bluuebunny/crossref_metadata_2025 huggingface dataset:
An energy-conserving two-temperature model of radiation damage in single-component and binary Lennard-Jones crystals
Authors: Phillips Carolyn L. , Crozier Paul S.
Published: August 2009

Two-temperature models are used to represent the interaction between atoms and free electrons during thermal transients such as radiation damage, laser heating, and cascade simulations. In this paper, we introduce an energy-conserving version of an inhomogeneous finite reservoir two-temperature model using a Langevin thermostat to communicate energy between the electronic and atomic subsystems. This energy-conserving modification allows the inhomogeneous two-temperature model to be used for longer and larger simulations and simulations of small energy phenomena, without introducing nonphysical energy fluctuations that may affect simulation results. We test this model on the annealing of Frenkel defects. We find that Frenkel defect annealing is largely indifferent to the electronic subsystem, unless the electronic subsystem is very tightly coupled to the atomic subsystem. We also consider radiation damage due to local deposition of heat in two idealized systems. We first consider radiation damage in a large face-centered-cubic Lennard-Jones (LJ) single-component crystal that readily recrystallizes. Second, we consider radiation damage in a large binary glass-forming LJ crystal that retains permanent damage. We find that the electronic subsystem parameters can influence the way heat is transported through the system and have a significant impact on the number of defects after the heat deposition event. We also find that the two idealized systems have different responses to the electronic subsystem. The single-component LJ system anneals most rapidly with an intermediate electron-ion coupling and a high electronic thermal conductivity. If sufficiently damaged, the binary glass-forming LJ system retains the least permanent damage with both a high electron-ion coupling and a high electronic thermal conductivity. In general, we find that the presence of an electronic gas can affect short and long term material annealing.
Indium migration paths in V-defects of InAlN grown by metal-organic vapor phase epitaxy
Authors: Kehagias Th. , Dimitrakopulos G. P. , Kioseoglou J. , Kirmse H. , Giesen C. , Heuken M. , Georgakilas A. , Neumann W. , Karakostas Th. , Komninou Ph.
Published: August 2009

InAlN thin films grown on GaN/Al2O3 (0001) templates by metal-organic vapor phase epitaxy were studied by transmission electron microscopy techniques. V-defects in the form of hexagonal inverted pyramids with {101¯1} sidewalls were observed on the films’ surfaces linked to the termination of threading dislocations. Their origin is explained by the different surface atom mobility of In and Al and the built-in strain relaxation. Indium segregation in the films is influenced by the formation of V-defects, the edges and the apexes of which function as paths of migrating indium atoms diffusing along nanopipes formed at the open-core threading dislocations.
Nucleation via an unstable intermediate phase
Authors: Sear Richard P.
Published: August 2009

The pathway for crystallization from dilute vapors and solutions is often observed to take a detour via a liquid or concentrated-solution phase. For example, in moist subzero air, droplets of liquid water form, which then freeze. In this example and in many others, an intermediate phase (here liquid water) is dramatically accelerating the kinetics of a phase transition between two other phases (water vapor and ice). Here we study this phenomenon via exact computer simulations of a simple lattice model. Surprisingly, we find that the rate of nucleation of the new equilibrium phase is actually fastest when the intermediate phase is slightly unstable in the bulk, i.e., has a slightly higher free energy than the phase we start in. Nucleation occurs at a concave part of the surface and microscopic amounts of the intermediate phase can form there even before the phase is stable in the bulk. As the nucleus of the equilibrium phase is microscopic, this allows nucleation to occur effectively in the intermediate phase before it is stable in the bulk.
Observation of negative differential transconductance in tunneling emitter bipolar transistors
Authors: van Veenhuizen Marc J. , Locatelli Nicolas , Moodera Jagadeesh , Chang Joonyeon
Published: August 2009

We report on measurement of negative differential transconductance (NDTC) of iron (Fe)/magnesium-oxide (MgO)/silicon tunneling emitter NPN bipolar transistors. Device simulations reveal that the NDTC is a consequence of an inversion layer at the tunneling-oxide/P-silicon interface for low base voltages. Electrons travel laterally through the inversion layer into the base and give rise to an increase in collector current. The NDTC results from the recombination of those electrons at the interface between emitter and base contact which is dependent on the base voltage. For larger base voltages, the inversion layer disappears marking the onset of normal bipolar transistor behavior.
Nanoscale doping of InAs via sulfur monolayers
Authors: Ho Johnny C. , Ford Alexandra C. , Chueh Yu-Lun , Leu Paul W. , Ergen Onur , Takei Kuniharu , Smith Gregory , Majhi Prashant , Bennett Joseph , Javey Ali
Published: August 2009

One of the challenges for the nanoscale device fabrication of III-V semiconductors is controllable postdeposition doping techniques to create ultrashallow junctions. Here, we demonstrate nanoscale, sulfur doping of InAs planar substrates with high dopant areal dose and uniformity by using a self-limiting monolayer doping approach. From transmission electron microscopy and secondary ion mass spectrometry, a dopant profile abruptness of ∼3.5 nm/decade is observed without significant defect density. The n+/p+ junctions fabricated by using this doping scheme exhibit negative differential resistance characteristics, further demonstrating the utility of this approach for device fabrication with high electrically active sulfur concentrations of ∼8×1018 cm−3.
Strong nonlinear optical response of graphene in the terahertz regime
Authors: Wright A. R. , Xu X. G. , Cao J. C. , Zhang C.
Published: August 2009

We demonstrate that within the model of massless Dirac fermions, graphene has a strong nonlinear optical response in the terahertz regime. It is found that the nonlinear contribution significantly alters both the single frequency and frequency tripled optical response at experimentally relevant field strengths. The optical activity of single layer graphene is significantly enhanced by nonlinear effects, and the frequency tripled response opens the gateway to photonic and optoelectronic device applications.
Experimental validation of a higher dimensional theory of electrical contact resistance
Authors: Gomez Matthew R. , French David M. , Tang Wilkin , Zhang Peng , Lau Y. Y. , Gilgenbach R. M.
Published: August 2009

The increased resistance of a cylindrical conducting channel due to constrictions of various radii and axial lengths was measured experimentally. The experimental data corroborate the higher dimensional contact resistance theory that was recently developed.
Characterization of field emission from carbon nanofibers on a metal tip
Authors: Sakai Y. , Tone D. , Nagatsu S. , Endo T. , Kita S. , Okuyama F.
Published: August 2009

Field electron emission from carbon nanofibers (CNFs) grown on a tungsten tip has been characterized by measuring emission current-voltage (I-V) curves and observing emission patterns on a phosphor screen. CNFs were vertically grown on the tip by plasma-enhanced chemical vapor deposition. Field emission from the CNFs over 100 μA was strongly dependent on emitter-anode distance, and the dominant field electrons were emitted within an angular spread of Δθ∼25°, indicating the electron emission took place mainly from the emitter’s apex area. By analyzing the I-V curves with the aid of the Fowler–Nordheim theory, the maximum current density was estimated to be about J=2×109 A/m2.
Bridging oxygen as a site for proton adsorption on the vitreous silica surface
Authors: Lockwood Glenn K. , Garofalini Stephen H.
Published: August 2009

Molecular dynamics computer simulations were used to study the protonation of bridging oxygen (Si–O–Si) sites present on the vitreous silica surface in contact with water using a dissociative water potential. In contrast to first-principles calculations based on unconstrained molecular analogs, such as H7Si2O7+ molecules, the very limited flexibility of neighboring SiO4 tetrahedra when embedded in a solid surface means that there is a relatively minor geometric response to proton adsorption, requiring sites predisposed to adsorption. Simulation results indicate that protonation of bridging oxygen occurs at predisposed sites with bridging angles in the 125°–135° range, well below the bulk silica mean of ∼150°, consistent with various ab initio calculations, and that a small fraction of such sites are present in all ring sizes. The energy differences between dry and protonated bridges at various angles observed in the simulations coincide completely with quantum calculations over the entire range of bridging angles encountered in the vitreous silica surface. Those sites with bridging angles near 130° support adsorbed protons more stably, resulting in the proton remaining adsorbed for longer periods of time. Vitreous silica has the necessary distribution of angular strain over all ring sizes to allow protons to adsorb onto bridging oxygen at the surface, forming acidic surface groups that serve as ideal intermediate steps in proton transfer near the surface. In addition to hydronium formation and water-assisted proton transfer in the liquid, protons can rapidly move across the water-silica interface via strained bridges that are predisposed to transient proton adsorption. Thus, an excess proton at any given location on a silica surface can move by either water-assisted or strained bridge-assisted diffusion depending on the local environment. The result of this would be net migration that is faster than it would be if only one mechanism is possible. These simulation results indicate the importance of performing large size and time scale simulations of the structurally heterogeneous vitreous silica exposed to water to describe proton transport at the interface between water and the silica surface.
Neural network approach to quantum-chemistry data: Accurate prediction of density functional theory energies
Authors: Balabin Roman M. , Lomakina Ekaterina I.
Published: August 2009

Artificial neural network (ANN) approach has been applied to estimate the density functional theory (DFT) energy with large basis set using lower-level energy values and molecular descriptors. A total of 208 different molecules were used for the ANN training, cross validation, and testing by applying BLYP, B3LYP, and BMK density functionals. Hartree–Fock results were reported for comparison. Furthermore, constitutional molecular descriptor (CD) and quantum-chemical molecular descriptor (QD) were used for building the calibration model. The neural network structure optimization, leading to four to five hidden neurons, was also carried out. The usage of several low-level energy values was found to greatly reduce the prediction error. An expected error, mean absolute deviation, for ANN approximation to DFT energies was 0.6±0.2 kcal mol−1. In addition, the comparison of the different density functionals with the basis sets and the comparison of multiple linear regression results were also provided. The CDs were found to overcome limitation of the QD. Furthermore, the effective ANN model for DFT/6-311G(3df,3pd) and DFT/6-311G(2df,2pd) energy estimation was developed, and the benchmark results were provided.
Electron acceleration by intense short laser pulse in the preplasma of a target
Authors: Liu Ming-Ping , Wu Hai-Cheng , Xie Bai-Song , Hong Xue-Ren , Zhang Shan , Yu M. Y.
Published: August 2009

Electron acceleration in the low-density preplasma of a thin solid target by a short intense laser pulse is investigated by particle-in-cell simulation. Electrons in the preplasma are trapped and accelerated by the laser ponderomotive force as well as the wake bubble field. When the laser pulse is stopped and reflected by the target, the trapped electrons continue to move forward inertially, passing through the target with small energy spread and emittance. The use of the present scheme in practical applications is discussed.
InGaN laser diodes with 50 mW output power emitting at 515 nm
Authors: Avramescu Adrian , Lermer Teresa , Müller Jens , Tautz Sönke , Queren Désirée , Lutgen Stephan , Strauß Uwe
Published: August 2009

We demonstrate direct green laser operation from InGaN based diodes at wavelengths as long as 515.9 nm with 50 mW output power in pulse operation. A factor of ∼10 defect reduction for the In-rich InGaN quantum wells based on improvements of the epitaxial growth process and design of the active layers on c-plane GaN-substrates makes it possible to demonstrate laser operation at room temperature. Micrometer-scale photoluminescence mappings and electro-optical measurements confirm the reduction of nonradiative defects in the emitting layers. The 11 μm broad-area gain-guided laser structures were driven in pulse operation to minimize thermal effects and to accurately measure the laser temperature dependence. The threshold current density was ∼9 kA/cm2 and the fitted slope efficiency had a value of ∼130 mW/A for an optical output up to 50 mW.
Drastic improvement in the S-band relativistic magnetron operation
Authors: Sayapin A. , Hadas Y. , Krasik Ya. E.
Published: August 2009

The superior operation of a S-band relativistic magnetron powered by a Linear Induction Accelerator with ≤400 kV, ≤4 kA, and ∼150 ns output pulses was revealed when the magnetron was coupled with a resonance load and a part of the generated microwave power stored in the resonator was reflected back to the magnetron. It is shown that, under optimal conditions, the efficiency of the magnetron operation increases by ∼40% and the generated microwave power reaches the power of the electron beam.
High performance thin film transistor with cosputtered amorphous Zn–In–Sn–O channel: Combinatorial approach
Authors: Ryu Min Ki , Yang Shinhyuk , Park Sang-Hee Ko , Hwang Chi-Sun , Jeong Jae Kyeong
Published: August 2009

Thin film transistors with a channel of Zn–In–Sn–O were fabricated via a combinatorial rf sputtering method. It was found that the role of the In atoms is to enhance the mobility and to shift the threshold voltage (Vth) negatively. On the other hand, the Sn fraction is critical for improving the overall trap density including the density-of-states of the bulk channel layer and the interfacial trap density at the ZnInSnO interface. The optimized transistor was obtained at a compositional ratio of Zn:In:Sn=40:20:40, which exhibited an excellent subthreshold gate swing of 0.12 V/decade, Vth of −0.4 V, and high Ion/off ratio of >109 as well as a high field-effect mobility of 24.6 cm2/V s.
An asymmetry model for the highly viscous flow
Authors: Buchenau U.
Published: August 2009

The shear flow is modeled in terms of local structural rearrangements. Most of these rearrangements are strongly asymmetric, because the embedding matrix tends to be elastically adapted to the initial state and to have a marked elastic misfit with regard to the final state. As one approaches the Maxwell time, the asymmetry becomes time dependent, thus enabling the system to leave the initial state. The model explains the Kohlrausch behavior at the main peak in terms of the interaction between different local structural rearrangements.
A statistical theory for self-condensing vinyl polymerization
Authors: Zhao Zuo-Fei , Wang Hai-Jun , Ba Xin-Wu
Published: August 2009

The method of statistical mechanics is used to investigate several properties of self-condensing vinyl polymerization system. Under the framework of mean field theory, two types of canonical partition functions of the system are constructed from viewpoints of functional groups and polymers, and by which the explicit expressions of equilibrium free energy and the law of mass action are obtained. Based on the free energy, the same size distribution function of hyperbranched polymers is derived by two different methods, which is identical with the previous result given by solving the kinetic differential equations. This implies that the two partition functions are consistent with each other. Furthermore, in terms of the size distribution function, the kth radius of gyration as well as its scaling behavior near the critical point are studied, and the corresponding scaling law is given. As an application, the isothermal compressibility is derived on the basis of equation of state, which indicates that the spatial correlation between monomers increases with the increasing of conversion of the double bonds, and reaches the maximum at the critical point. In addition, it is shown that a usual treatment on the polydispersity index would lead it to infinite, which is not agreement with the true result of 1 at the end of the reaction system. To clarify this fact, we find that the correlation length plays an important role, and then by using asymptotic forms of the size distribution and the second moment, the reasonable result can be carried out.
Tricritical behavior of the smectic-A to smectic-C∗ transition
Authors: Mukherjee Prabir K.
Published: August 2009

A phenomenological Landau-like theory is presented, which describes the tricritical behavior of the smectic-A to smectic-C∗ transition in a liquid crystal mixture. The influence of the concentration on this transition is discussed by varying the coupling between the concentration variable and the order parameters. It was observed from the theoretical calculations that for a particular value of the concentration, the first order smectic-A to smectic-C∗ transition becomes second order at a tricritical point. Calculations based on this model agree qualitatively with experiment.
Columnar phases of discotics with orientation-dependent interactions
Authors: Martínez-Haya Bruno , Cuetos Alejandro
Published: August 2009

The liquid crystal phase diagram of fluids of rigid discotics with soft interactions has been investigated by means of Monte Carlo simulations. The particles are modeled by spherocylinders or Gay–Berne ellipsoids with thickness/diameter aspect ratios of L/D=0.2. The study includes a variety of pair interaction potentials, featuring different energetic dependencies on the orientation of the particles. Three distinct types of models are considered: (i) models with a homogeneous interaction around the molecular core, (ii) models favoring stacked pair configurations, and (iii) models favoring edge-to-edge configurations. The stability and internal structure of the isotropic, nematic, and the different hexatic columnar phases exhibited by these fluids are discussed. The results indicate that the spherocylinder and ellipsoidal models differ in fundamental trends of their phase behavior. The spherocylinder fluids display more extended ranges of stability and longer pair correlation lengths in the columnar phases than the ellipsoidal models. As a consequence, as opposed to ellipsoids, the nematic phase for spherocylinders with the title aspect ratio tends to be entropically suppressed, even under favorable energetics.
Simultaneous two-level lasing in GaInAsSb/GaSb strained quantum-well lasers
Authors: Vizbaras Kristijonas , Kashani-Shirazi Kaveh , Amann Markus-Christian
Published: August 2009

Simultaneous two-level lasing, corresponding to ground level and excited level transitions in GaInAsSb/GaSb quantum well lasers under continuous wave operation is reported. The effect is attributed to a slowed-down intersubband relaxation in the quantum wells due to buildup of hot phonon population resulting in an incomplete clamping of the excited state population above the ground level lasing threshold.
Single-beam coherent anti-Stokes Raman scattering spectroscopy of N2 using a shaped 7 fs laser pulse
Authors: Roy Sukesh , Wrzesinski Paul , Pestov Dmitry , Gunaratne Tissa , Dantus Marcos , Gord James R.
Published: August 2009

The feasibility is explored by single-beam coherent anti-Stokes Raman scattering (CARS) spectroscopy of gas-phase diatomic molecules related to combusting flows, with implications for gas-phase thermometry. We demonstrate CARS of gas-phase N2 using a shaped ∼7 fs laser pulse, investigate the dependence of the CARS signal on the total pressure of the probed environment, both in pure N2 and in mixtures with Ar, discuss the observed signal-to-noise ratio, and suggest improvements to be considered for reliable single-shot measurements at flame temperatures.
Random hcp and fcc structures in thermoresponsive microgel crystals
Authors: Brijitta J. , Tata B. V. R. , Joshi R. G. , Kaliyappan T.
Published: August 2009

Monodisperse thermoresponsive poly(N-isopropylacrylamide) (PNIPAM) microgel particles having a diameter of 520 nm were synthesized by free-radical precipitation polymerization and centrifuged to obtain a concentrated suspension. The centrifuged mother suspension was made to self-order into a crystalline state by repeated annealing beyond the volume phase transition (VPT) of the particles. We report here the three-dimensional (3D) real space structure, determined using a confocal laser scanning microscope, of PNIPAM microgel crystal samples prepared by two different recrystallized routes: (1) solidifying a shear melted colloidal liquid (referred as as-prepared sample) and (2) slow cooling of a colloidal liquid (referred as recrystallized sample). We have recorded images of several regions of the crystal with each region containing 15 horizontal crystal planes for determining the in-plane [two-dimensional (2D)] and 3D pair-correlation functions. The 2D pair-correlation function g(r) revealed hexagonal long-range order of particles in the layers with a lattice constant of 620 nm. The analysis of stacking sequence of layers recorded on as-prepared sample has revealed the existence of stacking disorder with an average stacking probability α∼0.42. This value of α together with the analysis of 3D pair-correlation function determined from particle positions revealed the structure of microgel crystals in the as-prepared sample to be random hexagonal close packing. We report the first observation of a split second peak in the 3D g(r) of the microgel crystals obtained from a shear melted liquid. Upon melting the sample above VPT and recrystallizing it the split second peak disappeared and the crystals are found to have a face centered cubic (fcc) structure with α∼0.95. From simulations, the split second peak is shown to arise from the displacement of some of the B-planes from the ideal hcp positions. The present results are discussed in light of those reported for charged and hard sphere colloidal crystals and plausible reasons for observing two different structures are also explained.
Large eddy simulation of flow in an unbaffled stirred tank for different Reynolds numbers
Authors: Yoon Hyun Sik , Balachandar S. , Ha Man Yeong
Published: August 2009

Large eddy simulation of flow in a stirred tank has been carried out for three different Reynolds numbers of 4000, 16 000, and 64 000 using a spectral multidomain method in order to observe the effect of Reynolds numbers on the flow fields. As the Reynolds number increases, each large ring vortex at the upper and lower parts of the tank has been broken up into smaller vortices. With increasing Reynolds number, the ring vortex in the mean field becomes a slightly more oblate and increases in height until it reaches the lid of the tank. The isosurface of swirling strength has been adopted to identify the instantaneous and mean tip-vortex structures. Due to the time-dependent jitter in the position of tip vortices, the time-averaged vortex structure appears to decay much faster. This decay is more rapid with increasing Reynolds number. The increment of the ratio of time and volume-averaged resolved scale dissipation and subgrid scaled dissipation was governed by the linear function of Reynolds number.
Compensation of interfacial states located inside the “buffer-free” GaSb/GaAs (001) heterojunction via δ-doping
Authors: Jallipalli A. , Nunna K. , Kutty M. N. , Balakrishnan G. , Lush G. B. , Dawson L. R. , Huffaker D. L.
Published: August 2009

We report the compensation of interfacial states formed by interfacial misfit dislocation (IMF) arrays via δ-doping. The IMF arrays are located inside the “buffer-free” heterojunction of GaSb/GaAs (001). The interfacial states are measured using surface photovoltage measurements and are positioned at 0.41, 0.49, and 0.61 eV. A higher reverse bias leakage current (IRB) was observed in the heterogeneous GaSb/GaAs IMF sample (73 μA at −5 V) compared to the homogeneous GaAs control sample (3.9 μA), which does not contain IMF. This increase in IRB is attributed to the interfacial states. Hence, the interfacial states are compensated by δ-doping the GaSb/GaAs interface using Te atoms. A low turn-on voltage of 0.85 V and a very low IRB of 0.1 nA were achieved for the δ-doped sample compared to the control and IMF samples. Hence, for optoelectronic applications, such as lasers, solar cells, and detectors, this compensated IMF technology is useful for integration of buffer-free III-Sb devices on an inexpensive GaAs platform.
Subtle interplay between native point defects and magnetism in ZnO:Co
Authors: Assadi M. H. N. , Zhang Y. B. , Li S.
Published: August 2009

Distribution of Co ions and its effect on magnetic properties of ZnO:Co in the presence of native point defects, oxygen vacancy, and interstitial hydrogen, have been investigated using first-principles density functional calculations. The study provides a fundamental theoretical understanding on the correlation between magnetism and the distribution of magnetic ions and the native point defects in the semiconducting host. Results show that Co ions have a strong tendency toward aggregation via oxygen within ab plane in the presence of point defects. The room temperature ferromagnetism observed experimentally in ZnO:Co is mainly dominated by the interstitial hydrogen rather than oxygen vacancy.
Effect of efficiency “droop” in violet and blue InGaN laser diodes
Authors: Grzanka S. , Perlin P. , Czernecki R. , Marona L. , Boćkowski M. , Łucznik B. , Leszczyński M. , Suski T.
Published: August 2009

We have studied two types of InGaN laser diodes emitting at 410 and 440 nm. Each device was characterized by measuring light-current characteristics in two geometries for which the light was collected: along the resonator and perpendicularly to the cavity. In the first configuration, the 410 nm device displays no reduction of differential efficiency while 440 nm laser shows evidence of droop. In the perpendicular configuration both devices show the pronounced droop. We associate the suppression of the droop for 410 nm laser in the “along cavity” configuration with the appearance of the stimulated recombination.
Reference interaction site model study of self-aggregating cyanine dyes
Authors: Chuev Gennady N. , Fedorov Maxim V.
Published: August 2009

Using the reference interaction site model and supramolecular approach, we modeled the aggregation of thea-monomethinecyanine dyes in water. Various modifications of the hypernetted-closure expression for the excess free energy have been studied. We found that the partial wave approximation with semiempirical corrections for excluded volume and hydrogen bonding effects provides estimations of the binding and dimerization energies of the aggregates, which are in agreement with available experimental data. The hydrated H-dimers are obtained to be more stable than the hydrated J-dimers. However, the complexes consisting from more than four monomers change their arrangement while self-assembling in water and form ladderlike structures. We propose a model explaining this structural transition.
Tolerance and M2 (alternative) macrophage polarization are related processes orchestrated by p50 nuclear factor κB
Authors: Porta Chiara , Rimoldi Monica , Raes Geert , Brys Lea , Ghezzi Pietro , Di Liberto Diana , Dieli Francesco , Ghisletti Serena , Natoli Gioacchino , De Baetselier Patrick , Mantovani Alberto , Sica Antonio
Published: August 2009

Cells of the monocyte–macrophage lineage play a central role in the orchestration and resolution of inflammation. Plasticity is a hallmark of mononuclear phagocytes, and in response to environmental signals these cells undergo different forms of polarized activation, the extremes of which are called classic or M1 and alternative or M2. NF-κB is a key regulator of inflammation and resolution, and its activation is subject to multiple levels of regulation, including inhibitory, which finely tune macrophage functions. Here we identify the p50 subunit of NF-κB as a key regulator of M2-driven inflammatory reactions in vitro and in vivo. p50 NF-κB inhibits NF-κB–driven, M1-polarizing, IFN-β production. Accordingly, p50-deficient mice show exacerbated M1-driven inflammation and defective capacity to mount allergy and helminth-driven M2-polarized inflammatory reactions. Thus, NF-κB p50 is a key component in the orchestration of M2-driven inflammatory reactions.
Inferring friendship network structure by using mobile phone data
Authors: Eagle Nathan , Pentland Alex (Sandy) , Lazer David
Published: August 2009

Data collected from mobile phones have the potential to provide insight into the relational dynamics of individuals. This paper compares observational data from mobile phones with standard self-report survey data. We find that the information from these two data sources is overlapping but distinct. For example, self-reports of physical proximity deviate from mobile phone records depending on the recency and salience of the interactions. We also demonstrate that it is possible to accurately infer 95% of friendships based on the observational data alone, where friend dyads demonstrate distinctive temporal and spatial patterns in their physical proximity and calling patterns. These behavioral patterns, in turn, allow the prediction of individual-level outcomes such as job satisfaction.
TLR4-mediated expulsion of bacteria from infected bladder epithelial cells
Authors: Song Jeongmin , Bishop Brian L. , Li Guojie , Grady Richard , Stapleton Ann , Abraham Soman N.
Published: August 2009

UropathogenicEscherichia coliinvade bladder epithelial cells (BECs) by direct entry into specialized cAMP regulated exocytic compartments. Remarkably, a significant number of these intracellular bacteria are subsequently expelled in a nonlytic and piecemeal fashion by infected BECs. Here, we report that expulsion of intracellularE. coliby infected BECs is initiated by the pattern recognition receptor, Toll-like receptor (TLR)4, after activation by LPS. Also, we reveal that caveolin-1, Rab27b, PKA, and MyRIP are components of the exocytic compartment, and that they form a complex involved in the exocytosis of bacteria. This capacity of TLR4 to mediate the expulsion of intracellular bacteria from infected cells represents a previously unrecognized function for this innate immune receptor.
Expanding wave solutions of the Einstein equations that induce an anomalous acceleration into the Standard Model of Cosmology
Authors: Temple Blake , Smoller Joel
Published: August 2009

We derive a system of three coupled equations that implicitly defines a continuous one-parameter family of expanding wave solutions of the Einstein equations, such that the Friedmann universe associated with the pure radiation phase of the Standard Model of Cosmology is embedded as a single point in this family. By approximating solutions near the center to leading order in the Hubble length, the family reduces to an explicit one-parameter family of expanding spacetimes, given in closed form, that represents a perturbation of the Standard Model. By introducing a comoving coordinate system, we calculate the correction to the Hubble constant as well as the exact leading order quadratic correction to the redshift vs. luminosity relation for an observer at the center. The correction to redshift vs. luminosity entails an adjustable free parameter that introduces an anomalous acceleration. We conclude (by continuity) that corrections to the redshift vs. luminosity relation observed after the radiation phase of the Big Bang can be accounted for, at the leading order quadratic level, by adjustment of this free parameter. The next order correction is then a prediction. Since nonlinearities alone could actuate dissipation and decay in the conservation laws associated with the highly nonlinear radiation phase and since noninteracting expanding waves represent possible time-asymptotic wave patterns that could result, we propose to further investigate the possibility that these corrections to the Standard Model might be the source of the anomalous acceleration of the galaxies, an explanation not requiring the cosmological constant or dark energy.
Mental retardation linked to mutations in the
HSD17B10
gene interfering with neurosteroid and isoleucine metabolism
Authors: Yang Song-Yu , He Xue-Ying , Olpin Simon E. , Sutton Vernon R. , McMenamin Joe , Philipp Manfred , Denman Robert B. , Malik Mazhar
Published: August 2009

Mutations in the
HSD17B10
gene were identified in two previously described mentally retarded males. A point mutation c.776G>C was found from a survivor (SV), whereas a potent mutation, c.419C>T, was identified in another deceased case (SF) with undetectable hydroxysteroid (17β) dehydrogenase 10 (HSD10) activity. Protein levels of mutant HSD10(R130C) in patient SF and HSD10(E249Q) in patient SV were about half that of HSD10 in normal controls. The E249Q mutation appears to affect HSD10 subunit interactions, resulting in an allosteric regulatory enzyme. For catalyzing the oxidation of allopregnanolone by NAD
+
the Hill coefficient of the mutant enzyme is ≈1.3. HSD10(E249Q) was unable to catalyze the dehydrogenation of 2-methyl-3-hydroxybutyryl-CoA and the oxidation of allopregnanolone, a positive modulator of the γ-aminobutyric acid type A receptor, at low substrate concentrations. Neurosteroid homeostasis is critical for normal cognitive development, and there is increasing evidence that a blockade of isoleucine catabolism alone does not commonly cause developmental disabilities. The results support the theory that an imbalance in neurosteroid metabolism could be a major cause of the neurological handicap associated with hydroxysteroid (17β) dehydrogenase 10 deficiency.
Structural and biological mimicry of protein surface recognition by α/β-peptide foldamers
Authors: Horne W. Seth , Johnson Lisa M. , Ketas Thomas J. , Klasse Per Johan , Lu Min , Moore John P. , Gellman Samuel H.
Published: August 2009

Unnatural oligomers that can mimic protein surfaces offer a potentially useful strategy for blocking biomedically important protein-protein interactions. Here we evaluate an approach based on combining α- and β-amino acid residues in the context of a polypeptide sequence from the HIV protein gp41, which represents an excellent testbed because of the wealth of available structural and biological information. We show that α/β-peptides can mimic structural and functional properties of a critical gp41 subunit. Physical studies in solution, crystallographic data, and results from cell-fusion and virus-infectivity assays collectively indicate that the gp41-mimetic α/β-peptides effectively block HIV-cell fusion via a mechanism comparable to that of gp41-derived α-peptides. An optimized α/β-peptide is far less susceptible to proteolytic degradation than is an analogous α-peptide. Our findings show how a two-stage design approach, in which sequence-based α→β replacements are followed by site-specific backbone rigidification, can lead to physical and biological mimicry of a natural biorecognition process.
Cholesterol modulates the recruitment of Kv1.5 channels from Rab11-associated recycling endosome in native atrial myocytes
Authors: Balse Elise , El-Haou Saïd , Dillanian Gilles , Dauphin Aurélien , Eldstrom Jodene , Fedida David , Coulombe Alain , Hatem Stéphane N.
Published: August 2009

Cholesterol is an important determinant of cardiac electrical properties. However, underlying mechanisms are still poorly understood. Here, we examine the hypothesis that cholesterol modulates the turnover of voltage-gated potassium channels based on previous observations showing that depletion of membrane cholesterol increases the atrial repolarizing current
I
Kur
. Whole-cell currents and single-channel activity were recorded in rat adult atrial myocytes (AAM) or after transduction with hKv1.5-EGFP. Channel mobility and expression were studied using fluorescence recovery after photobleaching (FRAP) and 3-dimensional microscopy. In both native and transduced-AAMs, the cholesterol-depleting agent MβCD induced a delayed (≈7 min) increase in
I
Kur
; the cholesterol donor LDL had an opposite effect. Single-channel recordings revealed an increased number of active Kv1.5 channels upon MβCD application. Whole-cell recordings indicated that this increase was not dependent on new synthesis but on trafficking of existing pools of intracellular channels whose exocytosis could be blocked by both
N
-ethylmaleimide and nonhydrolyzable GTP analogues. Rab11 was found to coimmunoprecipitate with hKv1.5-EGFP channels and transfection with Rab11 dominant negative (DN) but not Rab4 DN prevented the MβCD-induced
I
Kur
increase. Three-dimensional microscopy showed a decrease in colocalization of Kv1.5 and Rab11 in MβCD-treated AAM. These results suggest that cholesterol regulates Kv1.5 channel expression by modulating its trafficking through the Rab11-associated recycling endosome. Therefore, this compartment provides a submembrane pool of channels readily available for recruitment into the sarcolemma of myocytes. This process could be a major mechanism for the tuning of cardiac electrical properties and might contribute to the understanding of cardiac effects of lipid-lowering drugs.
Cleavage of RseA by RseP requires a carboxyl-terminal hydrophobic amino acid following DegS cleavage
Authors: Li Xiaochun , Wang Boyuan , Feng Lihui , Kang Hui , Qi Yang , Wang Jiawei , Shi Yigong
Published: August 2009

Regulated intramembrane proteolysis (RIP) by the Site-2 protease (S2P) results in the release of a transmembrane signaling protein. Curiously, however, S2P cleavage must be preceded by the action of the Site-1 protease (S1P). To decipher the underlying mechanism, we reconstituted sequential, in vitro cleavages of the
Escherichia coli
transmembrane protein RseA by DegS (S1P) and RseP (S2P). After DegS cleavage, the newly exposed carboxyl-terminal residue Val-148 of RseA plays an essential role for RseP cleavage, and its mutation to charged or dissimilar amino acids crippled the Site-2 cleavage. By contrast, the identity of residues 146 and 147 of RseA has no impact on Site-2 cleavage. These results explain why Site-1 cleavage must precede Site-2 cleavage. Structural analysis reveals that the putative peptide-binding groove in the second, but not the first, PDZ domain of RseP is poised for binding to a single hydrophobic amino acid. These observations suggest that after DegS cleavage, the newly exposed carboxyl terminus of RseA may facilitate Site-2 cleavage through direct interaction with the PDZ domain.
Explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa
Authors: DeGiorgio Michael , Jakobsson Mattias , Rosenberg Noah A.
Published: August 2009

Studies of worldwide human variation have discovered three trends in summary statistics as a function of increasing geographic distance from East Africa: a decrease in heterozygosity, an increase in linkage disequilibrium (LD), and a decrease in the slope of the ancestral allele frequency spectrum. Forward simulations of unlinked loci have shown that the decline in heterozygosity can be described by a serial founder model, in which populations migrate outward from Africa through a process where each of a series of populations is formed from a subset of the previous population in the outward expansion. Here, we extend this approach by developing a retrospective coalescent-based serial founder model that incorporates linked loci. Our model both recovers the observed decline in heterozygosity with increasing distance from Africa and produces the patterns observed in LD and the ancestral allele frequency spectrum. Surprisingly, although migration between neighboring populations and limited admixture between modern and archaic humans can be accommodated in the model while continuing to explain the three trends, a competing model in which a wave of outward modern human migration expands into a series of preexisting archaic populations produces nearly opposite patterns to those observed in the data. We conclude by developing a simpler model to illustrate that the feature that permits the serial founder model but not the archaic persistence model to explain the three trends observed with increasing distance from Africa is its incorporation of a cumulative effect of genetic drift as humans colonized the world.
The human IgM pentamer is a mushroom-shaped molecule with a flexural bias
Authors: Czajkowsky Daniel M. , Shao Zhifeng
Published: August 2009

The textbook planar model of pentameric IgM, a potent activator of complement C1q, is based upon the crystallographic structure of IgG. Although widely accepted, key predictions of this model have not yet been directly confirmed, which is particularly important since IgG lacks a major Ig fold domain in its Fc region that is present in IgM. Here, we construct a homology-based structural model of the IgM pentamer using the recently obtained crystallographic structure of IgE Fc, which has this additional Ig domain, under the constraint that all of the cysteine residues known to form disulfide bridges both within each monomer and between monomers are bonded together. In contrast to the planar model, this model predicts a non-planar, mushroom-shaped complex, with the central portion formed by the C-terminal domains protruding out of the plane formed by the Fab domains. This unexpected conformation of IgM is, however, directly confirmed by cryo-atomic force microscopy of individual human IgM molecules. Further analysis of this model with free energy calculations of out-of-plane Fab domain rotations reveals a pronounced asymmetry favoring flexions toward the central protrusion. This bias, together with polyvalent attachment to cell surface antigen, would ensure that the IgM pentamer is oriented on the cell membrane with its C1q binding sites fully exposed to the solution, and thus provides a mechanistic explanation for the first steps of C1q activation by IgM.
Structure of ERA in complex with the 3′ end of 16S rRNA: Implications for ribosome biogenesis
Authors: Tu Chao , Zhou Xiaomei , Tropea Joseph E. , Austin Brian P. , Waugh David S. , Court Donald L. , Ji Xinhua
Published: August 2009

ERA, composed of an N-terminal GTPase domain followed by an RNA-binding KH domain, is essential for bacterial cell viability. It binds to 16S rRNA and the 30S ribosomal subunit. However, its RNA-binding site, the functional relationship between the two domains, and its role in ribosome biogenesis remain unclear. We have determined two crystal structures of ERA, a binary complex with GDP and a ternary complex with a GTP-analog and the
1531
AUCACCUCCUUA
1542
sequence at the 3′ end of 16S rRNA. In the ternary complex, the first nine of the 12 nucleotides are recognized by the protein. We show that GTP binding is a prerequisite for RNA recognition by ERA and that RNA recognition stimulates its GTP-hydrolyzing activity. Based on these and other data, we propose a functional cycle of ERA, suggesting that the protein serves as a chaperone for processing and maturation of 16S rRNA and a checkpoint for assembly of the 30S ribosomal subunit. The AUCA sequence is highly conserved among bacteria, archaea, and eukaryotes, whereas the CCUCC, known as the anti-Shine-Dalgarno sequence, is conserved in noneukaryotes only. Therefore, these data suggest a common mechanism for a highly conserved ERA function in all three kingdoms of life by recognizing the AUCA, with a “twist” for noneukaryotic ERA proteins by also recognizing the CCUCC.
Reactions of ozone with human skin lipids: Sources of carbonyls, dicarbonyls, and hydroxycarbonyls in indoor air
Authors: Wisthaler Armin , Weschler Charles J.
Published: August 2009

This study has used proton transfer reaction-mass spectrometry (PTR-MS) for direct air analyses of volatile products resulting from the reactions of ozone with human skin lipids. An initial series of small-scale in vitro and in vivo experiments were followed by experiments conducted with human subjects in a simulated office. The latter were conducted using realistic ozone mixing ratios (≈15 ppb with occupants present). Detected products included mono- and bifunctional compounds that contain carbonyl, carboxyl, or
α
-hydroxy ketone groups. Among these, three previously unreported dicarbonyls have been identified, and two previously unreported
α
-hydroxy ketones have been tentatively identified. The compounds detected in this study (excepting acetone) have been overlooked in surveys of indoor pollutants, reflecting the limitations of the analytical methods routinely used to monitor indoor air. The results are fully consistent with the Criegee mechanism for ozone reacting with squalene, the single most abundant unsaturated constituent of skin lipids, and several unsaturated fatty acid moieties in their free or esterified forms. Quantitative product analysis confirms that squalene is the major scavenger of ozone at the interface between room air and the human envelope. Reactions between ozone and human skin lipids reduce the mixing ratio of ozone in indoor air, but concomitantly increase the mixing ratios of volatile products and, presumably, skin surface concentrations of less volatile products. Some of the volatile products, especially the dicarbonyls, may be respiratory irritants. Some of the less volatile products may be skin irritants.
Transmission dynamics and economics of rabies control in dogs and humans in an African city
Authors: Zinsstag J. , Dürr S. , Penny M. A. , Mindekem R. , Roth F. , Gonzalez S. Menendez , Naissengar S. , Hattendorf J.
Published: August 2009

Human rabies in developing countries can be prevented through interventions directed at dogs. Potential cost-savings for the public health sector of interventions aimed at animal-host reservoirs should be assessed. Available deterministic models of rabies transmission between dogs were extended to include dog-to-human rabies transmission. Model parameters were fitted to routine weekly rabid-dog and exposed-human cases reported in N′Djaména, the capital of Chad. The estimated transmission rates between dogs (βd) were 0.0807 km2/(dogs·week) and between dogs and humans (βdh) 0.0002 km2/(dogs·week). The effective reproductive ratio (Re) at the onset of our observations was estimated at 1.01, indicating low-level endemic stability of rabies transmission. Human rabies incidence depended critically on dog-related transmission parameters. We simulated the effects of mass dog vaccination and the culling of a percentage of the dog population on human rabies incidence. A single parenteral dog rabies-mass vaccination campaign achieving a coverage of least 70% appears to be sufficient to interrupt transmission of rabies to humans for at least 6 years. The cost-effectiveness of mass dog vaccination was compared to postexposure prophylaxis (PEP), which is the current practice in Chad. PEP does not reduce future human exposure. Its cost-effectiveness is estimated at US $46 per disability adjusted life-years averted. Cost-effectiveness for PEP, together with a dog-vaccination campaign, breaks even with cost-effectiveness of PEP alone after almost 5 years. Beyond a time-frame of 7 years, it appears to be more cost-effective to combine parenteral dog-vaccination campaigns with human PEP compared to human PEP alone.