bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative imaging of stray fields and magnetization distributions in hard magnetic element arrays
Authors: Dreyer S. , Norpoth J. , Jooss C. , Sievers S. , Siegner U. , Neu V. , Johansen T. H.
Published: May 2007

In order to determine magnetic stray field and magnetization distributions of thin magnetic patterns and arrays, we developed a new quantitative imaging technique based on magneto-optical indicator films (MOIF) combined with inverse magnetostatic methods. The method is applied to hard magnetic FePt and PrCo5 films which exhibit out-of-plane and in-plane easy magnetization axes, respectively. The films are patterned with standard electron beam lithography into square shaped elements with sizes between 10 μm and 500 nm. The magnetization values obtained from the MOIF method are compared to those of integral magnetometer measurements and show a good agreement, if the sensor properties are taken into account, properly. As an outlook, a concept for combining MOIF imaging with magnetic force microscopy is demonstrated which allows for quantitative magnetization imaging with a resolution down to 10 nm.
Computational study of the melting-freezing transition in the quantum hard-sphere system for intermediate densities. II. Structural features
Authors: Sesé Luis M. , Bailey Lorna E.
Published: May 2007

The structural features of the quantum hard-sphere system in the region of the fluid–face-centered-cubic-solid transition, for reduced number densities 0.45<ρN*⩽0.9 (reduced de Broglie wavelengths λB*⩽0.8), are presented. The parameters obtained with path-integral Monte Carlo simulations for the fluid, amorphous, and solid phases are related to the distinct sorts of pair correlations that can be defined in a path-integral quantum fluid (instantaneous, continuous linear response and centroids). These parameters cover the pair radial correlation functions, the configurational structure factors, the order parameters Q4 and Q6, and the radii of gyration of the path-integral necklaces. Also, the fluid static structure factors have been computed by solving appropriate Ornstein-Zernike equations. A number of significant regularities in the above parameters involving both sides of the crystallization line are reported, and a comparison with results for Lennard-Jones quantum systems that can be found in the literature is made. On the other hand, the main amplitudes of the quantum fluid structure factors follow a complex behavior along the crystallization line, which points to difficulties in identifying a neat rule, similar to that of Hansen-Verlet for classical fluids, for these quantum amplitudes. To complete this study a further analysis of the instantaneous and centroid triplet correlations in the vicinities of the fluid–face-centered-cubic-solid phase transition of hard spheres has been performed, and some interesting differences between the classical and quantum melting-freezing transition are observed.
Dendritic-pattern formation in anodic aluminum oxide templates
Authors: Friedman Adam L. , Menon Latika
Published: May 2007

Formation of disordered and ordered pore patterns in two dimensions have been reported in pore growth in nanoporous alumina templates. This is explained in terms of instability in the pattern formation. Here, we report our observation of instability in the pattern formation in three dimensions, that is, along the cylindrical axis of the pores. The instability is revealed in the form of dendrites in the pore pattern under certain fabrication conditions. We examine the conditions under which two- and three-dimensional instability occurs and compare our observations of the two dimensional case with existing models in the literature.
Effect of the concentration of organic dyes on their surface plasmon enhanced two-photon absorption cross section using activated Au nanoparticles
Authors: Cohanoschi Ion , Yao Sheng , Belfield Kevin D. , Hernández Florencio E.
Published: May 2007

In this article we present the study of the surface plasmon enhanced two-photon absorption of a hydrophilic stilbene derivative (trans-4,4’-diaminostilbene) in aqueous solution at different concentrations. The observed exponential growth of the effective two-photon absorption cross section [σ2′(Au)] is attributed to the electric-field augmentation via surface plasmon resonance between nanoparticles, i.e., hot spots, and the molecular density on Au nanospheres. An unprecedented σ2′(Au)=550 000 GM has been measured. This result opens a new universe of applications in multiphoton imaging, photodynamic therapy, telecommunications, optical limiting, and multidimensional data storage using hybrid systems.
Electron and hole mobility determination in organic layers by analysis of admittance spectroscopy
Authors: Schmeits M.
Published: May 2007

We present results of a theoretical study on the simultaneous determination of the electron and hole mobilities in organic layers by admittance spectroscopy. By solving the basic semiconductor equations under steady-state and small-signal conditions for a typical system composed of an organic layer sandwiched between two electrodes, we show that it is effectively possible to obtain by admittance measurements on the same organic device, both the electron and hole mobilities. The analysis of the effect of the various parameters characterizing the structure allows determining the conditions for the simultaneous appearance of two resonance peaks in the curve representing the negative differential susceptance −ΔB a as function of the modulation frequency f. The frequency position of the two peaks allows us to obtain the transit time of both types of carriers and to deduce the mobility of the electrons and holes. Three major conditions have to be realized: injection of both electrons and holes at the respective electrodes, recombination rates of appropriate strength, and trap state modulation not masking the resonance peak of the slowest carrier.
Dependence of strength, elongation, and toughness on grain size in metallic structural materials
Authors: Li S. X. , Cui G. R.
Published: May 2007

The dependence of yield strength, uniform elongation, and toughness on grain size in metallic structural materials was discussed. The toughness is defined as the product of yield strength and uniform elongation. The yield strength versus grain size can be well described by the Hall-Petch relation; however, the uniform elongation versus grain size is not well understood yet. A simple model involving the densities of geometrically necessary dislocations and statistically stored dislocations was proposed to estimate the uniform elongation versus grain size. Existing data for low carbon steels and aluminum indicate that, in the grain size less than 1μm, the materials usually exhibit high strength and low uniform elongation and, in the grain size greater than 10μm, the materials usually exhibit low strength and high elongation; in either case the toughness is low. However, in the grain size of several micrometers, the toughness is the highest. It is suggested that we should pay more attention to develop the metallic materials with grain size of several micrometers for structural applications.
Hamiltonian dynamics of thermostated systems: Two-temperature heat-conducting ϕ4 chains
Authors: Hoover Wm. G. , Hoover Carol G.
Published: May 2007

We consider and compare four Hamiltonian formulations of thermostated mechanics, three of them kinetic, and the other one configurational. Though all four approaches “work” at equilibrium, their application to many-body nonequilibrium simulations can fail to provide a proper flow of heat. All the Hamiltonian formulations considered here are applied to the same prototypical two-temperature “ϕ4” model of a heat-conducting chain. This model incorporates nearest-neighbor Hooke’s-Law interactions plus a quartic tethering potential. Physically correct results, obtained with the isokinetic Gaussian and Nosé-Hoover thermostats, are compared with two other Hamiltonian results. The latter results, based on constrained Hamiltonian thermostats, fail to model correctly the flow of heat.
Grain size effect on the dielectric behavior of nanostructured Ni0.5Zn0.5Fe2O4
Authors: Sivakumar N. , Narayanasamy A. , Ponpandian N. , Govindaraj G.
Published: May 2007

The dielectric properties of nanocrystalline Ni0.5Zn0.5Fe2O4 spinel ferrite with various grain sizes, obtained by mechanically milling, have been studied using impedance measurements in the frequency range from 1 Hz to 10 MHz and in the temperature range from 300 to 823 K. The effect of milling, frequency, and temperature on the dielectric properties of nanocrystalline Ni-Zn ferrite is discussed. The real part of dielectric constant (ε′) for the 14 nm grain size sample is found to be about an order of magnitude smaller than that of the bulk nickel zinc ferrite. The anomalous frequency dependence of ε′ has been explained on the basis of hopping of both electrons and holes. The unusual increase in dielectric loss with milling is because of the increase in electrical conductivity due to oxygen vacancies introduced upon milling. The electrical modulus has been fitted to a stretched exponential function and the results clearly reveal the presence of the non-Debye type of dielectric relaxation in this material. The relaxation frequency is observed to decrease with milling due to increasing interaction between charge carriers arising out of oxygen vacancies introduced by milling. The mechanism for the electrical conduction is found to be the same as that for the dielectric polarization.
Phase evolution in SrTiO3-PbZrO3 solid solution
Authors: Smirnova E. P. , Sotnikov A. V. , Kvyatkovskii O. E. , Weihnacht M. , Lemanov V. V.
Published: May 2007

The article is focused on the compositional evolution and interrelation of phases in (1−x)SrTiO3-xPbZrO3 solid solution. The results of dielectric and ultrasonic wave velocity measurements in a temperature range from 4.2 to 600 K are reported. Experimental evidences of a ferroelectric phase transition at the critical concentration xc1=0.0028, the transformation from the ferroelectric to relaxor ferroelectric state at 0.08≤x<0.1 and crossover from the relaxor to the antiferroelectric state at x>0.6 are obtained. It was also shown that antiferrodistortive (improper ferroelastic) phase exists up to the concentrations 0.08<x<0.1 and is suppressed at higher concentrations, in the relaxor state. The antiferroelectric (the second antiferrodistortive) phase transition is suppressed also in the relaxor region at x<0.7. The experimental phase diagram and interrelations between the phases in the system are analyzed within the phenomenological Lifshits model.
Charge transfer reactions in Xe plasma expansion
Authors: Jiao C. Q. , Garscadden A. , Ganguly B. N.
Published: May 2007

Charge transfer reactions of fast Xe ions with hydrocarbons including methane (CH4), ethene (C2H4), and propane (C3H8) are studied by adding these hydrocarbon gases into a cross flowing Xe plasma expansion. Branching ratios and relative reaction rates for the charge transfers of fast Xe+ with each of the three hydrocarbon gases are measured under different rf powers of the inductively coupled Xe discharge. For CH4∕Xe system, we find that fast Xe+ reacts readily with CH4 generating CH4+ and CH3+ in a ratio of 1:0.56, with an estimated rate coefficient of (2.3±0.3)×10−10cm3∕s at 75W rf power which slowly increases to (2.9±0.3)×10−10cm3∕s at 250W (error bars reflect only the uncertainties due to the unknown extent of the ion recombination that follows the charge transfer reaction). These observed charge transfer reactions are made possible by the kinetically excited Xe ions produced by free expansion of the plasma. For the C2H4∕Xe system product ions C2H4+ and C2H2+ are observed, and for C3H8∕Xe, C2H4+ and C2H5+ and minor product ions including C2H2+ and C3H7+ are observed.
Heating and ablation of tokamak graphite by pulsed nanosecond Nd-YAG lasers
Authors: Semerok A. , Fomichev S. V. , Weulersse J.-M. , Brygo F. , Thro P.-Y. , Grisolia C.
Published: May 2007

The results on laser heating and ablation of graphite tiles of thermonuclear tokamaks are presented. Two pulsed Nd-YAG lasers (20 Hz repetition rate, 5 ns pulse duration and 10 kHz repetition rate, 100 ns pulse duration) were applied for ablation measurements. The ablation thresholds (1.0±0.5 J/cm2 for 5 ns and 2.5±0.5 J/cm2 for 100 ns laser pulses) were determined for the Tore Supra tokamak graphite tiles (backside) nonexposed to plasma. The high repetition rate Nd-YAG laser (10 kHz, 100 ns pulse duration) and the developed pyrometer system were applied for graphite heating measurements. Some unexpected features of laser heating of the graphite surface were observed. They were explained by the presence of a thin surface layer with the properties different from those of the bulk graphite. The theoretical models of laser heating and near-threshold ablation of graphite with imperfectly adhered layer were developed to interpret the experimental results.
Thermal relaxation kinetics of defects in single-wall carbon nanotubes
Authors: Uchida Takashi , Tachibana Masaru , Kojima Kenichi
Published: May 2007

The defects in single-wall carbon nanotubes irradiated with a 248 nm pulsed excimer laser were studied using Raman spectroscopy. The thermal relaxation kinetics of the laser-induced defects was examined at sample temperatures from 296 to 698 K. Two relaxation processes are revealed; one is the fast process with an activation energy of 0.4 eV and the other is the slow process with an activation energy of 0.7 eV. These two processes can correspond to vacancy-interstitial recombination and vacancy migration along the tube axis, respectively.
Dead-space corrected GaInP/GaAs composite collector double heterojunction bipolar transistors
Authors: Poh Z. S. , Yow H. K. , Ong D. S. , Houston P. A. , Krysa A. B.
Published: May 2007

GaInP/GaAs/GaInP double heterojunction bipolar transistors incorporating dead-space corrected composite collectors were investigated experimentally. The optimized DHBT with a 10-nm lowly doped GaAs spacer and a 5-nm highly doped GaInP spacer has extended the operating range of the collector-emitter voltage, VCE, by maximizing the collector-emitter voltage at the onset of the multiplication, VCE,onset, to 20 V, while minimizing the saturation voltage, VCE,sat (<1 V), and maintaining the nominal breakdown voltage, BVCEO, of the GaInP collector at 25 V. The design incorporating an Al0.11Ga0.89As spacer rather than a GaInP spacer within the lowly doped GaAs-GaInP composite collector demonstrated similar breakdown behavior.
Effects of a surfactant-templated nanoporous TiO2 interlayer on dye-sensitized solar cells
Authors: Ahn Kwang-Soon , Kang Moon-Sung , Lee Ji-Won , Kang Yong Soo
Published: May 2007

A 320 nm thick surfactant-templated nanoporous (STN) TiO2 layer prepared from block copolymer P123 [poly(ethylene oxide)20-poly(propylene oxide)70-poly(ethylene oxide)20] was used as an interlayer between a 21 μm thick mesoporous TiO2 layer and a transparent conducting oxide. The thin STN TiO2 interlayer had well-dispersed nanoporous features, which made it possible to adsorb dye molecules in the interlayer. In addition, it provided an enhanced electron lifetime, resulting in a reduced recombination rate and an increased diffusion length. The dye-sensitized solar cell with the thin STN interlayer resulted in a significantly increased overall energy conversion efficiency from 7.11% to 9.22% with an improvement of all parameters (short-circuit current, open circuit voltage, and fill factor).
Escape rate of metastable states in a driven NbN superconducting microwave resonator
Authors: Abdo Baleegh , Segev Eran , Shtempluck Oleg , Buks Eyal
Published: May 2007

We study thermal instability and formation of local hot spots in a driven nonlinear NbN superconducting microwave resonator. White noise injected into the resonator results in transitions between the metastable states via a process consisting of two stages. In the first stage, the input noise entering the system induces fluctuations in the resonator mode. While in the second one, these mode fluctuations result in phase transitions of the hot spot due to induced temperature fluctuations. The associated noise-activated escape rate is calculated theoretically and measured also experimentally by means of driving the system into stochastic resonance. A comparison between theory and experiment yields a partial agreement.
Variational approach for the quantum Zakharov system
Authors: Haas F.
Published: May 2007

The quantum Zakharov system is described in terms of a Lagrangian formalism. A time-dependent Gaussian trial function approach for the envelope electric field and the low-frequency part of the density fluctuation leads to a coupled, nonlinear system of ordinary differential equations. In the semiclassical case, linear stability analysis of this dynamical system shows a destabilizing role played by quantum effects. Arbitrary values of the quantum effects are also considered, yielding the ultimate destruction of the localized, Gaussian trial solution. Numerical simulations are shown for both the semiclassical and the full quantum cases.
Gas-liquid two-phase flow across a bank of micropillars
Authors: Krishnamurthy Santosh , Peles Yoav
Published: May 2007

Adiabatic nitrogen-water two-phase flow across a bank of staggered circular micropillars, 100μm long with a diameter of 100μm and a pitch-to-diameter ratio of 1.5, was investigated experimentally for Reynolds number ranging from 5 to 50. Flow patterns, void fraction, and pressure drop were obtained, discussed, and compared to large scale as well as microchannel results. Two-phase flow patterns were determined by flow visualization, and a flow map was constructed as a function of gas and liquid superficial velocities. Significant deviations from conventional scale systems, with respect to flow patterns and trend lines, were observed. A unique flow pattern, driven by surface tension, was observed and termed bridge flow. The applicability of conventional scale models to predict the void fraction and two-phase frictional pressure drop was also assessed. Comparison with a conventional scale void fraction model revealed good agreement, but was found to be in a physically wrong form. Thus, a modified physically based model for void fraction was developed. A two-phase frictional multiplier was found to be a strong function of mass flux, unlike in previous microchannel studies. It was observed that models from conventional scale systems did not adequately predict the two-phase frictional multiplier at the microscale, thus, a modified model accounting for mass flux was developed.
Preferred orientation of pores in ceramics under heating by a linearly polarized microwave field
Authors: Rybakov K. I. , Semenov V. E. , Link G. , Thumm M.
Published: May 2007

A spherical pore in the ionic crystalline material subjected to a linearly polarized microwave radiation is shown to flatten along the electric field vector. The deformation of the pore occurs due to rectification of high-frequency flows of charged vacancies in the course of their nonlinear interaction with the electric field near the pore surface. The estimates show that the effect is most pronounced in the materials with a significant contribution of mobile vacancies into microwave absorption. Preferred orientation of pores has been observed experimentally in a zirconia ceramic sample sintered under heating by a linearly polarized microwave radiation.
The paraelectric state in thin-film (Ba,Sr)TiO3
Authors: Tyunina M. , Levoska J.
Published: May 2007

Vertical capacitor heterostructures of (Ba,Sr)TiO3 thin films with different Ba:Sr ratios, microstructures, and thicknesses were grown by in situ pulsed laser deposition using MgO or Al2O3 substrates and La0.5Sr0.5CoO3 or Pt electrodes. The low-frequency dielectric response was experimentally studied as a function of frequency, temperature, and applied field. High-temperature Curie-Weiss behavior, temperature evolution of the dynamic dielectric nonlinearity, and dielectric hysteresis were observed and analyzed. The observed high-temperature relaxorlike state and relaxational nature of dielectric hysteresis are discussed.
Differential force microscope for long time-scale biophysical measurements
Authors: Choy Jason L. , Parekh Sapun H. , Chaudhuri Ovijit , Liu Allen P. , Bustamante Carlos , Footer Matthew J. , Theriot Julie A. , Fletcher Daniel A.
Published: May 2007

Force microscopy techniques including optical trapping, magnetic tweezers, and atomic force microscopy (AFM) have facilitated quantification of forces and distances on the molecular scale. However, sensitivity and stability limitations have prevented the application of these techniques to biophysical systems that generate large forces over long times, such as actin filament networks. Growth of actin networks drives cellular shape change and generates nano-Newtons of force over time scales of minutes to hours, and consequently network growth properties have been difficult to study. Here, we present an AFM-based differential force microscope with integrated epifluorescence imaging in which two adjacent cantilevers on the same rigid support are used to provide increased measurement stability. We demonstrate 14nm displacement control over measurement times of 3hours and apply the instrument to quantify actin network growth in vitro under controlled loads. By measuring both network length and total network fluorescence simultaneously, we show that the average cross-sectional density of the growing network remains constant under static loads. The differential force microscope presented here provides a sensitive method for quantifying force and displacement with long time-scale stability that is useful for measurements of slow biophysical processes in whole cells or in reconstituted molecular systems in vitro.
Molecular simulation with variable protonation states at constant pH
Authors: Stern Harry A.
Published: May 2007

A new method is presented for performing molecular simulations at constant pH. The method is a Monte Carlo procedure where trial moves consist of relatively short molecular dynamics trajectories, using a time-dependent potential energy that interpolates between the old and new protonation states. Conformations and protonation states are sampled from the correct statistical ensemble independent of the trial-move trajectory length, which may be adjusted to optimize efficiency. Because moves are not instantaneous, the method does not require the use of a continuum solvation model. It should also be useful in describing buried titratable groups that are not directly exposed to solvent, but have strong interactions with neighboring hydrogen bond partners. The feasibility of the method is demonstrated for a simple test case: constant-pH simulations of acetic acid in aqueous solution with an explicit representation of water molecules.
Modelling the probability of sustained flaming: predictive value of fire weather index components compared with observations of site weather and fuel moisture conditions
Authors: Beverly Jennifer L. , Wotton B. Mike
Published: May 2007

We investigated the likelihood that short-duration sustained flaming would develop in forest ground fuels that had direct contact with a small and short-lived flame source. Data from 1027 small-scale experimental test fires conducted in field trials at six sites in British Columbia and the North-West Territories between 1958 and 1961 were used to develop logistic regression models for ten fuel categories that represent unique combinations of forest cover, ground fuel type, and in some cases, season. Separate models were developed using two subsets of independent variables: (1) weather variables and fuel moisture measurements taken at the site of the test fire; and (2) Canadian Fire Weather Index (FWI) system components calculated from weather observations recorded at a nearby station. Results indicated that models developed with FWI system components were as effective as models developed with site variables at predicting the probability of short-duration sustained flaming in most fuel categories. FWI system components were not useful for predicting sustained flaming in spring grass fuels and had limited usefulness for modelling the probability of sustained flaming in aspen leaf ground fuels during summer conditions. For all other fuel categories, FWI system components were highly effective substitutes for site variables for modelling the probability of sustained flaming.
Precipitation associated with lightning-ignited wildfires in Arizona and New Mexico
Authors: Hall Beth L.
Published: May 2007

From 1990 to 1998, over 17000 naturally ignited wildfires were observed in Arizona and New Mexico on US federal land during the fire season of April through October. Lightning strikes associated with these fires accounted for less than 0.35% of all recorded cloud-to-ground lightning strikes that occurred during the fire season during that time. Given the high aridity of this region, why do some lightning strikes ignite fires and others not? Natural wildfire ignitions in this region are often attributed to what is referred to as ‘dry’ lightning, or lightning with little or no precipitation. This study used daily and hourly gridded precipitation derived from historical gauge data to compare the amount of precipitation associated with natural wildfires and the amount of precipitation associated with lightning strikes that were not associated with natural wildfire events. Climatology of natural ignitions tend to peak before the time of the seasonal maximum lightning flashes and precipitation, suggesting ‘dry’ ignitions in the early part (e.g. late June, early July) of the wildfire season. Observed natural wildfires were more often associated with conditions of <2 mm of precipitation on the day of the event than were cases without an associated ignition. The majority of lightning flashes that did not cause a discovered wildfire were associated with a higher precipitation rate after the timing of the event, which suggests the possibility of the precipitation extinguishing the wildfires before discovery. Most lightning flashes that were not associated with a discovered ignition had twice as many hours with some measurable precipitation than where there were discovered ignitions, which eludes to the longer-term impact of preceding precipitation on the fuels than the lightning storm-associated precipitation. These results can be applied to gridded forecasts of amount of precipitation to indicate areas where there is an increased probability of natural wildfire ignition, assuming the other factors of ignition source and fuel availability are present.
Fire danger rating in the United States of America: an evolution since 1916
Authors: Hardy Colin C. , Hardy Charles E.
Published: May 2007

Fire scientists in the United States began exploring the relationships of fire-danger and hazard with weather, fuel moisture, and ignition probabilities as early as 1916. Many of the relationships identified then persist today in the form of our National Fire-Danger-Rating System. This paper traces the evolution of fire-danger rating in the United States, including discussions of significant developmental milestones, innovative instrumentation, and a succession of analogue fire-danger meters, or calculators. Although the primary theme of this paper is an historical review of pioneering efforts leading up to our current state-of-knowledge, a common thread throughout this paper is the desire by every generation of developer to achieve a ‘purely analytical system’. A national system was first introduced in 1964. The current system used throughout the USA was implemented in 1978, with optional revisions added in 1988. We present this evolution within the context of three periods of development: first, the pioneering efforts initiated at the Priest River Experiment Station in northern Idaho; second, the implementation of a national, standardised fire-danger-rating system; and third, spatially explicit delivery systems that provide a national view of weather and fire potential, which include national fire-danger and weather maps and satellite-derived maps that reflect the state of live vegetation across the United States.
Climatological and statistical characteristics of the Haines Index for North America
Authors: Winkler Julie A. , Potter Brian E. , Wilhelm Dwight F. , Shadbolt Ryan P. , Piromsopa Krerk , Bian Xindi
Published: May 2007

The Haines Index is an operational tool for evaluating the potential contribution of dry, unstable air to the development of large or erratic plume-dominated wildfires. The index has three variants related to surface elevation, and is calculated from temperature and humidity measurements at atmospheric pressure levels. To effectively use the Haines Index, fire forecasters and managers must be aware of the climatological and statistical characteristics of the index for their location. However, a detailed, long-term, and spatially extensive analysis of the index does not currently exist. To meet this need, a 40-year (1961–2000) climatology of the Haines Index was developed for North America. The climatology is based on gridded (2.5° latitude × 2.5° longitude) temperature and humidity fields from the NCEP/NCAR reanalysis. The climatology illustrates the large spatial variability in the Haines Index both within and between regions using the different index variants. These spatial variations point to the limitations of the index and must be taken into account when using the Haines Index operationally.
Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by
Escherichia coli
RNA polymerase
Authors: Davis Caroline A. , Bingman Craig A. , Landick Robert , Record M. Thomas , Saecker Ruth M.
Published: May 2007

The architecture of cellular RNA polymerases (RNAPs) dictates that transcription can begin only after promoter DNA bends into a deep channel and the start site nucleotide (+1) binds in the active site located on the channel floor. Formation of this transcriptionally competent “open” complex (RP
o
) by
Escherichia coli
RNAP at the λP
R
promoter is greatly accelerated by DNA upstream of base pair −47 (with respect to +1). Here we report real-time hydroxyl radical (·OH) and potassium permanganate (KMnO
4
) footprints obtained under conditions selected for optimal characterization of the first kinetically significant intermediate (I
1
) in RP
o
formation. ·OH footprints reveal that the DNA backbone from −71 to −81 is engulfed by RNAP in I
1
but not in RP
o
; downstream protection extends to approximately +20 in both complexes. KMnO
4
footprinting detects solvent-accessible thymine bases in RP
o
, but not in I
1
. We conclude that upstream DNA wraps more extensively on RNAP in I
1
than in RP
o
and that downstream DNA (−11 to +20) occupies the active-site channel in I
1
but is not yet melted. Mapping of the footprinting data onto available x-ray structures provides a detailed model of a kinetic intermediate in bacterial transcription initiation and suggests how transient contacts with upstream DNA in I
1
might rearrange the channel to favor entry of downstream duplex DNA.
Structure of the heterotrimeric complex that regulates type III secretion needle formation
Authors: Quinaud Manuelle , Plé Sophie , Job Viviana , Contreras-Martel Carlos , Simorre Jean-Pierre , Attree Ina , Dessen Andréa
Published: May 2007

Type III secretion systems (T3SS), found in several Gram-negative pathogens, are nanomachines involved in the transport of virulence effectors directly into the cytoplasm of target cells. T3SS are essentially composed of basal membrane-embedded ring-like structures and a hollow needle formed by a single polymerized protein. Within the bacterial cytoplasm, the T3SS needle protein requires two distinct chaperones for stabilization before its secretion, without which the entire T3SS is nonfunctional. The 2.0-Å x-ray crystal structure of the PscE-PscF
55–85
-PscG heterotrimeric complex from
Pseudomonas aeruginosa
reveals that the C terminus of the needle protein PscF is engulfed within the hydrophobic groove of the tetratricopeptide-like molecule PscG, indicating that the macromolecular scaffold necessary to stabilize the T3SS needle is totally distinct from chaperoned complexes between pilus- or flagellum-forming molecules. Disruption of specific PscG–PscF interactions leads to impairment of bacterial cytotoxicity toward macrophages, indicating that this essential heterotrimer, which possesses homologs in a wide variety of pathogens, is a unique attractive target for the development of novel antibacterials.
Hippocampal place cell assemblies are speed-controlled oscillators
Authors: Geisler Caroline , Robbe David , Zugaro Michaël , Sirota Anton , Buzsáki György
Published: May 2007

The phase of spikes of hippocampal pyramidal cells relative to the local field θ oscillation shifts forward (“phase precession”) over a full θ cycle as the animal crosses the cell's receptive field (“place field”). The linear relationship between the phase of the spikes and the travel distance within the place field is independent of the animal's running speed. This invariance of the phase–distance relationship is likely to be important for coordinated activity of hippocampal cells and space coding, yet the mechanism responsible for it is not known. Here we show that at faster running speeds place cells are active for fewer θ cycles but oscillate at a higher frequency and emit more spikes per cycle. As a result, the phase shift of spikes from cycle to cycle (i.e., temporal precession slope) is faster, yet spatial-phase precession stays unchanged. Interneurons can also show transient-phase precession and contribute to the formation of coherently precessing assemblies. We hypothesize that the speed-correlated acceleration of place cell assembly oscillation is responsible for the phase–distance invariance of hippocampal place cells.
A highly efficient form of the selenocysteine insertion sequence element in protozoan parasites and its use in mammalian cells
Authors: Novoselov Sergey V. , Lobanov Alexey V. , Hua Deame , Kasaikina Marina V. , Hatfield Dolph L. , Gladyshev Vadim N.
Published: May 2007

Selenoproteins are an elite group of proteins containing a rare amino acid, selenocysteine (Sec), encoded by the codon, UGA. In eukaryotes, incorporation of Sec requires a Sec insertion sequence (SECIS) element, a stem–loop structure located in the 3′-untranslated regions of selenoprotein mRNAs. Here we report identification of a noncanonical form of SECIS element in
Toxoplasma gondii
and
Neospora canine
, single-celled apicomplexan parasites of humans and domestic animals. This SECIS has a GGGA sequence in the SBP2-binding site in place of AUGA previously considered invariant. Using a combination of computational and molecular techniques, we show that
Toxoplasma
and
Neospora
possess both canonical and noncanonical SECIS elements. The GGGA-type SECIS element supported Sec insertion in mammalian HEK 293 and NIH 3T3 cells and did so more efficiently than the natural mammalian SECIS elements tested. In addition, mammalian type I and type II SECIS elements mutated into the GGGA forms were functional but manifested decreased Sec insertion efficiency. We carried out computational searches for both AUGA and GGGA forms of SECIS elements in
Toxoplasma
and detected five selenoprotein genes, including one coding for a previously undescribed selenoprotein, designated SelQ, and two containing the GGGA form of the SECIS element. In contrast, the GGGA-type SECIS elements were not detected in mammals and nematodes. As a practical outcome of the study, we developed pSelExpress1, a vector for convenient expression of selenoproteins in mammalian cells. It contains an SBP2 gene and the most efficient tested SECIS element: an AUGA mutant of the GGGA-type
Toxoplasma
SelT structure.
Three-dimensional structure of cofilin bound to monomeric actin derived by structural mass spectrometry data
Authors: Kamal J. K. Amisha , Benchaar Sabrina A. , Takamoto Keiji , Reisler Emil , Chance Mark R.
Published: May 2007

The cytoskeletal protein, actin, has its structure and function regulated by cofilin. In the absence of an atomic resolution structure for the actin/cofilin complex, the mechanism of cofilin regulation is poorly understood. Theoretical studies based on the similarities of cofilin and gelsolin segment 1 proposed the cleft between subdomains 1 and 3 in actin as the cofilin binding site. We used radiolytic protein footprinting with mass spectrometry and molecular modeling to provide an atomic model of how cofilin binds to monomeric actin. Footprinting data suggest that cofilin binds to the cleft between subdomains 1 and 2 in actin and that cofilin induces further closure of the actin nucleotide cleft. Site-specific fluorescence data confirm these results. The model identifies key ionic and hydrophobic interactions at the binding interface, including hydrogen-bonding between His-87 of actin to Ser-89 of cofilin that may control the charge dependence of cofilin binding. This model and its implications fill an especially important niche in the actin field, owing to the fact that ongoing crystallization efforts of the actin/cofilin complex have so far failed. This 3D binary complex structure is derived from a combination of solution footprinting data and computational approaches and outlines a general method for determining the structure of such complexes.
Solution structure and mutational analysis of pituitary adenylate cyclase-activating polypeptide binding to the extracellular domain of PAC1-RS
Authors: Sun Chaohong , Song Danying , Davis-Taber Rachel A. , Barrett Leo W. , Scott Victoria E. , Richardson Paul L. , Pereda-Lopez Ana , Uchic Marie E. , Solomon Larry R. , Lake Marc R. , Walter Karl A. , Hajduk Philip J. , Olejniczak Edward T.
Published: May 2007

The pituitary adenylate cyclase-activating polypeptide (PACAP) receptor is a class II G protein-coupled receptor that contributes to many different cellular functions including neurotransmission, neuronal survival, and synaptic plasticity. The solution structure of the potent antagonist PACAP (residues 6′–38′) complexed to the N-terminal extracellular (EC) domain of the human splice variant hPAC1-R-short (hPAC1-RS) was determined by NMR. The PACAP peptide adopts a helical conformation when bound to hPAC1-RSwith a bend at residue A18′ and makes extensive hydrophobic and electrostatic interactions along the exposed β-sheet and interconnecting loops of the N-terminal EC domain. Mutagenesis data on both the peptide and the receptor delineate the critical interactions between the C terminus of the peptide and the C terminus of the EC domain that define the high affinity and specificity of hormone binding to hPAC1-RS. These results present a structural basis for hPAC1-RSselectivity for PACAP versus the vasoactive intestinal peptide and also differentiate PACAP residues involved in binding to the N-terminal extracellular domain versus other parts of the full-length hPAC1-RSreceptor. The structural, mutational, and binding data are consistent with a model for peptide binding in which the C terminus of the peptide hormone interacts almost exclusively with the N-terminal EC domain, whereas the central region makes contacts to both the N-terminal and other extracellular parts of the receptor, ultimately positioning the N terminus of the peptide to contact the transmembrane region and result in receptor activation.
The phi complex as a neuromarker of human social coordination
Authors: Tognoli Emmanuelle , Lagarde Julien , DeGuzman Gonzalo C. , Kelso J. A. Scott
Published: May 2007

Many social interactions rely upon mutual information exchange: one member of a pair changes in response to the other while at the same time producing actions that alter the behavior of the other. However, little is known about how such social processes are integrated in the brain. Here, we used a specially designed dual-electroencephalogram system and the conceptual framework of coordination dynamics to identify neural signatures of effective, real-time coordination between people and its breakdown or absence. High-resolution spectral analysis of electrical brain activity before and during visually mediated social coordination revealed a marked depression in occipital alpha and rolandic mu rhythms during social interaction that was independent of whether behavior was coordinated or not. In contrast, a pair of oscillatory components (phi
1
and phi
2
) located above right centro-parietal cortex distinguished effective from ineffective coordination: increase of phi
1
favored independent behavior and increase of phi
2
favored coordinated behavior. The topography of the phi complex is consistent with neuroanatomical sources within the human mirror neuron system. A plausible mechanism is that the phi complex reflects the influence of the other on a person's ongoing behavior, with phi
1
expressing the inhibition of the human mirror neuron system and phi
2
its enhancement.
Scaling theory of transport in complex biological networks
Authors: Gallos Lazaros K. , Song Chaoming , Havlin Shlomo , Makse Hernán A.
Published: May 2007

Transport is an important function in many network systems and understanding its behavior on biological, social, and technological networks is crucial for a wide range of applications. However, it is a property that is not well understood in these systems, probably because of the lack of a general theoretical framework. Here, based on the finding that renormalization can be applied to bionetworks, we develop a scaling theory of transport in self-similar networks. We demonstrate the networks invariance under length scale renormalization, and we show that the problem of transport can be characterized in terms of a set of critical exponents. The scaling theory allows us to determine the influence of the modular structure on transport in metabolic and protein-interaction networks. We also generalize our theory by presenting and verifying scaling arguments for the dependence of transport on microscopic features, such as the degree of the nodes and the distance between them. Using transport concepts such as diffusion and resistance, we exploit this invariance, and we are able to explain, based on the topology of the network, recent experimental results on the broad flow distribution in metabolic networks.
Class IA phosphoinositide 3-kinases are obligate p85-p110 heterodimers
Authors: Geering Barbara , Cutillas Pedro R. , Nock Gemma , Gharbi Severine I. , Vanhaesebroeck Bart
Published: May 2007

Class IA phosphoinositide 3-kinases (PI3Ks) signal downstream of tyrosine kinases and Ras and control a wide variety of biological responses. In mammals, these heterodimeric PI3Ks consist of a p110 catalytic subunit (p110α, p110β, or p110δ) bound to any of five distinct regulatory subunits (p85α, p85β, p55γ, p55α, and p50α, collectively referred to as “p85s”). The relative expression levels of p85 and p110 have been invoked to explain key features of PI3K signaling. For example, free (i.e., non-p110-bound) p85α has been proposed to negatively regulate PI3K signaling by competition with p85/p110 for recruitment to phosphotyrosine docking sites. Using affinity and ion exchange chromatography and quantitative mass spectrometry, we demonstrate that the p85 and p110 subunits are present in equimolar amounts in mammalian cell lines and tissues. No evidence for free p85 or p110 subunits could be obtained. Cell lines contain 10,000–15,000 p85/p110 complexes per cell, with p110β and p110δ being the most prevalent catalytic subunits in nonleukocytes and leukocytes, respectively. These results argue against a role of free p85 in PI3K signaling and provide insights into the nonredundant functions of the different class IA PI3K isoforms.
Membrane association is a determinant for substrate recognition by PMT4 protein
O
-mannosyltransferases
Authors: Hutzler Johannes , Schmid Maria , Bernard Thomas , Henrissat Bernard , Strahl Sabine
Published: May 2007

Protein O-mannosylation represents an evolutionarily conserved, essential posttranslational modification with immense impact on a variety of cellular processes. In humans, O-mannosylation defects result in Walker–Warburg syndrome, a severe recessive congenital muscular dystrophy associated with defects in neuronal migration that produce complex brain and eye abnormalities. In mouse and yeasts, loss of O-mannosylation causes lethality. Protein
O
-mannosyltransferases (PMTs) initiate the assembly of
O
-mannosyl glycans. The evolutionarily conserved PMT family is classified into PMT1, PMT2, and PMT4 subfamilies, which mannosylate distinct target proteins. In contrast to other types of glycosylation, signal sequences for O-mannosylation have not been identified to date. In the present study, we identified signals that determine PMT4-dependent O-mannosylation. Using specific model proteins, we demonstrate that in yeast Pmt4p mediates O-mannosylation of Ser/Thr-rich membrane-attached proteins. The nature of the membrane-anchoring sequence is nonrelevant, as long as it is flanked by a Ser/Thr-rich domain facing the endoplasmic reticulum lumen. Our work shows that, in contrast to several other types of glycosylation, PMT4 O-mannosylation signals are not just linear protein's primary structure sequences but rather are highly complex. Based on these findings, we performed
in silico
analyses of the
Saccharomyces cerevisiae
proteome and identified previously undescribed Pmt4p substrates. This tool for proteome-wide identification of O-mannosylated proteins is of general interest because several of these proteins are major players of a wide variety of cellular processes.
Combinatorial regulation of genes essential for
Myxococcus xanthus
development involves a response regulator and a LysR-type regulator
Authors: Viswanathan Poorna , Ueki Toshiyuki , Inouye Sumiko , Kroos Lee
Published: May 2007

Myxococcus xanthus
is a bacterium that undergoes multicellular development. C-signaling influences gene expression and movement of cells into aggregates. Expression of the
dev
operon, which includes genes essential for efficient sporulation, depends in part on C-signaling and reaches its highest level in cells within aggregates, ensuring that spores form within fruiting bodies. Here, an upstream DNA element was found to be essential for
dev
promoter activity and was bound by FruA, a response regulator in the C-signaling pathway. A second positive regulatory element, located ≈350 bp downstream of the
dev
transcriptional start site, was bound by LadA, a newly identified transcription factor in the LysR family. Typically, LysR-type transcription factors bind upstream of the promoter and activate transcription in response to a coinducer. LadA appears to activate transcription from an unusual location for a LysR family member and likely subjects
dev
transcription to a different cue than does FruA. A
ladA
mutant exhibited similar developmental defects as
dev
mutants, suggesting that LadA may be devoted to
dev
regulation, unlike FruA, which regulates many developmental genes. FruA and LadA act on a regulatory region spanning >400 bp to bring about proper temporal and spatial expression of the
dev
operon, resembling the regulation of developmental genes in multicellular eukaryotes.