Hood Andrew , Delaunay Pierre-Yves , Hoffman Darin , Nguyen Binh-Minh , Wei Yajun , Razeghi Manijeh , Nathan Vaidya
Published: June 2007

Effective surface passivation of type-II InAs∕GaSb superlattice photodiodes with cutoff wavelengths in the long-wavelength infrared is presented. A stable passivation layer, the electrical properties of which do not change as a function of the ambient environment nor time, has been prepared by a solvent-based surface preparation, vacuum desorption, and the application of an insulating polyimide layer. Passivated photodiodes, with dimensions ranging from 400×400to25×25μm2, with a cutoff wavelength of ∼11μm, exhibited near bulk-limited R0A values of ∼12Ωcm2, surface resistivities in excess of 104Ωcm, and very uniform current-voltage behavior at 77K.
Correlation between optoelectronic and structural properties and epilayer thickness of AlN
Authors: Pantha B. N. , Dahal R. , Nakarmi M. L. , Nepal N. , Li J. , Lin J. Y. , Jiang H. X. , Paduano Q. S. , Weyburne David
Published: June 2007

AlN epilayers were grown by metal organic chemical vapor deposition on sapphire substrates. X-ray diffraction measurements revealed that the threading dislocation (TD) density, in particular, the edge TD density, decreases considerably with increasing the epilayer thickness. Photoluminescence results showed that the intensity ratio of the band edge emission to the defect related emission increases linearly with increasing the epilayer thickness. Moreover, the dark current of the fabricated AlN metal-semiconductor-metal deep ultraviolet (DUV) photodetectors decreases drastically with the AlN epilayer thickness. The results suggested that one effective way for attaining DUV optoelectronic devices with improved performance is to increase the thickness of the AlN epilayer template, which results in the reduction of the TD density.
Phosphorescent organic light-emitting device with an ambipolar oxadiazole host
Authors: Lee Jiun-Haw , Tsai Hsin-Hung , Leung Man-Kit , Yang Chih-Chiang , Chao Chun-Chieh
Published: June 2007

In this latter, the authors demonstrated a phosphorescent organic light-emitting device (OLED) with a lower driving voltage and a longer operation lifetime based on 2,2′-bis[5-phenyl-2-(1,3,4)oxadazolyl]biphenyl, an oxadiazole (OXD) derivative, as the host of the emitting layer doped with a common green-emitting phosphorescent dopant, fac-tris(2-phenylpyridine) iridium [Ir(ppy)3]. Rather than an electron transporting materials, the OXD exhibits an ambipolar transport characteristic with suitable Ir(ppy)3 concentrations due to its low highest occupied molecular orbital value (5.9eV) and the hole-transporting characteristics of Ir(ppy)3. It results in a 2.4V voltage reduction and a 2.6 times lifetime elongation of the OXD-based device, as compared to the conventional phosphorescent OLED.
Fabrication of thin-film organic transistor on flexible substrate via ultraviolet transfer embossing
Authors: Zhang Jun , Li Chang Ming , Chan-Park Mary B. , Zhou Qin , Gan Ye , Qin Fang , Ong Beng , Chen Tupei
Published: June 2007

Organic field-effect transistors with large-area coverage on flexible plastic substrates are fabricated by ultraviolet transfer embossing printing method. The source and drain electrodes are formed on the plastic substrate with gold by means of transfer embossing. The active layer is spin coated from 5wt% poly(3-hexylthiophene)-chloroform solution. Poly(4-vinylphenol) is used as the dielectric layer and a thin layer of silver paste is applied to cover the channel area as the gate electrode. The device shows good saturation behavior and gives an on/off ratio of 102 and the extracted field-effect mobility of the transistor is 0.0016cm2∕Vs.
Interface mechanism of ultrasonic flip chip bonding
Authors: Li J. , Han L. , Duan J. , Zhong J.
Published: June 2007

The authors demonstrate that the ultrasonic vibration in flip chip (FC) bonding results in the generation of dislocations, and the atomic diffusion can be activated more easily along the dislocation lines which perform the fast diffusion channels, thus the dislocation diffusion is probably more prominent than the body diffusion during ultrasonic bonding. To minimize the intermetallic compound layer, the effectiveness of a different bonding approach is confirmed. Furthermore, an experiment-based mode of ultrasonic energy conversion was found that the ratio of up interface to down interface in ultrasonic FC bonding was about 2.3:1.
Single-wall carbon nanotube networks as a transparent back contact in CdTe solar cells
Authors: Barnes T. M. , Wu X. , Zhou J. , Duda A. , van de Lagemaat J. , Coutts T. J. , Weeks C. L. , Britz D. A. , Glatkowski P.
Published: June 2007

Single-wall carbon nanotube (SWCNT) networks form a highly transparent and electrically conductive thin film that can be used to replace traditional transparent conducting oxides (TCOs) in a variety of applications. Here, the authors demonstrate their use as a transparent back contact in a near-infrared (NIR) transparent CdTe solar cell. SWCNT networks are hole-selective conductors and have a significantly greater NIR transparency than TCOs—qualities which could both make them very useful in tandem thin-film solar cells. SWCNT networks can be incorporated into single-junction CdTe devices and in CdTe top cells for mechanically stacked thin-film tandem devices, as described here. The best device efficiency using SWCNTs in the back contact was 12.4%, with 40%–50% transmission between 800 and 1500nm.
Analysis of diffuse phase transition and relaxorlike behaviors in Pb0.5Sr0.5TiO3 films through dc electric-field dependence of dielectric response
Authors: Yang Jing , Chu Junhao , Shen Mingrong
Published: June 2007

The pulsed-laser deposited Pb0.5Sr0.5TiO3 (PST) films with typical diffuse phase transition (DPT) and relaxorlike characteristics have been investigated by dc electric-field dependence of dielectric response. It was found that the butterfly hysteresis still persists above the Curie temperature on the curves of dielectric constant changing with the dc electric field. This result was correlated with the existence of polar nanoregions (PNRs) in the PST films, as well established in terms of a multipolarization mechanism model. Consequently, the existence of PNRs may be one of the crucial causes of the DPT and relaxorlike behaviors in PST ferroelectric films.
V
5
+
ionic displacement induced ferroelectric behavior in V-doped ZnO films
Authors: Yang Y. C. , Song C. , Zeng F. , Pan F. , Xie Y. N. , Liu T.
Published: June 2007

V-doped ZnO films have been prepared on Si(111) substrates by direct current reactive magnetron cosputtering. Hysteresis loops of polarization–applied field characteristics with a remnant polarization of 0.2μC∕cm2 were obtained in (2.5at.%) V-doped ZnO films, indicating the ferroelectric behavior exists in this system. This is demonstrated by displacement-voltage curves, which show typical butterfly shapes. X-ray absorption near-edge structure (XANES) spectrum at V K edge shows that V is in the 5+ state replacing Zn. Furthermore, the calculations of the XANES spectra indicate that a V5+ ionic displacement of 0.15Å is responsible for the ferroelectric behavior.
Finite element analysis of resistivity measurement with van der Pauw method in a diamond anvil cell
Authors: Huang Xiaowei , Gao Chunxiao , Han Yonghao , Li Ming , He Chunyuan , Hao Aimin , Zhang Dongmei , Yu Cuiling , Zou Guangtian , Ma Yanzhang
Published: June 2007

Using finite element analysis, the authors studied the steady current field distribution under the configuration of van der Pauw method [L. J. van der Pauw, Philips Tech. Rev. 20, 220 (1958)] for resistivity measurement in a diamond anvil cell. Based on the theoretical analysis, the authors obtained the theoretical accuracy curve of the van der Pauw method. This method provides accurate determination of sample resistivity when the ratio of sample thickness to its diameter is less than 0.45. They found that the contact area between electrode and sample is a key factor in the resistivity measurement accuracy and its size is dependent on the sample diameter for a given measurement accuracy.
Amplified spontaneous emission in para-sexiphenyl bulk single crystals
Authors: Losio Paolo A. , Hunziker Christoph , Günter Peter
Published: June 2007

Amplified spontaneous emission (ASE) in single crystals of para-sexiphenyl grown in the β phase by vapor transport is demonstrated upon photoexcitation at 355nm. Excitation with femtosecond laser pulses leads to dual wavelength ASE at 427 and 450nm, while excitation with nanosecond laser pulses leads to ASE only at 450nm. The threshold fluences for nanosecond and femtosecond pumpings are determined to be 885 and 110μJ∕cm2, respectively. Additionally, the singlet exciton annihilation rate is measured to be γss=(1.2±0.1)×10−6cm3s−1.
Discrete monolayer light emission from GaSb wetting layer in GaAs
Authors: Lo Ming-Cheng , Huang Shyh-Jer , Lee Chien-Ping , Lin Sheng-Di , Yen Shun-Tung
Published: June 2007

Distinct light emission peaks from monolayers of GaSb quantum wells in GaAs were observed. Discrete atomic layers of GaSb for the wetting layer prior to quantum dot formation give rise to transition peaks corresponding to quantum wells with 1, 2, and 3 ML. From the transition energies the authors were able to deduce the band offset parameter between GaSb and GaAs. By fitting the experimental data with the theoretical calculated result using an 8×8 k∙p Burt’s Hamiltonian along with the Bir-Picus deformation potentials, the strain-free (fully strained) valence band discontinuity for this type-II heterojunction was determined to be 0.45eV (0.66eV).
Trapping of dielectric particles with light-induced space-charge fields
Authors: Eggert H. A. , Kuhnert F. Y. , Buse K. , Adleman J. R. , Psaltis D.
Published: June 2007

Light-induced space-charge fields in lithium niobate crystals are used to trap and manipulate dielectric particles on the surface of such crystals. Without any external voltage source, strong field gradients are present in the proximity of the crystal surface. These are used to trap particles with diameters in the range between 100nm and some tens of micrometers.
Elimination of negative differential conductance in an asymmetric molecular transistor by an ac voltage
Authors: Dong Bing , Lei X. L. , Horing N. J. M.
Published: June 2007

The authors analyze resonant tunneling subject to a nonadiabatic time-dependent bias voltage through an asymmetric single molecular quantum dot with coupling between the electronic and vibrational degrees of freedom using a Tien-Gordon-type rate equation. The results clearly exhibit the appearance of photon-assisted satellites in the current-voltage characteristics and the elimination of hot-phonon-induced negative differential conductance with increasing ac driving amplitude for an asymmetric system. This can be ascribed to an ac-induced suppression of unequilibrated (hot) phonons in an asymmetric system.
Visual-infrared electroluminescence emission from ZnO∕GaAs heterojunctions grown by metal-organic chemical vapor deposition
Authors: Du Guotong , Cui Yongguo , Xiaochuan Xia , Li Xiangping , Zhu Huichao , Zhang Baolin , Zhang Yuantao , Ma Yan
Published: June 2007

The light-emitting diode of p-ZnO∕n-GaAs heterojunction was grown by metal-organic chemical vapor deposition. The p-ZnO films have been formed by the doping As atoms which diffuse into ZnO film from GaAs substrate. The p-type behavior of As-doped ZnO films based on As-doped p-ZnO∕n-GaAs, p-ZnO∕p-GaAs heterojunction was studied by carrying out I-V measurements and x-ray photoelectron spectroscopy. The I-V characteristic of p-ZnO∕n-GaAs heterojunction showed characteristic of rectifying diode and visual-infrared electroluminescence emission under forward current injection at room temperature. The I-V of the heterounction had a threshold voltage of ∼2.5V.
Realization of highly reproducible ZnO nanowire field effect transistors with n-channel depletion and enhancement modes
Authors: Hong Woong-Ki , Hwang Dae-Kue , Park Il-Kyu , Jo Gunho , Song Sunghoon , Park Seong-Ju , Lee Takhee , Kim Bong-Joong , Stach Eric A.
Published: June 2007

The authors demonstrate the highly reproducible fabrication of n-channel depletion-mode (D-mode) and enhancement-mode (E-mode) field effect transistors (FETs) created from ZnO nanowires (NWs). ZnO NWs were grown by the vapor transport method on two different types of substrates. It was determined that the FETs created from ZnO NWs grown on an Au-coated sapphire substrate exhibited an n-channel D mode, whereas the FETs of ZnO NWs grown on an Au-catalyst-free ZnO film exhibited an n-channel E mode. This controlled fabrication of the two operation modes of ZnO NW-FETs is important for the wide application of NW-FETs in logic circuits.
Cation, dipole, and spin order in Pb(Fe2∕3W1∕3)O3-based magnetoelectric multiferroic compounds
Authors: Wongmaneerung R. , Tan X. , McCallum R. W. , Ananta S. , Yimnirun R.
Published: June 2007

Long range 1:1 cation order was developed in Pb(Fe2(1−x)∕3Sc2x∕3W1∕3)O3 solid solution compounds by high temperature solid state reaction. It is found that the degree of cation order directly influences the saturation magnetization in these single phase compounds. A high saturation magnetization (∼0.61μB∕f.u.) was observed for x=0.15 at 10K under 5T. A ferrimagnetic structure was suggested to take into account for the observed magnetic behavior. These compounds also display a saturated electrical polarization of ∼15μC∕cm2 at 40kV∕cm at 120K.
Nearly full density Ni52.5Nb10Zr15Ti15Pt7.5 bulk metallic glass obtained by spark plasma sintering of gas atomized powders
Authors: Xie Guoqiang , Louzguine-Luzgin Dmitri V. , Kimura Hisamichi , Inoue Akihisa
Published: June 2007

Ni-based bulk metallic glasses (BMGs) with a large size were fabricated by spark plasma sintering (SPS) of a gas-atomized Ni52.5Nb10Zr15Ti15Pt7.5 glassy alloy powder. The structure and thermal stability of the sintered specimens as well as the interface characteristics between powder particles were investigated. The sintered glassy specimens with nearly 100% relative density were obtained by the SPS process at a sintering temperature of 773K with a loading pressure of 600MPa. It was achieved using relatively low sintering temperature, short holding time, and rapid cooling during the SPS process. The results suggest that the BMGs fabricated by the SPS process opens possibilities of application as structural materials offering excellent properties and satisfying large-size requirements.
Transformation media that rotate electromagnetic fields
Authors: Chen Huanyang , Chan C. T.
Published: June 2007

The authors suggest a way to manipulate electromagnetic waves by introducing a rotation mapping of coordinates that can be realized by a specific transformation of the permittivity and permeability of a shell surrounding an enclosed domain. Inside the enclosed domain, the information from the outside will appear as if it is coming from a different angle. Numerical simulations were performed to illustrate these properties.
Improved long-term thermal stability of InGaN∕GaN multiple quantum well light-emitting diodes using TiB2- and Ir-based p-Ohmic contacts
Authors: Stafford L. , Voss L. F. , Pearton S. J. , Wang H. T. , Ren F.
Published: June 2007

In Ga N ∕ Ga N multiple quantum well light-emitting diodes (MQW-LEDs) were fabricated with either Ni∕Au∕TiB2∕Ti∕Au or Ni∕Au∕Ir∕Au p-Ohmic contacts and annealed at 200 and 350°C for 45days. By comparison with companion devices with conventional Ni∕Au Ohmic contacts fabricated on the same wafer, MQW-LEDs with TiB2- and Ir-based Ohmic metallization schemes showed superior long-term thermal stability as judged by the change in turn-on voltage, leakage current, and output power, a promising result for applications where reliable operation at high temperature is required.
Localized switching mechanism in resistive switching of atomic-layer-deposited TiO2 thin films
Authors: Kim Kyung Min , Choi Byung Joon , Hwang Cheol Seong
Published: June 2007

The resistance switching mechanism of TiO2 films under voltage sweep mode was investigated. From the observed soft set of Pt∕TiO2∕Pt sample and from the polarity-dependant switching behavior of Ir(O)∕TiO2∕Pt sample, local rupture and recovery of conducting filaments near the anode interface wer identified as the switching mechanism. This is consistent with the authors’ recent observation [K. Kim et al., Electrchem. Solid-State Lett. 9, G343 (2006)] of the resistance switching property of Al2O3∕TiO2 multilayers, where switching was controlled by the layer close to the anode. It appears that most parts of the filaments are preserved during switching and only a small portion of the film near the anode contributes to switching.
Effects of pulsed-excitation applied voltage rise time on argon metastable production efficiency in a high pressure dielectric barrier discharge
Authors: Leiweke Robert J. , Ganguly Biswa N.
Published: June 2007

The authors have quantified the effect of pressure scaling on Ar metastable production efficiency in a dielectric barrier discharge with and without dielectric component losses. Estimates of the volume averaged deposited energy were performed for both short or long rise time voltage pulses, using the same total applied voltages of ∼10 and ∼150ns, respectively. The metastable production efficiencies of long-pulse discharge exhibit smaller decrease over the 100–500Torr pressure range, compared to those of the short-pulse one to the extent that the efficiency values and scaling for both cases are essentially the same within the experimental uncertainty.
Evidence of internal Bauschinger test in nanocomposite wires during in situ macroscopic tensile cycling under synchrotron beam
Authors: Thilly L. , Renault P. O. , Van Petegem S. , Brandstetter S. , Schmitt B. , Van Swygenhoven H. , Vidal V. , Lecouturier F.
Published: June 2007

In situ multiple tensile load-unload cycles under synchrotron radiation are performed on nanocomposite Cu∕Nb wires. The phase specific lattice strains and peak widths demonstrate the dynamics of the load-sharing mechanism where the fine Cu channels and the Nb nanotubes store elastic energy, leading to a continuous buildup of internal stress. The in situ technique reveals the details of the macroscopically observed Bauschinger effect.
Electron lifetime measurements of heavily C-doped InGaAs and GaAsSb as a function of the doping density
Authors: Vignaud D. , Yarekha D. A. , Lampin J. F. , Zaknoune M. , Godey S. , Mollot F.
Published: June 2007

The electron lifetime has been measured by time-resolved differential transmission experiments in heavily carbon-doped p-type InGaAs and GaAsSb, grown lattice matched on InP by molecular beam epitaxy. It is found inversely proportional to the square of the doping in both alloys, a result typical of Auger recombination dominated processes. It is shown that the electron lifetime is almost twice larger in GaAsSb than in InGaAs for large p-type doping, thus confirming that GaAsSb is a strong contender for the base material of double heterostructure bipolar transistors on InP.
Structural and magnetic properties of Co2FeAl1−xSix
Authors: Balke Benjamin , Fecher Gerhard H. , Felser Claudia
Published: June 2007

This work reports about the structural and magnetic properties of the quaternary Heusler alloy Co2FeAl1−xSix with varying Si concentration. The structure of the Co2FeAl1−xSix solid solution was investigated by means of x-ray diffraction and differential scanning calorimetry. It is found that the alloys exhibit the L21 structure for x⩾0.4. Depending on the Si concentration x, a structural phase transition is found at temperatures between 1000 and 1200K. The transition temperature decreases with increasing Si content x. The magnetic properties were studied using low temperature magnetometry. For x⩾0.4, the magnetization of the compounds is in agreement with a Slater-Pauling-like behavior and with the values obtained from ab initio calculations. For x⩽0.4, enlarged magnetic moments are found due to disorder. The enlarged values are explained by an increase of the Co spin moments and enhanced orbital moments.
Particle transport in a nonuniform flow field: Retardation and clogging
Authors: Valdes Julio R. , Carlos Santamarina J.
Published: June 2007

The authors examine the time delays experienced by migratory particles inside nonuniform flow fields using experimental and numerical methods. Particle trajectories are affected by the particle-fluid density ratio and the flow direction, such that particles may precede or trail the fluid. In flow toward an orifice, the time delay suffered by a single particle is a function of the Froude number Fr and the Archimedes number Ar. When multiple particles are transported radially through a porous medium, time delays manifest through localized annular clogging when 0.05<Ar−1<0.15 and Fr<6. Gradual particle sedimentation occurs when Ar−1>1. Applications include filtration and reservoir fluid extraction.
Protein folding under confinement: A role for solvent
Authors: Lucent Del , Vishal V. , Pande Vijay S.
Published: June 2007

Although most experimental and theoretical studies of protein folding involve proteins
in vitro
, the effects of spatial confinement may complicate protein folding
in vivo
. In this study, we examine the folding dynamics of villin (a small fast folding protein) with explicit solvent confined to an inert nanopore. We have calculated the probability of folding before unfolding (
P
fold
) under various confinement regimes. Using
P
fold
correlation techniques, we observed two competing effects. Confining protein alone promotes folding by destabilizing the unfolded state. In contrast, confining both protein and solvent gives rise to a solvent-mediated effect that destabilizes the native state. When both protein and solvent are confined we see unfolding to a compact unfolded state different from the unfolded state seen in bulk. Thus, we demonstrate that the confinement of solvent has a significant impact on protein kinetics and thermodynamics. We conclude with a discussion of the implications of these results for folding in confined environments such as the chaperonin cavity
in vivo
.
Salinity-dependent diatom biosilicification implies an important role of external ionic strength
Authors: Vrieling Engel G. , Sun Qianyao , Tian Mingwen , Kooyman Patricia J. , Gieskes Winfried W. C. , van Santen Rutger A. , Sommerdijk Nico A. J. M.
Published: June 2007

The role of external ionic strength in diatom biosilica formation was assessed by monitoring the nanostructural changes in the biosilica of the two marine diatom species
Thalassiosira punctigera
and
Thalassiosira weissflogii
that was obtained from cultures grown at two distinct salinities. Using physicochemical methods, we found that at lower salinity the specific surface area, the fractal dimensions, and the size of mesopores present in the biosilica decreased. Diatom biosilica appears to be denser at the lower salinity that was applied. This phenomenon can be explained by assuming aggregation of smaller coalescing silica particles inside the silica deposition vesicle, which would be in line with principles in silica chemistry. Apparently, external ionic strength has an important effect on diatom biosilica formation, making it tempting to propose that uptake of silicic acid and other external ions may take place simultaneously. Uptake and transport of reactants in the proximity of the expanding silica deposition vesicle, by (macro)pinocytosis, are more likely than intracellular stabilization and transport of silica precursors at the high concentrations that are necessary for the formation of the siliceous frustule components.
Fueling protein–DNA interactions inside porous nanocontainers
Authors: Cisse Ibrahim , Okumus Burak , Joo Chirlmin , Ha Taekjip
Published: June 2007

Vesicle encapsulation offers a biologically relevant environment for many soluble proteins and nucleic acids and an optimal immobilization medium for single-molecule fluorescence assays. Furthermore, the confinement of biomolecules within small volumes opens up new avenues to unique experimental configurations. Nevertheless, the vesicles' impermeability, even toward ions and other small molecules such as ATP, hinders more general applications. We therefore developed methods to induce pores into vesicles. Porous vesicles were then used to modulate the interaction between
Escherichia coli
RecA proteins and ssDNA by changing the extravesicular nucleotides. Repetitive binding and dissociation of the same RecA filament on the DNA was observed with a rebinding rate two orders of magnitude greater than in the absence of confinement, suggesting a previously unreported nucleation pathway for RecA filament. This method provides a biofriendly and simple alternative to surface tethering that is ideal for the study of transient and weakly interacting biological complexes.
Caenorhabditis elegans
SID-2 is required for environmental RNA interference
Authors: Winston William M. , Sutherlin Marie , Wright Amanda J. , Feinberg Evan H. , Hunter Craig P.
Published: June 2007

In plants and in the nematode
Caenorhabditis elegans
, an RNAi signal can trigger gene silencing in cells distant from the site where silencing is initiated. In plants, this signal is known to be a form of dsRNA, and the signal is most likely a form of dsRNA in
C. elegans
as well. Furthermore, in
C. elegans
, dsRNA present in the environment or expressed in ingested bacteria is sufficient to trigger RNAi (environmental RNAi). Ingestion and soaking delivery of dsRNA has also been described for other invertebrates. Here we report the identification and characterization of SID-2, an intestinal luminal transmembrane protein required for environmental RNAi in
C. elegans
. SID-2, when expressed in the environmental RNAi defective species
Caenorhabditis briggsae
, confers environmental RNAi.
IQGAP1 modulates activation of B-Raf
Authors: Ren Jian-Guo , Li Zhigang , Sacks David B.
Published: June 2007

IQGAP1 modulates several cellular functions, including cell–cell adhesion, transcription, cytoskeletal architecture, and selected signaling pathways. We previously documented that IQGAP1 binds ERK and MAPK kinase (MEK) and regulates EGF-stimulated MEK and ERK activity. Here we characterize the interaction between IQGAP1 and B-Raf, the molecule immediately upstream of MEK in the Ras/MAPK signaling cascade. B-Raf binds directly to IQGAP1
in vitro
and coimmunoprecipitates with IQGAP1 from cell lysates. Importantly, IQGAP1 modulates B-Raf function. EGF is unable to stimulate B-Raf activity in IQGAP1-null cells and in cells transfected with an IQGAP1 mutant construct that is unable to bind B-Raf. Interestingly, binding to IQGAP1 significantly enhances B-Raf activity
in vitro
. Our data identify a previously unrecognized interaction between IQGAP1 and B-Raf and suggest that IQGAP1 is a scaffold necessary for activation of B-Raf by EGF.
Light-controlled self-assembly of reversible and irreversible nanoparticle suprastructures
Authors: Klajn Rafal , Bishop Kyle J. M. , Grzybowski Bartosz A.
Published: June 2007

Nanoparticles (NPs) decorated with ligands combining photoswitchable dipoles and covalent cross-linkers can be assembled by light into organized, three-dimensional suprastructures of various types and sizes. NPs covered with only few photoactive ligands form metastable crystals that can be assembled and disassembled “on demand” by using light of different wavelengths. For higher surface concentrations, self-assembly is irreversible, and the NPs organize into permanently cross-linked structures including robust supracrystals and plastic spherical aggregates.
Single molecule detection of intermediates during botulinum neurotoxin translocation across membranes
Authors: Fischer Audrey , Montal Mauricio
Published: June 2007

The dynamics of
Clostridium botulinum
neurotoxins (BoNTs) protein-translocation across membranes was investigated by using a single molecule assay with millisecond resolution on excised patches of neuronal cells. Translocation of BoNT/A light chain (LC) by heavy chain (HC) was observed in real time as an increase of channel conductance: the HC channel is occluded by the LC during transit, then unoccluded after completion of translocation and release of LC-cargo. We identified an entirely unknown succession of intermediate conductance stages during LC translocation. For the single-chain BoNT/E, by contrast to the di-chain BoNT/A, we demonstrate that productive translocation requires proteolysis of the LC cargo from the HC chaperone. We propose a model for the set of protein–protein interactions between translocase and cargo at each step of translocation that supports the notion of an interdependent, tight interplay between the HC chaperone and the LC cargo preventing LC aggregation and dictating the outcome of translocation: productive passage of cargo or abortive channel occlusion by cargo.
Reburn severity in managed and unmanaged vegetation in a large wildfire
Authors: Thompson Jonathan R. , Spies Thomas A. , Ganio Lisa M.
Published: June 2007

Debate over the influence of postwildfire management on future fire severity is occurring in the absence of empirical studies. We used satellite data, government agency records, and aerial photography to examine a forest landscape in southwest Oregon that burned in 1987 and then was subject, in part, to salvage-logging and conifer planting before it reburned during the 2002 Biscuit Fire. Areas that burned severely in 1987 tended to reburn at high severity in 2002, after controlling for the influence of several topographical and biophysical covariates. Areas unaffected by the initial fire tended to burn at the lowest severities in 2002. Areas that were salvage-logged and planted after the initial fire burned more severely than comparable unmanaged areas, suggesting that fuel conditions in conifer plantations can increase fire severity despite removal of large woody fuels.
Development of a technique for the investigation of folding dynamics of single proteins for extended time periods
Authors: Kinoshita Masahito , Kamagata Kiyoto , Maeda Akio , Goto Yuji , Komatsuzaki Tamiki , Takahashi Satoshi
Published: June 2007

A technique was developed for the detection of fluorescence signals from free single molecules for extended time periods and was applied to the characterization of the unfolded states of iso-1-cytochrome
c
(cyt
c
). Protein molecules labeled with fluorescent dye were slowly injected into a capillary at concentrations that allow for the observation of one molecule at a time. A laser was introduced into the capillary coaxially, and the fluorescence was imaged as traces by using a lens with a large focal depth and wide field of view. Thus, the traces reflect the time-dependent changes in the fluorescence signals from single proteins. Cyt
c
was labeled with Alexa Fluor 532 at the C-terminal cysteine (cyt
c
-Alexa). In bulk experiments, cyt
c
-Alexa was shown to possess different fluorescence intensity for the native state, the unfolded state (U), and the intermediate state. Single-molecule traces of cyt
c
-Alexa were recorded by using the device. Intensity histograms of the traces revealed two distributions with broad and narrow widths, which were interpreted to correspond to the U and intermediate state, respectively, observed in the bulk measurements. The broad width of the U suggested the existence of a relatively slow conformational dynamics, which might be consistent with the correlation time (≈15 ms) estimated from the traces assignable to the U. The technique was expected to reveal dynamics of proteins along the folding processes without artifacts caused by immobilization.
Computer modeling of siRNA knockdown effects indicates an essential role of the Ca
2+
channel α
2
δ-1 subunit in cardiac excitation–contraction coupling
Authors: Tuluc Petronel , Kern Georg , Obermair Gerald J. , Flucher Bernhard E.
Published: June 2007

L-type Ca
2+
currents determine the shape of cardiac action potentials (AP) and the magnitude of the myoplasmic Ca
2+
signal, which regulates the contraction force. The auxiliary Ca
2+
channel subunits α
2
δ-1 and β
2
are important regulators of membrane expression and current properties of the cardiac Ca
2+
channel (Ca
V
1.2). However, their role in cardiac excitation–contraction coupling is still elusive. Here we addressed this question by combining siRNA knockdown of the α
2
δ-1 subunit in a muscle expression system with simulation of APs and Ca
2+
transients by using a quantitative computer model of ventricular myocytes. Reconstitution of dysgenic muscle cells with Ca
V
1.2 (GFP-α
1C
) recapitulates key properties of cardiac excitation–contraction coupling. Concomitant depletion of the α
2
δ-1 subunit did not perturb membrane expression or targeting of the pore-forming GFP-α
1C
subunit into junctions between the outer membrane and the sarcoplasmic reticulum. However, α
2
δ-1 depletion shifted the voltage dependence of Ca
2+
current activation by 9 mV to more positive potentials, and it slowed down activation and inactivation kinetics approximately 2-fold. Computer modeling revealed that the altered voltage dependence and current kinetics exert opposing effects on the function of ventricular myocytes that in total cause a 60% prolongation of the AP and a 2-fold increase of the myoplasmic Ca
2+
concentration during each contraction. Thus, the Ca
2+
channel α
2
δ-1 subunit is not essential for normal Ca
2+
channel targeting in muscle but is a key determinant of normal excitation and contraction of cardiac muscle cells, and a reduction of α
2
δ-1 function is predicted to severely perturb normal heart function.
Pulmonary expression of CXC chemokine ligand 13, CC chemokine ligand 19, and CC chemokine ligand 21 is essential for local immunity to influenza
Authors: Rangel-Moreno Javier , Moyron-Quiroz Juan E. , Hartson Louise , Kusser Kim , Randall Troy D.
Published: June 2007

CXC chemokine ligand 13 (CXCL13), CC chemokine ligand 21 (CCL21), and CCL19 are constitutively expressed in secondary lymphoid organs, where they control the placement of lymphocytes and dendritic cells. However, these chemokines are also inducibly expressed in the lung after influenza infection. Here we show that, in the absence of spleen and lymph nodes, the expression of homeostatic chemokines in the lung is essential for local B and T cell responses to influenza and for the development and organization of inducible bronchus-associated lymphoid tissue (iBALT). Surprisingly, despite the association between local CXCL13 expression and the formation of ectopic lymphoid tissues, the loss of CXCL13 in the lung had minimal impact on either the development or function of iBALT. In contrast, the loss of CCL19 and CCL21 impaired iBALT formation as well as B and T cell responses. These results demonstrate that the local expression of homeostatic chemokines in nonlymphoid organs, such as the lung, plays an important role in protective immune responses.
Structure-based discovery of an inhibitor of Arf activation by Sec7 domains through targeting of protein–protein complexes
Authors: Viaud Julien , Zeghouf Mahel , Barelli Hélène , Zeeh Jean-Christophe , Padilla André , Guibert Bernard , Chardin Pierre , Royer Catherine A. , Cherfils Jacqueline , Chavanieu Alain
Published: June 2007

Small molecules that produce nonfunctional protein–protein complexes are an alternative to competitive inhibitors for the inhibition of protein functions. Here we target the activation of the small GTP-binding protein Arf1, a major regulator of membrane traffic, by the Sec7 catalytic domain of its guanine nucleotide exchange factor ARNO. The crystal structure of the Arf1-GDP/ARNO complex, which initiates the exchange reaction, was used to discover an inhibitor, LM11, using
in silico
screening of a flexible pocket near the Arf1/ARNO interface. Using fluorescence kinetics and anisotropy, NMR spectroscopy and mutagenesis, we show that LM11 acts following a noncompetitive mechanism in which the inhibitor targets both Arf1-GDP and the Arf1-GDP/ARNO complex and produces a nonfunctional Arf-GDP/ARNO complex whose affinity is similar to that of the native complex. In addition, LM11 recognizes features of both Arf and ARNO near the Arf/Sec7 interface, a characteristic reminiscent of the paradigm interfacial inhibitor Brefeldin A. We then show that LM11 is a cell-active inhibitor that impairs Arf-dependent trafficking structures at the Golgi. Furthermore, LM11 inhibits ARNO-dependent migration of Madin–Darby canine kidney (MDCK) cells, demonstrating that ARNO is a target of LM11 in cells. Remarkably, LM11 inhibits the activation of Arf1 but not Arf6
in vitro
, pointing to a possible synergy between Arf1 and Arf6 activation by ARNO in cell migration. Our design method shows that flexible regions in protein–protein complexes provide drugable sites with the potential to develop novel tools for investigating and inhibiting signaling pathways.
Structural basis for recruitment of tandem hotdog domains in acyl-CoA thioesterase 7 and its role in inflammation
Authors: Forwood Jade K. , Thakur Anil S. , Guncar Gregor , Marfori Mary , Mouradov Dmitri , Meng Weining , Robinson Jodie , Huber Thomas , Kellie Stuart , Martin Jennifer L. , Hume David A. , Kobe Bostjan
Published: June 2007

Acyl-CoA thioesterases (Acots) catalyze the hydrolysis of fatty acyl-CoA to free fatty acid and CoA and thereby regulate lipid metabolism and cellular signaling. We present a comprehensive structural and functional characterization of mouse acyl-CoA thioesterase 7 (Acot7). Whereas prokaryotic homologues possess a single thioesterase domain, mammalian Acot7 contains a pair of domains in tandem. We determined the crystal structures of both the N- and C-terminal domains of the mouse enzyme, and inferred the structure of the full-length enzyme using a combination of chemical cross-linking, mass spectrometry, and molecular modeling. The quaternary arrangement in Acot7 features a trimer of hotdog fold dimers. Both domains of Acot7 are required for activity, but only one of two possible active sites in the dimer is functional. Asn-24 and Asp-213 (from N- and C-domains, respectively) were identified as the catalytic residues through site-directed mutagenesis. An enzyme with higher activity than wild-type Acot7 was obtained by mutating the residues in the nonfunctional active site. Recombinant Acot7 was shown to have the highest activity toward arachidonoyl-CoA, suggesting a function in eicosanoid metabolism. In line with the proposal, Acot7 was shown to be highly expressed in macrophages and up-regulated by lipopolysaccharide. Overexpression of Acot7 in a macrophage cell line modified the production of prostaglandins D2 and E2. Together, the results link the molecular and cellular functions of Acot7 and identify the enzyme as a candidate drug target in inflammatory disease.