bluuebunny/crossref_metadata_2025 huggingface dataset:
Mechanochemical mechanism for fast reaction of metastable intermolecular composites based on dispersion of liquid metal
Authors: Levitas Valery I. , Asay Blaine W. , Son Steven F. , Pantoya Michelle
Published: May 2007

An unexpected mechanism for fast reaction of Al nanoparticles covered by a thin oxide shell during fast heating is proposed and justified theoretically and experimentally. For nanoparticles, the melting of Al occurs before the oxide fracture. The volume change due to melting induces pressures of 1–2 GPa and causes dynamic spallation of the shell. The unbalanced pressure between the Al core and the exposed surface creates an unloading wave with high tensile pressures resulting in dispersion of atomic scale liquid Al clusters. These clusters fly at high velocity and their reaction is not limited by diffusion (this is the opposite of traditional mechanisms for micron particles and for nanoparticles at slow heating). Physical parameters controlling the melt dispersion mechanism are found by our analysis. In addition to an explanation of the extremely short reaction time, the following correspondence between our theory and experiments are obtained: (a) For the particle radius below some critical value, the flame propagation rate and the ignition time delay are independent of the radius; (b) damage of the oxide shell suppresses the melt dispersion mechanism and promotes the traditional diffusive oxidation mechanism; (c) nanoflakes react more like micron size (rather than nanosize) spherical particles. The reasons why the melt dispersion mechanism cannot operate for the micron particles or slow heating of nanoparticles are determined. Methods to promote the melt dispersion mechanism, to expand it to micron particles, and to improve efficiency of energetic metastable intermolecular composites are formulated. In particular, the following could promote the melt dispersion mechanism in micron particles: (a) Increasing the temperature at which the initial oxide shell is formed; (b) creating initial porosity in the Al; (c) mixing of the Al with a material with a low (even negative) thermal expansion coefficient or with a phase transformation accompanied by a volume reduction; (d) alloying the Al to decrease the cavitation pressure; (e) mixing nano- and micron particles; and (f) introducing gasifying or explosive inclusions in any fuel and oxidizer. A similar mechanism is expected for nitridation and fluorination of Al and may also be tailored for Ti and Mg fuel.
Theoretical and experimental analyses of the synergism in the dielectric strength for C3F8∕C2HF5 mixtures
Authors: Larin A. V. , Meurice N. , Gentils F. , Fievet C. , Vercauteren D. P.
Published: May 2007

Two theoretical approaches are applied in order to describe the behavior of the experimental breakdown voltage in C3F8∕C2HF5 mixtures. First, available cross section data of the electron-molecule processes are scaled to simulate the dielectric strength (DS) behavior in both C3F8 and C2HF5 gases at the level of the Boltzmann equation (BE) solution corresponding to a homogeneous electric field model. Then, the DS of C3F8∕C2HF5 mixtures is evaluated and compared to the experimental breakdown voltage measured using different electrode geometries as sphere/plane type via experimental techniques, i.e., power frequency and negative or positive polarity lightning impulse. Due to the limitation of the BE approach to describe the observed experimental data, the Hunter-Christophorou [J. Appl. Phys. 57, 4377 (1985)] model regarding the positive synergism phenomenon is finally applied. Both models allow us to compare relative values of the “chemical” and “physical” DS components in C3F8∕C2HF5 mixtures.
One-dimensional analysis of the rate of plasma-assisted sputter deposition
Authors: Palmero A. , Rudolph H. , Habraken F. H. P. M.
Published: May 2007

In this article a recently developed model [A. Palmero, H. Rudolph, and F. H. P. M. Habraken, Appl. Phys. Lett. 89, 211501 (2006)] is applied to analyze the transport of sputtered material from the cathode toward the growing film when using a plasma-assisted sputtering deposition technique. The argon pressure dependence of the deposition rate of aluminum, silicon, vanadium, chromium, germanium, tantalum, and tungsten under several different experimental conditions has been analyzed by fitting experimental results from the literature to the above-mentioned theory. Good fits are obtained. Three quantities are deduced from the fit: the temperature of the cathode and of the growing film, and the value of the effective cross section for thermalization due to elastic scattering of a sputtered particle on background gas atoms. The values derived from the fits for the growing film and cathode temperature are very similar to those experimentally determined and reported in the literature. The effective cross sections have been found to be approximately the corresponding geometrical cross section divided by the average number of collisions required for the thermalization, implying that the real and effective thermalization lengths have a similar value. Finally, the values of the throw distance appearing in the Keller-Simmons model, as well as its dependence on the deposition conditions have been understood invoking the values of the cathode and film temperature, as well as of the value of the effective cross section. The analysis shows the overall validity of this model for the transport of sputtered particles in sputter deposition.
Coupling of laser energy into plasma channels
Authors: Dimitrov D. A. , Giacone R. E. , Bruhwiler D. L. , Busby R. , Cary J. R. , Geddes C. G. R. , Esarey E. , Leemans W. P.
Published: May 2007

Diffractive spreading of a laser pulse imposes severe limitations on the acceleration length and maximum electron energy in the laser wake field accelerator (LWFA). Optical guiding of a laser pulse via plasma channels can extend the laser-plasma interaction distance over many Rayleigh lengths. Energy efficient coupling of laser pulses into and through plasma channels is very important for optimal LWFA performance. Results from simulation parameter studies on channel guiding using the particle-in-cell (PIC) code VORPAL [C. Nieter and J. R. Cary, J. Comput. Phys. 196, 448 (2004)] are presented and discussed. The effects that density ramp length and the position of the laser pulse focus have on coupling into channels are considered. Moreover, the effect of laser energy leakage out of the channel domain and the effects of tunneling ionization of a neutral gas on the guided laser pulse are also investigated. Power spectral diagnostics were developed and used to separate pump depletion from energy leakage. The results of these simulations show that increasing the density ramp length decreases the efficiency of coupling a laser pulse to a channel and increases the energy loss when the pulse is vacuum focused at the channel entrance. Then, large spot size oscillations result in increased energy leakage. To further analyze the coupling, a differential equation is derived for the laser spot size evolution in the plasma density ramp and channel profiles are simulated. From the numerical solution of this equation, the optimal spot size and location for coupling into a plasma channel with a density ramp are determined. This result is confirmed by the PIC simulations. They show that specifying a vacuum focus location of the pulse in front of the top of the density ramp leads to an actual focus at the top of the ramp due to plasma focusing, resulting in reduced spot size oscillations. In this case, the leakage is significantly reduced and is negligibly affected by ramp length, allowing for efficient use of channels with long ramps.
Dislocation dynamics analysis of dislocation intersections in nanoscale metallic multilayered composites
Authors: Akasheh F. , Zbib H. M. , Hirth J. P. , Hoagland R. G. , Misra A.
Published: May 2007

In this work, dislocation dynamics (DD) analysis is used to investigate the strength of nanoscale metallic multilayered composites. Several possible interactions between threading (glide) dislocations and intersecting interfacial dislocations are considered and found to lead to strength predictions in better agreement with experimental trends and significantly higher than the predictions of the simplified confined layer plasticity model based on Orowan bowing of single dislocation in a rigid channel. The strongest interaction occurs when threading and intersecting interfacial dislocations have collinear Burgers’ vector and involves an annihilation reaction at their crossing points followed by the resumption of threading with a new dislocation configuration. The other possible dislocation intersections involve the formation of junctions, which are found to be more complex than simple models suggest. When the layer interfaces are modeled as impenetrable walls, as in existing analytical and some dislocation dynamics (DD) models, the predicted strengthening effect is weaker than that predicted by DD with more physical boundary conditions at the interfaces.
Electrical transport and thermoelectric properties of Y1−xCaxCoO3 (⩽x⩽0.1) at high temperatures
Authors: Liu Y. , Qin X. Y. , Xin H. X. , Zhang J. , Li H. J. , Wang Y. F.
Published: May 2007

The effects of Ca substitution for Y on the electrical transport and thermoelectric properties of Y1−xCaxCoO3 (0⩽x⩽0.1), prepared by using the sol-gel process, were investigated in the temperature range from 300to780K. The results indicated that direct current electrical resistivity ρ of Y1−xCaxCoO3 decreased remarkably with increasing Ca content x as x⩽0.01, which could mainly be attributed to the increase of hole concentration due to substitution of Ca2+ for Y3+. The temperature dependences of the resistivity for Y1−xCaxCoO3 were all found to be basically consistent with small-polaron hopping conduction model. Although Seebeck coefficient S of Y1−xCaxCoO3 at low temperatures T<∼550K decreased remarkably with increasing x, it approached a limit value ∼150μV∕K at ∼800K for all the samples with different x, which was consistent well with the thermopower resulting from the degeneracy of electron configuration estimated from Heikes formula by assuming that Co3+ and Co4+ exist in low spin state. Experiments showed that thermal conductivity κ of Y1−xCaxCoO3 came mainly from its lattice component, whose decrease with increasing x could be chiefly ascribed to impurity-scattering effect due to Ca doping. The thermoelectric figure of merit ZT (=S2T∕ρκ) of Y1−xCaxCoO3 changed nonmonotonously with increasing doping content of Ca, and Y0.95Ca0.05CoO3 was found to have optimum thermoelectric properties with ZT=0.019 at 660K, which was about ten-fold greater than that of YCoO3, indicating that its thermoelectric properties could be improved effectively by appropriate substitution of Ca for Y in this compound.
Influences of annealing in reducing and oxidizing ambients on flatband voltage properties of HfO2 gate stack structures
Authors: Ohmori K. , Ahmet P. , Yoshitake M. , Chikyow T. , Shiraishi K. , Yamabe K. , Watanabe H. , Akasaka Y. , Nara Y. , Chang K.-S. , Green M. L. , Yamada K.
Published: May 2007

We have applied a combinatorial technique to fabricate work function (WF) tuned Pt-W alloy films and used the films as metal electrodes for HfO2∕SiO2∕Si capacitors. As the ratio, RPt, of Pt to W changes from 0 to 1, the WF value varies continuously from 4.7 to 5.5 eV. This tunability enables us to systematically investigate the effect of WF variation on electrical properties. After a forming gas annealing process, the values of flatband voltage (Vfb) from capacitance-voltage properties are almost constant, regardless of the WF variation, because of oxygen vacancy formation that results in Fermi level pinning. On additional oxidizing gas annealing (OGA), the effect of WF value on Vfb becomes dominant. However, the difference in Vfb between W and Pt is 0.34 V, which is much smaller than the observed WF difference of 0.8 eV. We attribute this phenomenon to the lowering of the effective WF due to an electric dipole, induced by oxygen vacancy formation at the metal/HfO2 interface. Moreover, a decrease in Vfb in W-rich regions was observed following the OGA, suggesting the formation of a W-O bond at the interface. These results clearly indicate that the control of bonding states at the metal/HfO2 interfaces on an atomic scale is essential for the realization of a combination of metal and high-k dielectric films in future complementary metal-oxide-semiconductor devices.
Topography imaging with a heated atomic force microscope cantilever in tapping mode
Authors: Park Keunhan , Lee Jungchul , Zhang Zhuomin M. , King William P.
Published: May 2007

This article describes tapping mode atomic force microscopy (AFM) using a heated AFM cantilever. The electrical and thermal responses of the cantilever were investigated while the cantilever oscillated in free space or was in intermittent contact with a surface. The cantilever oscillates at its mechanical resonant frequency, 70.36 kHz, which is much faster than its thermal time constant of 300 μs, and so the cantilever operates in thermal steady state. The thermal impedance between the cantilever heater and the sample was measured through the cantilever temperature signal. Topographical imaging was performed on silicon calibration gratings of height 20 and 100 nm. The obtained topography sensitivity is as high as 200 μV∕nm and the resolution is as good as 0.5 nm∕Hz1∕2, depending on the cantilever power. The cantilever heating power ranges 0–7 mW, which corresponds to a temperature range of 25–700 °C. The imaging was performed entirely using the cantilever thermal signal and no laser or other optics was required. As in conventional AFM, the tapping mode operation demonstrated here can suppress imaging artifacts and enable imaging of soft samples.
Low temperature diffusion of impurities in hydrogen implanted silicon
Authors: Personnic S. , Bourdelle K. K. , Letertre F. , Tauzin A. , Laugier F. , Fortunier R. , Klocker H.
Published: May 2007

The effect of hydrogen implantation on the transport of impurities in silicon is studied. We use secondary ion mass spectrometry measurements to investigate the depth redistribution of oxygen, carbon, and fluorine during low temperature, ≤450 °C, isothermal anneals. Their fast migration toward the projected range region of H implants points to the existence of a strong interaction of the impurities with H-induced defects. Significantly enhanced, as compared to the literature values, diffusivities of the investigated impurities were obtained. The results reveal that hydrogen implantation can be advantageously used for the impurity profile engineering and gettering studies in silicon in the low temperatures annealing regime.
Low-frequency noise in epitaxially grown Schottky junctions
Authors: Young A. C. , Zimmerman J. D. , Brown E. R. , Gossard A. C.
Published: May 2007

The low-frequency power spectrum has been measured for ErAs:InAlGaAs diodes and shows at least a ten-times reduction of 1∕f noise compared to traditional Al Schottky diodes on the same semiconductor material. These junctions are grown by molecular beam epitaxy, preventing oxidation and other contamination at the junction. The major noise source for these devices is attributed to the sidewalls and not the junction itself. Low-frequency oscillations have also been observed and associated with a deep trap level estimated to be ∼200 meV below the conduction band edge by the comparison of diodes with different InAlGaAs compositions and confirmed by deep level transient spectroscopy. This deep level could be associated to erbium incorporation in the depletion region.
First-principles study on secondary electron emission of MgO surface
Authors: Cho Youngmi , Kim Changwook , Ahn Hyo-Shin , Cho Eunae , Kim Tae-Eun , Han Seungwu
Published: May 2007

We theoretically investigate secondary-electron-emission properties of MgO when noble gases are incident on the surface. We consider both potential and kinetic emission mechanisms. For the potential emission through Auger neutralization, densities of states and vacuum level are obtained from the first-principles calculations. It is found that secondary-emission coefficients decrease in the following sequence of surface directions; (111)-OH>(100)>(110), a tendency that is in agreement with experimental observations. For a surface model including F center, the secondary-emission coefficient substantially increases for Kr and Xe. To investigate the kinetic emission mechanism by an energetic ion impinging on MgO surfaces, first-principles molecular dynamics simulations are performed. Dynamic up-shifts of antibonding states between ions and oxygen atoms are found to lead to the secondary-electron emission at kinetic energies as low as 30 eV. Various collision conditions are compared based on the temporal interval during which excited states stay within the conduction band.
Strain analysis of Ge/Si(001) islands after initial Si capping by Raman spectroscopy
Authors: Lin J. H. , Yang H. B. , Qin J. , Zhang B. , Fan Y. L. , Yang X. J. , Jiang Z. M.
Published: May 2007

The shape of the self-assembled GeSi/Si(001) islands changed from a dome to a pyramid bounded with {103} or {105} facets after initial Si capping at 640 °C. The strains in the islands with initial Si capping are investigated by Raman spectroscopy. Compared with those of the uncapped islands, both peaks of Ge-Ge and Ge-Si vibration modes in the capped islands show blueshifts, corresponding to the Ge content decrease and the compressive strain increase in the capped islands. The total strain energy in an island is found to increase remarkably after Si capping. After simple analysis, it is found that the surface energy change could not overwhelm this large strain energy increase, making the shape transition favorable. It implies that the strain energy in the substrate in association with an island formation as well as evolution should be considered in accounting for the resulting island shape changes after Si capping.
Global nonambipolar flow: Plasma confinement where all electrons are lost to one boundary and all positive ions to another boundary
Authors: Baalrud S. D. , Hershkowitz N. , Longmier B.
Published: May 2007

A new mode of plasma confinement is demonstrated in which essentially all positive ions leave the plasma to only one boundary while essentially all electrons are lost to a different boundary. Sheaths near the plasma boundaries are entirely responsible for this global nonambipolar flow. The bulk plasma remains quasineutral and unperturbed even when all electrons are lost to only one, physically small, location. A necessary condition for global nonambipolar flow depends on the ratio of electron collection area to ion collection area. The plasma electron temperature is significantly higher in the global nonambipolar mode than in the typical ambipolar mode due to a relative increase in confinement of high-energy electrons and a relative decrease in confinement of low-energy electrons.
Application of superlattice multipliers for high-resolution terahertz spectroscopy
Authors: Endres C. P. , Lewen F. , Giesen T. F. , Schlemmer S. , Paveliev D. G. , Koschurinov Y. I. , Ustinov V. M. , Zhucov A. E.
Published: May 2007

Frequency multipliers based on superlattice (SL) devices as nonlinear elements have been developed as radiation sources for a terahertz (THz) laboratory spectrometer. Input frequencies of 100 and 250 GHz from backward wave oscillators have been multiplied up to the 11th harmonic, producing usable frequencies up to 2.7 THz. Even at these high frequencies the output power is sufficient for laboratory spectroscopy. Comparisons to conventional high-resolution microwave spectroscopy methods reveal several superior features of this new device such as very high line frequency accuracies, broadband tunability, high output power levels at odd harmonics of the input frequency up to high orders, and a robust applicability.
Grating interferometer based scanning setup for hard x-ray phase contrast imaging
Authors: Kottler C. , Pfeiffer F. , Bunk O. , Grünzweig C. , David C.
Published: May 2007

In x-ray radiography, particularly for technical and industrial applications, a scanning setup is very often favorable when compared to a direct two-dimensional image acquisition. Here, we report on an efficient scanning method for grating based x-ray phase contrast imaging with tube based sources. It uses multiple line detectors for staggered acquisition of the individual phase-stepping images. We find that the total exposure time does not exceed the time needed in an equivalent scanning setup for absorption radiography. Therefore, we conclude that it should be possible to implement the method into a scanning system without affecting the scanning speed or significant increase in cost but with the advantage of providing both the phase contrast and the absorption information at once.
Effect of hydrogen treatment on the field emission of amorphous carbon film
Authors: Xie W. G. , Chen Jun , Chen Jian , Deng S. Z. , She J. C. , Xu N. S.
Published: May 2007

The field emission characteristics of amorphous carbon (a-C) films are studied before and after H plasma treatment. It is found that H plasma treatment lowered the turn-on field and improved the field emission uniformity. Surface sp2∕sp3 ratio, work function, and topography of the a-C films before and after H plasma treatment are studied using Raman spectroscopy, Kelvin probe, and atomic force microscopy, respectively. The results show that the etching effect of H plasma on a-C film is obvious, which is different from those of diamond and tetrahedral amorphous carbon (ta-C) films. We suggest that the surface component change and nanostructure of treated a-C films cause electron injection from sp2 sites to surface sp3 sites which are responsible for low macroelectrical field emission.
Identification of nanoindentation-induced phase changes in silicon by in situ electrical characterization
Authors: Ruffell S. , Bradby J. E. , Fujisawa N. , Williams J. S.
Published: May 2007

In situ electrical measurements during nanoindentation of Czochralski grown p-type crystalline silicon (100) have been performed using a conducting diamond Berkovich indenter tip. Through-tip current monitoring with a sensitivity of ∼10pA and extraction of current-voltage curves at various points on the complete load-unload cycle have been used to track the phase transformations of silicon during the loading and unloading cycle. Postindent current-voltage curves prove to be extremely sensitive to phase changes during indentation, as well as to the final phase composition within the indented volume. For example, differences in the final structure are detected by current-voltage measurements even in an unloading regime in which only amorphous silicon is expected to form. The electrical measurements are interpreted with the aid of previously reported transmission electron microscopy and Raman microspectroscopy measurements.
Island-induced bootstrap current on the saturation of a thin magnetic island in tokamaks
Authors: Shaing K. C.
Published: May 2007

It is shown that island-induced bootstrap current density, which results from the symmetry breaking of the ∣B∣ when an island is embedded in the equilibrium magnetic field B, modifies the evolution equation and the saturation level for a thin magnetic island in tokamaks. This modification is independent of the fraction of the equilibrium bootstrap current density. It is found that island-induced bootstrap current density increases the saturation level for modes with positive values of Δ′. Here, Δ′ is the stability parameter for the linear tearing modes.
Methanol adsorption on Cu(110) and the angular distribution of the reaction products
Authors: Demirci E. , Stettner J. , Kratzer M. , Schennach R. , Winkler A.
Published: May 2007

Integral and angle resolved thermal desorption spectroscopies were used to study methanol adsorption and oxidation on clean and oxygen covered Cu(110) surfaces. Special emphasis was put on the Cu–CuO stripe phase, which forms when the Cu(110) surface is covered with 0.25 ML of oxygen. In the temperature regime between 200 and 300K associative desorption of methanol and water takes place, showing a normal desorption character with peaks shifting to lower temperature with increasing coverage and with a nearly cosine angular desorption distribution. In the temperature range of about 350K formaldehyde, hydrogen, and again methanol desorb nearly concomitantly in the form of a very narrow peak (full width at half maximum=10K), with peaks shifting to higher temperature with increasing methanol coverage. The angular distribution of these peaks is strongly forward focused, indicating activation barriers being involved. In the case of the Cu–CuO stripe phase the angular distribution of the desorption products is clearly different in the [11̱0] and [001] azimuthal directions, demonstrating the influence of the border lines between the copper and the copper oxide stripes on the desorption process.
Two-phase structure of polyelectrolyte gel/surfactant complexes
Authors: Tararyshkin Denis , Kramarenko Elena , Khokhlov Alexei
Published: May 2007

The behavior of lightly cross-linked polyelectrolyte hydrogel swelling in the solution of oppositely charged surfactants is studied theoretically. It is shown that if there is a lack of surfactant in the solution intragel separation into two phases differing in swelling ratios and surfactant content can take place. The surfactant ions concentrate and form micelles in a part of the gel and this part collapses while the rest of the gel remains swollen. The two-phase region widens with an increase of ionization degree of the gel subchains.
Fire-growth modelling using meteorological data with random and systematic perturbations
Authors: Anderson Kerry , Reuter Gerhard , Flannigan Mike D.
Published: May 2007

The focus of this investigation is to quantify the effects of perturbations in the meteorological data used in a fire-growth model. Observed variations of temperature, humidity, wind speed, and wind direction are applied as perturbations to hourly values within a simulated weather forecast to produce several forecasts. In turn, these are used by a deterministic eight-point fire-growth model to produce an ensemble of possible final fire perimeters. Two studies were conducted to assess the value of applying perturbations. In the first study, fire growth using detailed, one-minute data was compared to growth based on the more commonly used hourly data. Results showed that the detailed weather produced fire growth larger and wider than the hourly based data. By applying perturbations, variations in the flank and back-fire spread were captured by the random-perturbation model while the forward spread fell within the 20 to 30% probability prediction. A sensitivity analysis based on the observed variations showed that wind speed accounted for a 44% difference in area burned, while temperature accounted for only a 16% difference. In the second study, case studies were conducted on four observed forest fires in Wood Buffalo National Park. Results showed that daily fire-growth predictions using simulated weather forecasts over-predicted fire growth using actual hourly weather observations by 27%. Systematic-perturbation models best compensated for this with most fire growth falling within the predicted range of the models (52 out of 63 days).
Impact of climate change on area burned in Alberta's boreal forest
Authors: Tymstra Cordy , Flannigan Mike D. , Armitage Owen B. , Logan Kimberley
Published: May 2007

Eight years of fire weather data from sixteen representative weather stations within the Boreal Forest Natural Region of Alberta were used to compile reference weather streams for low, moderate, high, very high and extreme Fire Weather Index (FWI) conditions. These reference weather streams were adjusted to create daily weather streams for input into Prometheus – the Canadian Wildland Fire Growth Model. Similar fire weather analyses were completed using Canadian Regional Climate Model (CRCM) output for northern Alberta (174 grid cells) to generate FWI class datasets (temperature, relative humidity, wind speed, Fine Fuel Moisture Code, Duff Moisture Code and Drought Code) for 1 ×, 2 × and 3 × CO2 scenarios. The relative differences between the CRCM scenario outputs were then used to adjust the reference weather streams for northern Alberta. Area burned was calculated for 21 fires, fire weather classes and climate change scenarios. The area burned estimates were weighted based on the historical frequency of area burned by FWI class, and then normalized to derive relative area burned estimates for each climate change scenario. The 2 × and 3 × CO2 scenarios resulted in a relative increase in area burned of 12.9 and 29.4% from the reference 1 × CO2 scenario.
Electrophoresis of individual microtubules in microchannels
Authors: van den Heuvel M. G. L. , de Graaff M. P. , Lemay S. G. , Dekker C.
Published: May 2007

We use micrometer-sized fluidic channels to confine and measure electrophoresis of freely suspended individual microtubules. We measure orientation-dependent velocities of microtubules and the electro-osmotic flow mobility in our channels to infer the anisotropic electrophoretic mobility of microtubules under physiological conditions. We discuss the difference between electrophoresis and purely hydrodynamic motion and its implications for interpreting mobility measurements. We show that the mobility anisotropy is a factor of 0.83, clearly different from the well known anisotropy factor of 0.5 in Stokes drag coefficients for cylindrical objects. We also show that the velocity is independent of microtubule length, which would be different for hydrodynamic motion. We demonstrate that the electric force on the counterions has important consequences for the interpretation of electrophoresis experiments and that ignoring this can lead to an underestimation of the effective charge by orders of magnitude. From the electrophoresis measurements, we calculate an effective surface-charge density of −36.7 ± 0.4 mC/m
2
for microtubules. Electrophoretic measurements of subtilisin-digested microtubules, which have the negatively charged C termini on the outer surface removed, show a 24% decrease in mobility and, correspondingly, in surface charge, but no change in anisotropy.
Shear-induced unfolding triggers adhesion of von Willebrand factor fibers
Authors: Schneider S. W. , Nuschele S. , Wixforth A. , Gorzelanny C. , Alexander-Katz A. , Netz R. R. , Schneider M. F.
Published: May 2007

von Willebrand factor (VWF), a protein present in our circulatory system, is necessary to stop bleeding under high shear-stress conditions as found in small blood vessels. The results presented here help unravel how an increase in hydrodynamic shear stress activates VWF's adhesion potential, leading to the counterintuitive phenomena of enhanced adsorption rate under strong shear conditions. Using a microfluidic device, we were able to mimic a wide range of bloodflow conditions and directly visualize the conformational dynamics of this protein under shear flow. In particular, we find that VWF displays a reversible globule-stretch transition at a critical shear rate γ̇
crit
in the absence of any adsorbing surface. Computer simulations reproduce this sharp transition and identify the large size of VWF's repeating units as one of the keys for this unique hydrodynamic activation. In the presence of an adsorbing collagen substrate, we find a large increase in the protein adsorption at the same critical shear rate, suggesting that the globule unfolding in bulk triggers the surface adsorption in the case of a collagen substrate, which provides a sufficient density of binding sites. Monitoring the adsorption process of multiple VWF fibers, we were able to follow the formation of an immobilized network that constitutes a “sticky” grid necessary for blood platelet adhesion under high shear flow. Because areas of high shear stress coincide with a higher chance for vessel wall damage by mechanical forces, we identified the shear-induced increase in the binding probability of VWF as an effective self-regulating repair mechanism of our microvascular system.
Involvement of β-site APP cleaving enzyme 1 (BACE1) in amyloid precursor protein-mediated enhancement of memory and activity-dependent synaptic plasticity
Authors: Ma Huifang , Lesné Sylvain , Kotilinek Linda , Steidl-Nichols Jill V. , Sherman Mathew , Younkin Linda , Younkin Steven , Forster Colleen , Sergeant Nicolas , Delacourte André , Vassar Robert , Citron Martin , Kofuji Paulo , Boland Linda M. , Ashe Karen H.
Published: May 2007

The amyloid precursor protein (APP) undergoes sequential cleavages to generate various polypeptides, including the amyloid-β protein (Aβ), which forms amyloid plaques in Alzheimer's disease (AD), secreted APPα (sAPPα) which enhances memory, and the APP intracellular domain (AICD), which has been implicated in the regulation of gene transcription and calcium signaling. The β-site APP cleaving enzyme 1 (BACE1) cleaves APP in an activity-dependent manner to form Aβ, AICD, and secreted APPβ. Because this neural activity was shown to diminish synaptic transmissionin vitro[Kamenetz F, Tomita T, Hsieh H, Seabrook G, Borchelt D, Iwatsubo T, Sisodia S, Malinow R (2003)Neuron37:925–937], the prevailing notion has been that this pathway diminishes synaptic function. Here we investigated the role of this pathwayin vivo. We studied transgenic mice overproducing APP that do not develop AD pathology or memory deficits but instead exhibit enhanced spatial memory. We showed enhanced synaptic plasticity in the hippocampus that depends on prior synaptic activity. We found that the enhanced memory and synaptic plasticity are abolished by the ablation of one or both copies of the BACE1 gene, leading to a significant decrease in AICD but not of any other APP cleavage products. In contrast to the previously described negative effect of BACE1-mediated cleavage of APP on synaptic functionin vitro, ourin vivowork indicates that BACE1-mediated cleavage of APP can facilitate learning, memory, and synaptic plasticity.
A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome
c
oxidase
Authors: Muramoto Kazumasa , Hirata Kunio , Shinzawa-Itoh Kyoko , Yoko-o Shinji , Yamashita Eiki , Aoyama Hiroshi , Tsukihara Tomitake , Yoshikawa Shinya
Published: May 2007

Cytochrome
c
oxidase transfers electrons and protons for dioxygen reduction coupled with proton pumping. These electron and proton transfers are tightly coupled with each other for the effective energy transduction by various unknown mechanisms. Here, we report a coupling mechanism by a histidine (His-503) at the entrance of a proton transfer pathway to the dioxygen reduction site (D-pathway) of bovine heart cytochrome
c
oxidase. In the reduced state, a water molecule is fixed by hydrogen bonds between His-503 and Asp-91 of the D-pathway and is linked via two water arrays extending to the molecular surface. The microenvironment of Asp-91 appears in the x-ray structure to have a proton affinity as high as that of His-503. Thus, Asp-91 and His-503 cooperatively trap, on the fixed water molecule, the proton that is transferred through the water arrays from the molecular surface. On oxidation, the His-503 imidazole plane rotates by 180° to break the hydrogen bond to the protonated water and releases the proton to Asp-91. On reduction, Asp-91 donates the proton to the dioxygen reduction site through the D-pathway. The proton collection controlled by His-503 was confirmed by partial electron transfer inhibition by binding of Zn
2+
and Cd
2+
to His-503 in the x-ray structures. The estimated
K
d
for Zn
2+
binding to His-503 in the x-ray structure is consistent with the reported
K
d
for complete proton-pumping inhibition by Zn
2+
[Kannt A, Ostermann T, Muller H, Ruitenberg M (2001)
FEBS Lett
503:142–146]. These results suggest that His-503 couples the proton transfer for dioxygen reduction with the proton pumping.
Nonclassical estrogen receptor α signaling mediates negative feedback in the female mouse reproductive axis
Authors: Glidewell-Kenney C. , Hurley L. A. , Pfaff L. , Weiss J. , Levine J. E. , Jameson J. L.
Published: May 2007

Ovarian estrogen exerts both positive and negative feedback control over luteinizing hormone (LH) secretion during the ovulatory cycle. Estrogen receptor (ER) α but not ERβ knockout mice lack estrogen feedback. Thus, estrogen feedback appears to be primarily mediated by ERα. However, it is now recognized that, in addition to binding to estrogen response elements (EREs) in DNA to alter target gene transcription, ERα signals through ERE-independent or nonclassical pathways, and the relative contributions of these pathways in conveying estrogen feedback remain unknown. Previously we created a knockin mouse model expressing a mutant form of ERα (AA) with ablated ERE-dependent but intact ERE-independent activity. Breeding this allele onto the ERα-null (−/−) background, we examine the ability of ERE-independent ERα signaling pathways to convey estrogen feedback regulation of the female hypothalamic–pituitary axis
in vivo
. ERα
−/AA
exhibited 69.9% lower serum LH levels compared with ERα
−/−
mice. Additionally, like wild type, ERα
−/AA
mice exhibited elevated LH after ovariectomy (OVX). Furthermore, the post-OVX rise in serum LH was significantly suppressed by estrogen treatment in OVX ERα
−/AA
mice. However, unlike wild type, both ERα
−/AA
and ERα
−/−
mice failed to exhibit estrous cyclicity, spontaneous ovulation, or an afternoon LH surge response to estrogen. These results indicate that ERE-independent ERα signaling is sufficient to convey a major portion of estrogen's negative feedback actions, whereas positive feedback and spontaneous ovulatory cyclicity require ERE-dependent ERα signaling.
Multinuclear palladium compounds containing palladium centers ligated by five silicon atoms
Authors: Shimada Shigeru , Li Yong-Hua , Choe Yoong-Kee , Tanaka Masato , Bao Ming , Uchimaru Tadafumi
Published: May 2007

Palladium (Pd) generally prefers low oxidation states. So far, no stable Pd compound with a +5 oxidation state is known. Here, we report two multinuclear Pd compounds containing Pd centers ligated by five silicon (Si) atoms. A thermal condensation reaction of [{1,2-C
6
H
4
(SiMe
2
)(SiH
2
)}Pd
II
(Me
2
PCH
2
CH
2
PMe
2
)] (Me = methyl) afforded two stereoisomers of dinuclear Pd
II
compounds and a trinuclear Pd compound as major products and a tetranuclear Pd compound as a minor product. The structures of the four Pd compounds were confirmed by single-crystal x-ray structure analysis. The dinuclear Pd compounds have a dimeric structure of [{1,2-C
6
H
4
(SiMe
2
)(SiH)}Pd
II
(Me
2
PCH
2
CH
2
PMe
2
)] connected through a Si–Si single bond formed by dehydrogenation of two molecules of the starting compound. The trinuclear and tetranuclear Pd compounds proved to have Pd centers bonded to five Si atoms with normal Pd–Si single-bond distances. Theoretical calculations of the trinuclear and tetranuclear Pd compounds accurately reproduced their x-ray structures and suggested that all of the Pd–Si bonds of the central Pd atoms have a relatively high single-bond character.
A high-resolution genetic signature of demographic and spatial expansion in epizootic rabies virus
Authors: Biek Roman , Henderson J. Caroline , Waller Lance A. , Rupprecht Charles E. , Real Leslie A.
Published: May 2007

Emerging pathogens potentially undergo rapid evolution while expanding in population size and geographic range during the course of invasion, yet it is generally difficult to demonstrate how these processes interact. Our analysis of a 30-yr data set covering a large-scale rabies virus outbreak among North American raccoons reveals the long lasting effect of the initial infection wave in determining how viral populations are genetically structured in space. We further find that coalescent-based estimates derived from the genetic data yielded an amazingly accurate reconstruction of the known spatial and demographic dynamics of the virus over time. Our study demonstrates the combined evolutionary and population dynamic processes characterizing the spread of pathogen after its introduction into a fully susceptible host population. Furthermore, the results provide important insights regarding the spatial scale of rabies persistence and validate the use of coalescent approaches for uncovering even relatively complex population histories. Such approaches will be of increasing relevance for understanding the epidemiology of emerging zoonotic diseases in a landscape context.
Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-Å crystallographic resolution
Authors: Poon Billy K. , Chen Xiaorui , Lu Mingyang , Vyas Nand K. , Quiocho Florante A. , Wang Qinghua , Ma Jianpeng
Published: May 2007

Here we report a normal-mode-based protocol for modeling anisotropic thermal motions of proteins in x-ray crystallographic refinement. The foundation for this protocol is a recently developed elastic normal mode analysis that produces much more accurate eigenvectors without the tip effect. The effectiveness of the procedure is demonstrated on the refinement of a 3.42-Å structure of formiminotransferase cyclodeaminase, a 0.5-MDa homooctameric enzyme. Using an order of magnitude fewer adjustable thermal parameters than the conventional isotropic refinement, this protocol resulted in a decrease of the values of
R
cryst
and
R
free
and improvements of the density map. Several poorly resolved regions in the original isotropically refined structure became clearer so that missing side chains were fitted easily and mistraced backbone was corrected. Moreover, the distribution of anisotropic thermal ellipsoids revealed functionally important structure flexibility. This normal-mode-based refinement is an effective way of describing anisotropic thermal motions in x-ray structures and is particularly attractive for the refinement of very large and flexible supramolecular complexes at moderate resolutions.
Nootropic α7 nicotinic receptor allosteric modulator derived from GABA
A
receptor modulators
Authors: Ng Herman J. , Whittemore Edward R. , Tran Minhtam B. , Hogenkamp Derk J. , Broide Ron S. , Johnstone Timothy B. , Zheng Lijun , Stevens Karen E. , Gee Kelvin W.
Published: May 2007

Activation of brain α7 nicotinic acetylcholine receptors (α7 nAChRs) has broad therapeutic potential in CNS diseases related to cognitive dysfunction, including Alzheimer's disease and schizophrenia. In contrast to direct agonist activation, positive allosteric modulation of α7 nAChRs would deliver the clinically validated benefits of allosterism to these indications. We have generated a selective α7 nAChR-positive allosteric modulator (PAM) from a library of GABA
A
receptor PAMs. Compound
6
(
N
-(4-chlorophenyl)-α-[[(4-chloro-phenyl)amino]methylene]-3-methyl-5-isoxazoleacet-amide) evokes robust positive modulation of agonist-induced currents at α7 nAChRs, while preserving the rapid native characteristics of desensitization, and has little to no efficacy at other ligand-gated ion channels. In rodent models, it corrects sensory-gating deficits and improves working memory, effects consistent with cognitive enhancement. Compound 6 represents a chemotype for allosteric activation of α7 nAChRs, with therapeutic potential in CNS diseases with cognitive dysfunction.
Genomic abnormalities of the murine model of Fabry disease after disease-related perturbation, a systems biology approach
Authors: Moore David F. , Gelderman Monique P. , Ferreira Paulo A. , Fuhrmann Steven R. , Yi Haiqing , Elkahloun Abdel , Lix Lisa M. , Brady Roscoe O. , Schiffmann Raphael , Goldin Ehud
Published: May 2007

Fabry disease is a disorder of α-
d
-galactosyl-containing glycolipids resulting from a deficiency of α-galactosidase A. Patients have a poorly understood vascular dysregulation. We hypothesized that disease-related perturbation by using enzyme replacement therapy in the murine model of Fabry disease would provide insight into abnormal biological processes in Fabry disease. Gene expression analyses of the heart, aorta, and liver of male α-galactosidase A knockout mice 28 weeks of age were compared with that of WT mice. Microarray analyses were performed before and after six weekly injections of α-galactosidase A. Alteration of Rpgrip1 ranked highest statistically in all three organs when knockout mice were compared with WT, and its splice variants responded in a unique way to α-galactosidase A. Enzyme replacement therapy tended to not only normalize gene expression, e.g., reduce the overexpression of securin, but also specifically modified gene expression in each tissue examined. Following multiple comparison analysis, gene expression correlation graphs were constructed, and
a priori
hypotheses were examined by using structural equation modeling. This systems biology approach demonstrated multiple and complex parallel cellular abnormalities in Fabry disease. These abnormalities form the basis for informed, in a Bayesian sense, sequential, hypothesis-driven research that can be subsequently tested experimentally.
An eight-subunit COP9 signalosome with an intact JAMM motif is required for fungal fruit body formation
Authors: Busch Silke , Schwier Elke U. , Nahlik Krystyna , Bayram Özür , Helmstaedt Kerstin , Draht Oliver W. , Krappmann Sven , Valerius Oliver , Lipscomb William N. , Braus Gerhard H.
Published: May 2007

Fruit body formation in filamentous fungi is a complex and yet hardly understood process. We show here that protein turnover control is crucial for
Aspergillus nidulans
development. Deletion of genes encoding COP9 signalosome (CSN) subunits 1, 2, 4, or 5 resulted in identical blocks in fruit body formation. The CSN multiprotein complex controls ubiquitin-dependent protein degradation in eukaryotes. Six CSN subunits interacted in a yeast two-hybrid analysis, and the complete eight-subunit CSN was recruited by a functional tandem affinity purification tag fusion of subunit 5 (CsnE). The tagged CsnE was unable to recruit any CSN subunit in a strain deleted for subunit 1 or subunit 4. Mutations in the JAMM metalloprotease core of CsnE resulted in mutant phenotypes identical to those of
csn
deletion strains. We propose that a correctly assembled CSN including a functional JAMM links protein turnover to fungal sexual development.
MicroRNA genes are frequently located near mouse cancer susceptibility loci
Authors: Sevignani Cinzia , Calin George A. , Nnadi Stephanie C. , Shimizu Masayoshi , Davuluri Ramana V. , Hyslop Terry , Demant Peter , Croce Carlo M. , Siracusa Linda D.
Published: May 2007

MicroRNAs (miRNAs) are short 19- to 24-nt RNA molecules that have been shown to regulate the expression of other genes in a variety of eukaryotic systems. Abnormal expression of miRNAs has been observed in several human cancers, and furthermore, germ-line and somatic mutations in human miRNAs were recently identified in patients with chronic lymphocytic leukemia. Thus, human miRNAs can act as tumor suppressor genes or oncogenes, where mutations, deletions, or amplifications can underlie the development of certain types of leukemia. In addition, previous studies have shown that miRNA expression profiles can distinguish among human solid tumors from different organs. Because a single miRNA can simultaneously influence the expression of two or more protein-coding genes, we hypothesized that miRNAs could be candidate genes for cancer risk. Research in complex trait genetics has demonstrated that genetic background determines cancer susceptibility or resistance in various tissues, such as colon and lung, of different inbred mouse strains. We compared the genome positions of mouse tumor susceptibility loci with those of mouse miRNAs. Here, we report a statistically significant association between the chromosomal location of miRNAs and those of mouse cancer susceptibility loci that influence the development of solid tumors. Furthermore, we identified distinct patterns of flanking DNA sequences for several miRNAs located at or near susceptibility loci in inbred strains with different tumor susceptibilities. These data provide a catalog of miRNA genes in inbred strains that could represent genes involved in the development and penetrance of solid tumors.