bluuebunny/crossref_metadata_2025 huggingface dataset:
Phonon-defect scattering in doped silicon by molecular dynamics simulation
Authors: Yao M. , Watanabe T. , Schelling P. K. , Keblinski P. , Cahill D. G. , Phillpot S. R.
Published: July 2008

Molecular dynamics simulations are used to study the scattering of phonon wave packets of well-defined frequency and polarization from individual point defects and from a field of point defects in Si. The relative amounts of energy in the transmitted and reflected phonon fields are calculated and the parameters that influence the phonon scattering process are determined. The results show that the fractions of transmitted and reflected energies strongly depend on the frequency of the incident phonons and on the mass and concentration of the defects. These results are compared with the classic formula for the scattering strength for point defects derived by Klemens, which we find to be valid when each phonon-defect scattering event is independent. The Klemens formula fails when coupled multiple scattering dominates. The phonon density of states is used to characterize the effects of point defects on mode mixing.
Focused ion beam specimen preparation for off-axis electron holography using Si, Ga, and Au ions
Authors: Cooper David , Bertin Francois , Salles Phillipe , Benassayag Gerard
Published: July 2008

Silicon specimens containing p-n junctions have been prepared by focused ion beam milling using gallium, silicon, and gold ion sources. The specimens have been examined using off-axis electron holography and the total thickness of the electrically ‘inactive’ layer has been measured as 80, 140, and 410±15nm for the Au, Ga, and Si ions, respectively. We also show that the thickness of this damaged layer can be predicted using simulations.
Photoluminescence of InAs0.04P0.67Sb0.29
Authors: Tsai Gene , Wang De-Lun , Lin Hao-Hsiung
Published: July 2008

We report the results of a detailed photoluminescence (PL) study on quaternary InAs0.04P0.67Sb0.29 grown by gas-source molecular-beam epitaxy. The main PL peak at 10 K shows a transition energy that is lower than the calculated energy gap by 0.223 eV, which is attributed to the tail states recombination. Another PL band, which emerges as the temperature increases, is assigned to the self-activated luminescence from defect centers. Its features, namely, nearly temperature-independent peak energy, Gaussian-like lineshape, and square-root-of- temperature-dependent linewidth, can be illustrated by the configuration coordinate model. The vibration energy, calculated from the linewidth at low temperature, is 0.022 eV for the excited state of the defect centers. The self-activated luminescence shows a thermal quenching behavior that is usually exhibited by amorphous semiconductors, indicating that the defects are related to the compositional disorder. The defects responsible for the luminescence are most likely complexes consisting of a substitutional carbon and an In vacancy.
Heat capacity and latent heat measurements of CoMnSi using a microcalorimeter
Authors: Miyoshi Y. , Morrison K. , Moore J. D. , Caplin A. D. , Cohen L. F.
Published: July 2008

A new method of utilizing a commercial silicon nitride membrane calorimeter to measure the latent heat at a first order phase transition is presented. The method is a direct measurement of the thermoelectric voltage jump induced by the latent heat, in a thermally isolated system ideally suited for single crystal and small microgram samples. We show that when combined with the ac calorimetry technique previously developed, the resultant thermal measurement capabilities are extremely powerful. We demonstrate the applicability of the combined method with measurements on a 100μm size fragment of CoMnSi exhibiting a sizable magnetocaloric effect near room temperature, and obtain good agreement with previously reported values on bulk samples.
Ab initio study of the low lying electronic states of ZnF and ZnF−
Authors: Hayashi Shinsuke , Léonard Céline , Chambaud Gilberte
Published: July 2008

Highly correlated ab initio calculations have been performed for an accurate determination of the electronic structure and of the spectroscopy of the low lying electronic states of the ZnF system. Using effective core pseudopotentials and aug-cc-pVQZ basis sets for both atoms, the potential curves, the dipole moment functions, and the transition dipole moments between relevant electronic states have been calculated at the multireference-configuration-interaction level. The spectroscopic constants calculated for the XΣ+2 ground state are in good agreement with the most recent theoretical and experimental values. It is shown that, besides the XΣ+2 ground state, the BΣ+2, the CΠ2, and the DΣ+2 states are bound. The AΠ2 state, which has been mentioned in previous works, is not bound but its potential presents a shoulder in the Franck–Condon region of the XΣ+2 ground state. All of the low lying quartet states are found to be repulsive. The absorption transitions from the v=0 level of the XΣ+2 ground state toward the three bound states have been evaluated and the spectra are presented. The potential energy of the ZnF− molecular anion has been determined in the vicinity of its equilibrium geometry and the electronic affinity of ZnF (EA=1.843eV with the zero energy point correction) has been calculated in agreement with the photoelectron spectroscopy experiments.
Electronic and magnetic properties of manganese and iron-doped GanAsn nanocages (n=7–12)
Authors: Wang Jianguang , Ma Li , Zhao Jijun , Wang Guanghou , Chen Xiaoshuang , Bruce King R.
Published: July 2008

The electronic and magnetic properties of Mn- or Fe-doped GanAsn (n=7–12) nanocages were studied using gradient-corrected density-functional theory considering doping at substitutional, endohedral, and exohedral sites. When doped with one atom, the most energetically favorable site gradually moves from surface (n=7–11) to interior (n=12) sites for the Mn atom, while the most preferred doping site of the Fe atom alternates between the surface (n=7,9,11) and interior (n=8,10,12) sites. All of the ground-state structures of Mn@GanAsn have the atomlike magnetic moment of 5μB, while the total magnetic moments of the most stable Fe@GanAsn cages for each size are about 2μB except for the 4μB magnetic moment of Fe@Ga12As12. Charge transfer and hybridization between the 4s and 3d states of Mn or Fe and the 4s and 4p states of As were found. The antiferromagnetic (AFM) state of Mn2@GanAsn is more energetically favorable than the ferromagnetic (FM) state. However, for Fe2@GanAsn the FM state is more stable than the AFM state. The local magnetic moments of Mn and Fe atoms in the GanAsn cages are about 4μB and 3μB in the FM and AFM states, respectively. For both Mn and Fe bidoping, the most energetically favorable doping sites of the transition metal atoms are located on the surface of the GanAsn cages. The computed magnetic moments of the doped Fe and Mn atoms agree excellently with the theoretical and experimental values in the Fe(Mn)∕GaAs interface as well as (Ga, Mn)As dilute magnetic semiconductors.
Orbital energies and negative electron affinities from density functional theory: Insight from the integer discontinuity
Authors: Teale Andrew M. , De Proft Frank , Tozer David J.
Published: July 2008

Orbital energies in Kohn–Sham density functional theory (DFT) are investigated, paying attention to the role of the integer discontinuity in the exact exchange-correlation potential. A series of closed-shell molecules are considered, comprising some that vertically bind an excess electron and others that do not. High-level ab initio electron densities are used to calculate accurate orbital energy differences, Δϵ, between the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO), using the same potential for both. They are combined with accurate vertical ionization potentials, I0, and electron affinities, A0, to determine accurate “average” orbital energies. These are the orbital energies associated with an exchange-correlation potential that averages over a constant jump in the accurate potential, of magnitude ΔXC=(I0−A0)−Δϵ, as given by the discontinuity analysis. Local functional HOMO energies are shown to be almost an order of magnitude closer to these average values than to −I0, with typical discrepancies of just 0.02 a.u. For systems that do not bind an excess electron, this level of agreement is only achieved when A0 is set equal to the negative experimental affinity from electron transmission spectroscopy (ETS); it degrades notably when the zero ground state affinity is instead used. Analogous observations are made for the local functional LUMO energies, although the need to use the ETS affinities is less pronounced for systems where the ETS values are very negative. The application of an asymptotic correction recovers the preference, leading to positive LUMO energies (but bound orbitals) for these systems, consistent with the behavior of the average energies. The asymptotically corrected LUMO energies typically agree with the average values to within 0.02 a.u., comparable to that observed with the HOMOs. The study provides numerical support for the view that local functionals exhibit a near-average behavior based on a constant jump of magnitude ΔXC. It illustrates why a recently proposed DFT expression involving local functional frontier orbital energies and ionization potential yields reasonable estimates of negative ETS affinities and is consistent with earlier work on the failure of DFT for charge-transfer excited states. The near-average behavior of the exchange-correlation potential is explicitly illustrated for selected systems. The nature of hybrid functional orbital energies is also mentioned, and the results of the study are discussed in terms of the variation in electronic energy as a function of electron number. The nature of DFT orbital energies is of great importance in chemistry; this study contributes to the understanding of these quantities.
Equilibrium of non-neutral plasmas in a Malmberg–Penning trap with a weakly tilted magnetic field
Authors: Kotelnikov Igor , Romé Massimiliano
Published: July 2008

The effect of small asymmetric magnetic perturbations on the equilibrium of a non-neutral plasma confined in a Malmberg–Penning trap is analyzed. A constraint, known in the theory of tandem mirrors as the condition of current closure, is derived for non-neutral plasmas. Together with Poisson’s equation, this constraint provides a set of equations for determining self-consistent asymmetric equilibria of non-neutral plasmas in Malmberg–Penning traps. As an example of this approach, the non-neutral plasma equilibrium in the presence of a weak magnetic tilt is analyzed. Analytical and semianalytical solutions for the electric potential variations inside the trap are found in a paraxial limit for various radial density profiles of the plasma, including the case of global thermal equilibrium. The numerical procedure aimed to obtain self-consistent plasma equilibria for a magnetic field with a large asymmetry is also discussed. The newly developed method can be straightforwardly applied to determine plasma equilibria under the effect of the magnetic perturbations of higher multipolarity (such as, quadrupole or octupole fields).
Evolution of complex dynamics
Authors: Wilds Roy , Kauffman Stuart A. , Glass Leon
Published: July 2008

We study the evolution of complex dynamics in a model of a genetic regulatory network. The fitness is associated with the topological entropy in a class of piecewise linear equations, and the mutations are associated with changes in the logical structure of the network. We compare hill climbing evolution, in which only mutations that increase the fitness are allowed, with neutral evolution, in which mutations that leave the fitness unchanged are allowed. The simple structure of the fitness landscape enables us to estimate analytically the rates of hill climbing and neutral evolution. In this model, allowing neutral mutations accelerates the rate of evolutionary advancement for low mutation frequencies. These results are applicable to evolution in natural and technological systems.
Collisionless dynamics of zonal flows in stellarator geometry
Authors: Mishchenko Alexey , Helander Per , Könies Axel
Published: July 2008

The collisionless time evolution of zonal flows in stellarator systems is investigated. An analytical solution of the kinetic and quasineutrality equations describing the residual zonal flow is derived for arbitrary three-dimensional systems without approximations in the magnetic geometry. The theory allows for an arbitrary number of particle species. It has been found that in stellarators the residual zonal flows are not in general steady but oscillate with a certain frequency. This frequency is determined by the speed of the bounce-averaged radial drifts of the particles trapped in the magnetic field and vanishes in tokamaks, where such net drifts are absent. A reduction of the bounce-averaged radial drifts in configurations optimized with respect to neoclassical transport results in a smaller zonal-flow frequency.
Fast phase transitions induced by picosecond electrical pulses on phase change memory cells
Authors: Wang W. J. , Shi L. P. , Zhao R. , Lim K. G. , Lee H. K. , Chong T. C. , Wu Y. H.
Published: July 2008

The reversible and fast phase transitions induced by picosecond electrical pulses are observed in the nanostructured GeSbTe materials, which provide opportunities in the application of high speed nonvolatile random access memory devices. The mechanisms for fast phase transition are discussed based on the investigation of the correlation between phase transition speed and material size. With the shrinkage of material dimensions, the size effects play increasingly important roles in enabling the ultrafast phase transition under electrical activation. The understanding of how the size effects contribute to the phase transition speed is of great importance for ultrafast phenomena and applications.
Multiple negative resistances in trenched structures bridged with carbon nanotubes
Authors: Dragoman M. , Konstantinidis G. , Kostopoulos A. , Dragoman D. , Neculoiu D. , Buiculescu R. , Plana R. , Coccetti F. , Hartnagel H.
Published: July 2008

Field effect transistor (FET)-like structures with a trench as “gate” were fabricated on GaAs substrates. The bottom of the trench as well as the “source” and “drain” regions were metallized. Bundles of nanotubes were then suspended over the trench. At a certain threshold, these trenched FET-like structures display an S-shaped negative resistance, which breaks into parallel branches when the voltage is increased in equal steps. Several such steps were observed at room temperature and under normal pressure. The steps were reversibly enabled and disabled via changes in the applied voltage. A maximum stable gain with a quasilinear behavior was observed between 0.5 and 3.25GHz.
High thermal stability of vacancy clusters formed in MeV Si-self-ion-implanted Si
Authors: Shao Lin , Thompson P. E. , Chen Q. Y. , Ma K. B. , Liu J. R. , Chu Wei-Kan
Published: July 2008

We have shown that considerable vacancy defects, introduced by MeV Si self-ion implantation, can survive a 900°C∕5min annealing for gate formation. By analyzing the trap-limited Si interstitial diffusion, we have characterized these vacancy clusters. Furthermore, we show that the remaining vacancies are sufficient to reduce B diffusion. The study suggests that MeV ion implantation, a promising approach for ultrashallow junction formation in metal-oxide-semiconductor device fabrication, can be inserted before gate formation (involving high temperature annealing) to avoid irradiation damage on gate structures.
Wetting gradient induced separation of emulsions: A combined experimental and lattice Boltzmann computer simulation study
Authors: Varnik Fathollah , Truman Pagra , Wu Bin , Uhlmann Petra , Raabe Dierk , Stamm Manfred
Published: July 2008

Guided motion of emulsions is studied via combined experimental and theoretical investigations. The focus of the work is on basic issues related to driving forces generated via a stepwise (abrupt) change in wetting properties of the substrate along a given spatial direction. Experiments on binary emulsions unambiguously show that selective wettability of one of the fluid components (water in our experiments) with respect to the two different parts of the substrate is sufficient in order to drive the separation process. These studies are accompanied by approximate analytic arguments as well as lattice Boltzmann computer simulations, focusing on effects of a wetting gradient on internal droplet dynamics as well as its relative strength compared to volumetric forces driving the fluid flow. These theoretical investigations show a qualitatively different dependence of wetting gradient induced forces on contact angle and liquid volume in the case of an open substrate as opposed to a planar channel. In particular, for the parameter range of our experiments, slit geometry is found to give rise to considerably higher separation forces as compared to open substrate.
Carbon nanotube screening effects on the water-ion channels
Authors: Xu Yang , Aluru N. R.
Published: July 2008

A self-consistent tight-binding method is used to investigate the screening effects of semiconducting and metallic single-wall carbon nanotubes (SWCNTs) when the water molecules and various charged ions pass through the nanotubes. The trajectories of ions and water molecules are obtained from molecular dynamics simulations. It is shown that metallic SWCNTs have much stronger screening abilities than semiconducting SWCNTs. Our results indicate that it is possible to distinctly identify different ions and also to differentiate between armchair and zig-zag nanotubes.
High-capacity hydrogen storage by metallized graphene
Authors: Ataca C. , Aktürk E. , Ciraci S. , Ustunel H.
Published: July 2008

First-principles plane wave calculations predict that Li can be adsorbed on graphene forming a uniform and stable coverage on both sides. A significant part of the electronic charge of the Li 2s orbital is donated to graphene and is accommodated by its distorted π*-bands. As a result, semimetallic graphene and semiconducting graphene ribbons change into good metals. It is even more remarkable that Li covered graphene can serve as a high-capacity hydrogen storage medium with each adsorbed Li absorbing up to four H2 molecules amounting to a gravimetric density of 12.8wt%.
Flux-driven Josephson parametric amplifier
Authors: Yamamoto T. , Inomata K. , Watanabe M. , Matsuba K. , Miyazaki T. , Oliver W. D. , Nakamura Y. , Tsai J. S.
Published: July 2008

We have developed a Josephson parametric amplifier comprising a superconducting coplanar-waveguide resonator terminated by a dc superconducting quantum interference device (SQUID). An external field (the pump, ∼20 GHz) modulates the flux threading of the dc SQUID and, therefore, the resonant frequency of the cavity field (the signal, ∼10 GHz), which leads to the parametric signal amplification. We operated the amplifier at different band centers and observed amplification (17 dB at maximum) and deamplification depending on the relative phase between the pump and the signal. The noise temperature is estimated to be less than 0.87 K.
Three dimensional micromachining inside a transparent material by single pulse femtosecond laser through a hologram
Authors: Yamaji Masahiro , Kawashima Hayato , Suzuki Jun’ichi , Tanaka Shuhei
Published: July 2008

A basic pattern of a three dimensional (3D) photonic crystal, which consists of 16 capsule shaped elements in eight layers, is formed inside a silica glass using only a single pulse femtosecond laser through a computer generated hologram. The three parameters indispensable to the completely flexible 3D patterning, namely, “absolute position,” “relative position,” and “shape” of each element, are discussed on the basis of the measured optical axis elongation as functions of pulse duration and fluence.
Modes in a pulse-modulated radio-frequency dielectric-barrier glow discharge
Authors: Shi J. J. , Zhang J. , Qiu G. , Walsh J. L. , Kong M. G.
Published: July 2008

This letter reports an experimental study of a pulse-modulated radio-frequency dielectric-barrier discharge in atmospheric helium. By controlling the duty cycle at a modulation frequency of 10 and 100kHz, the 13.56MHz discharge is shown to operate in three different glow modes: the continuum mode, the discrete mode, and the transition mode. By investigating plasma ignition, residual electrons during power off are found to affect different glow modes. Duty cycle dependences of power density, gas temperature, optical emission intensities at 706 and 777nm are used to capture clearly the characteristics of the three glow modes.
Spatially resolved cathodoluminescence spectra of excitons in a ZnO microparticle
Authors: Hirai Takeshi , Ohno Nobuhito , Harada Yoshiyuki , Horii Taku , Sawada Yuji , Itoh Tadashi
Published: July 2008

Spatially resolved cathodoluminescence (CL) spectra of excitons in a ZnO microparticle, which consists of a number of small particles (primary particles), have been investigated at low temperature (15K). The spatially resolved CL spectra can be interpreted in terms of the influence of an internal electric field, which is likely caused by transfer of electrons from donor defects to surface states near the surface, on the radiative recombination of free and bound excitons in the ZnO microparticle.
High frequency and low frequency noise of AlGaN/GaN metal-oxide-semiconductor high-electron mobility transistors with gate insulator grown using photoelectrochemical oxidation method
Authors: Huang Li-Hsien , Yeh Su-Hao , Lee Ching-Ting
Published: July 2008

The AlGaN/GaN metal-oxide-semiconductor high-electron mobility transistors, which are fabricated using gate insulators directly grown by photoelectrochemical oxidation method, were studied for rf and low frequency noise applications. The drain-source current in saturation (IDSS) and maximum extrinsic transconductance gm(max) are 580 mA/mm and 76.72 mS/mm, respectively. The unity gain cutoff frequency (fT) and maximum frequency of oscillation (fmax) are 5.6 and 10.6 GHz, respectively. Furthermore, the low frequency noise in saturation region is measured and fitted well by 1/f law up to 10 kHz.
Distinct spins of substituent Co in polycrystalline Co- and Cu-codoped ZnO magnetic semiconductors
Authors: Zhang Y. B. , Li S.
Published: July 2008

Polycrystalline Zn0.938Co0.062O and Zn0.928Co0.062Cu0.01O oxides have been synthesized by solid state reaction. A single-phase wurtzite structure was formed in the polycrystalline samples with substituent Co and Cu in oxidation states of +2 and +1, respectively. The magnetization can be fitted with a paramagnetic Curie term, an antiferromagnetic Curie–Weiss term, and a diamagnetic constant. The results show that the substitution of Co at the Zn site does not occur randomly but Co ions appear to have a tendency to group, while the substitution of Cu at the Zn can reduce Co’s grouping tendency, resulting in more isolated free Co ions.
Critical nature of the giant field-induced pyroelectric response in Pb(Mg1/3Nb2/3)O3–xPbTiO3 single crystals
Authors: Raevskaya S. I. , Zakharov Yu. N. , Lutokhin A. G. , Emelyanov A. S. , Raevski I. P. , Panchelyuga M. S. , Titov V. V. , Prosandeev S. A.
Published: July 2008

We study the E-T phase diagram and dynamical pyroelectric coefficient of an (001)-oriented flux-grown 0.8Pb(Mg1/3Nb2/3)O3–0.2PbTiO3 single crystal. We found that the highest pyroelectric coefficient can be achieved at the point having quasicritical features. These data establish a quasicritical behavior of the field-induced pyroelectric coefficients in relaxors.
Interfacial electronic structures in an organic double-heterostructure photovoltaic cell
Authors: Tang J. X. , Zhou Y. C. , Liu Z. T. , Lee C. S. , Lee S. T.
Published: July 2008

The electronic structure of 2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline/fullerene/copper-phthalocyanine double heterostructure in a typical organic photovoltaic cell was studied by photoemission spectroscopy. The results show that the traditional vacuum energy level lineup is not valid for these organic heterojunctions, which suggests formation of interface dipole and energy level bending across the interface due to charge transfer. Based on the measured energy levels using x-ray and ultraviolet photoemission spectroscopies, important parameters such as the theoretical maximum of the open circuit voltage are extracted, and their impacts on charge photogeneration process are discussed.
Hyperthermal hydrogen atoms in argon-hydrogen atmospheric pressure microplasma jet
Authors: Oliveira C. , Souza Corrêa J. A. , Gomes M. P. , Sismanoglu B. N. , Amorim J.
Published: July 2008

An argon-hydrogen atmospheric pressure microplasma jet was constructed for the treatment of materials. The microplasma jet device operating at 50 W produced long plasma jet of 30 mm with gas temperatures measured, using OH emissions, from 1600 to 2600 K as a function of distance. Excitation temperature was found to be from 7000 to 10 000 K. Through the analysis of Hα line broadening mechanisms, surprising hot hydrogen atoms H (n=3) were found with temperatures ranging from 12 000 to 19 600 K.
Path integrals, Les Houches, and other adventures of Cécile DeWitt-Morette
Authors: Feder Toni
Published: July 2008

Entrée to Paris got Cécile DeWitt into physics. Working with great physicists kept her in the field.
The changing face of Titan
Authors: Lorenz Ralph D.
Published: July 2008

On Saturn’s hazy moon Titan, torrential downpours of methane punctuate centuries of drought on a landscape of sand dunes and badlands.
Iranian and US scientists keep channels of communication open
Authors: Kramer David
Published: July 2008

Visiting physicists and engineers are welcomed in Tehran and carry conciliatory messages from Iranian leaders back to the US.
Reversible interconversion of carbon dioxide and formate by an electroactive enzyme
Authors: Reda Torsten , Plugge Caroline M. , Abram Nerilie J. , Hirst Judy
Published: July 2008

Carbon dioxide (CO
2
) is a kinetically and thermodynamically stable molecule. It is easily formed by the oxidation of organic molecules, during combustion or respiration, but is difficult to reduce. The production of reduced carbon compounds from CO
2
is an attractive proposition, because carbon-neutral energy sources could be used to generate fuel resources and sequester CO
2
from the atmosphere. However, available methods for the electrochemical reduction of CO
2
require excessive overpotentials (are energetically wasteful) and produce mixtures of products. Here, we show that a tungsten-containing formate dehydrogenase enzyme (FDH1) adsorbed to an electrode surface catalyzes the efficient electrochemical reduction of CO
2
to formate. Electrocatalysis by FDH1 is thermodynamically reversible—only small overpotentials are required, and the point of zero net catalytic current defines the reduction potential. It occurs under thoroughly mild conditions, and formate is the only product. Both as a homogeneous catalyst and on the electrode, FDH1 catalyzes CO
2
reduction with a rate more than two orders of magnitude faster than that of any known catalyst for the same reaction. Formate oxidation is more than five times faster than CO
2
reduction. Thermodynamically, formate and hydrogen are oxidized at similar potentials, so formate is a viable energy source in its own right as well as an industrially important feedstock and a stable intermediate in the conversion of CO
2
to methanol and methane. FDH1 demonstrates the feasibility of interconverting CO
2
and formate electrochemically, and it is a template for the development of robust synthetic catalysts suitable for practical applications.
Shine–Dalgarno interaction prevents incorporation of noncognate amino acids at the codon following the AUG
Authors: Di Giacco Viviana , Márquez Viter , Qin Yan , Pech Markus , Triana-Alonso Francisco J. , Wilson Daniel N. , Nierhaus Knud H.
Published: July 2008

During translation, usually only one in ≈400 misincorporations affects the function of a nascent protein, because only chemically similar near-cognate amino acids are misincorporated in place of the cognate one. The deleterious misincorporation of a chemically dissimilar noncognate amino acid during the selection process is precluded by the presence of a tRNA at the ribosomal E-site. However, the selection of first aminoacyl-tRNA, directly after initiation, occurs without an occupied E-site, i.e., when only the P-site is filled with the initiator tRNA and thus should be highly error-prone. Here, we show how bacterial ribosomes have solved this accuracy problem: In the absence of a Shine–Dalgarno (SD) sequence, the first decoding step at the A-site after initiation is extremely error-prone, even resulting in the significant incorporation of noncognate amino acids. In contrast, when a SD sequence is present, the incorporation of noncognate amino acids is not observed. This is precisely the effect that the presence of a cognate tRNA at the E-site has during the elongation phase. These findings suggest that during the initiation phase, the SD interaction functionally compensates for the lack of codon–anticodon interaction at the E-site by reducing the misincorporation of near-cognate amino acids and prevents noncognate misincorporation.
Near-field infinity-simulating boundary conditions for the heat equation
Authors: Ditkowski Adi , Suhov Alexander
Published: July 2008

The numerical simulation of various physical phenomena in infinite domains poses great difficulties. Truncation of the domain is usually necessary in such cases. To ensure stability of the resulting problem on the restricted domain, appropriate boundary conditions should be applied. Here, we develop a boundary condition for the case in which the heat equation is satisfied outside the domain of interest with no restrictions on the equation inside. The condition employs a thin layer encasing the computational domain. The resulting condition, combined with techniques similar to those proposed by Jiang and Greengard [Jiang S, Greengard L (2004) Fast evaluation of nonreflecting boundary conditions for the Schrödinger equation in one dimension.
Comp Math Appl
47:955–966.] promises to be more accurate and computationally efficient than previously described techniques.
Quantifying neuronal network dynamics through coarse-grained event trees
Authors: Rangan Aaditya V. , Cai David , McLaughlin David W.
Published: July 2008

Animals process information about many stimulus features simultaneously, swiftly (in a few 100 ms), and robustly (even when individual neurons do not themselves respond reliably). When the brain carries, codes, and certainly when it decodes information, it must do so through some coarse-grained projection mechanism. How can a projection retain information about network dynamics that covers multiple features, swiftly and robustly? Here, by a coarse-grained projection to event trees and to the event chains that comprise these trees, we propose a method of characterizing dynamic information of neuronal networks by using a statistical collection of spatial–temporal sequences of relevant physiological observables (such as sequences of spiking multiple neurons). We demonstrate, through idealized point neuron simulations in small networks, that this event tree analysis can reveal, with high reliability, information about multiple stimulus features within short realistic observation times. Then, with a large-scale realistic computational model of V1, we show that coarse-grained event trees contain sufficient information, again over short observation times, for fine discrimination of orientation, with results consistent with recent experimental observation.
DNA polymorphisms at the
BCL11A
,
HBS1L-MYB
, and β-
globin
loci associate with fetal hemoglobin levels and pain crises in sickle cell disease
Authors: Lettre Guillaume , Sankaran Vijay G. , Bezerra Marcos André C. , Araújo Aderson S. , Uda Manuela , Sanna Serena , Cao Antonio , Schlessinger David , Costa Fernando F. , Hirschhorn Joel N. , Orkin Stuart H.
Published: July 2008

Sickle cell disease (SCD) is a debilitating monogenic blood disorder with a highly variable phenotype characterized by severe pain crises, acute clinical events, and early mortality. Interindividual variation in fetal hemoglobin (HbF) expression is a known and potentially heritable modifier of SCD severity. High HbF levels are correlated with reduced morbidity and mortality. Common single nucleotide polymorphisms (SNPs) at the
BCL11A
and
HBS1L-MYB
loci have been implicated previously in HbF level variation in nonanemic European populations. We recently demonstrated an association between a
BCL11A
SNP and HbF levels in one SCD cohort [Uda M,
et al.
(2008)
Proc Natl Acad Sci
USA 105:1620–1625]. Here, we genotyped additional
BCL11A
SNPs,
HBS1L-MYB
SNPs, and an SNP upstream of

G

γ-
globin
(
HBG2
; the
Xmn
I polymorphism), in two independent SCD cohorts: the African American Cooperative Study of Sickle Cell Disease (CSSCD) and an SCD cohort from Brazil. We studied the effect of these SNPs on HbF levels and on a measure of SCD-related morbidity (pain crisis rate). We strongly replicated the association between these SNPs and HbF level variation (in the CSSCD,
P
values range from 0.04 to 2 × 10
−42
). Together, common SNPs at the
BCL11A
,
HBS1L-MYB
, and β-
globin
(
HBB
) loci account for >20% of the variation in HbF levels in SCD patients. We also have shown that HbF-associated SNPs associate with pain crisis rate in SCD patients. These results provide a clear example of inherited common sequence variants modifying the severity of a monogenic disease.
A model for integrated implementation of activity-based costing and radio frequency identification technology in manufacturing
Authors: Buyurgan Nebil , Nachtmann Heather , Celikkol Selin
Published: July 2008

Activity-based costing (ABC) systems require extensive data collection and often rely heavily on estimated input data because gathering the necessary information is too costly. With its remarkable capabilities, radio frequency identification (RFID) technology presents an excellent opportunity to improve the ABC cost driver data collection process, especially in manufacturing environments. Typical, individual implementation methods of these systems can involve risks and difficulties. In order to overcome these risks and difficulties to profit from the benefits by leveraging the efforts, this paper focuses on a new managerial strategy and presents an integrated implementation model for manufacturing companies. Along with detailed adoption processes, this study also identifies opportunities where RFID technology can provide ABC systems with extensive data collection and ABC systems can avoid budget overruns of RFID projects. This study shows that in addition to the benefits of integrated implementation steps, opportunities provided by this integration offer the use of RFID technology for improving the ABC cost driver data collection process and the use of ABC systems for costing RFID projects.
Autonomously controlled storage management in vehicle logistics – applications of RFID and mobile computing systems
Authors: Böse Felix , Piotrowski Jakub , Scholz-Reiter Bernd
Published: July 2008

Today, planning and control of logistic processes on automobile terminals are generally executed by centralised logistics systems, which cannot cope with high requirements for flexible order processing due to increasing dynamics and complexity. The main business processes on automobile terminals – notification of vehicles by automobile manufacturer, transport to automobile terminal, storage and technical treatment as well as delivery to automobile dealer – are planned and controlled by centralised application software systems. In the context of this article, an innovative approach to autonomous control in automobile logistics is investigated, considering as example the logistic order processing of an idealised automobile terminal of the company E.H. Harms Automobile-Logistics. Within a simulation study, evidence of the existing application potential of autonomous control in the field of vehicle storage management is provided. Thereupon the technical feasibility of an autonomously controlled storage management system is examined. System requirements for technical implementation of an autonomously controlled storage management are deviated. Thereafter, results of an executed case study concerning the implementation and test of an autonomously controlled, radio frequency identification (RFID) based storage management system are presented and the remaining weaknesses of the implemented IT solution are identified. Finally, further research and development activities are introduced in the form of a wearable computing concept using smart clothes.
Tumor Necrosis Factor-α–elicited Stimulation of γ-Secretase Is Mediated by c-Jun N-terminal Kinase-dependent Phosphorylation of Presenilin and Nicastrin
Authors: Kuo Lan-Hsin , Hu Ming-Kuan , Hsu Wen-Ming , Tung Ying-Tsen , Wang Bo-Jeng , Tsai Wang-Wei , Yen Chen-Tung , Liao Yung-Feng
Published: July 2008

γ-Secretase is a multiprotein complex composed of presenilin (PS), nicastrin (NCT), Aph-1, and Pen-2, and it catalyzes the final proteolytic step in the processing of amyloid precursor protein to generate amyloid-β. Our previous results showed that tumor necrosis factor-α (TNF-α) can potently stimulate γ-secretase activity through a c-Jun N-terminal kinase (JNK)-dependent pathway. Here, we demonstrate that TNF-α triggers JNK-dependent serine/threonine phosphorylation of PS1 and NCT to stimulate γ-secretase activity. Blocking of JNK activity with a potent JNK inhibitor (SP600125) reduces TNF-α–triggered phosphorylation of PS1 and NCT. Consistent with this, we show that activated JNKs can be copurified with γ-secretase complexes and that active recombinant JNK2 can promote the phosphorylation of PS1 and NCT in vitro. Using site-directed mutagenesis and a synthetic peptide, we clearly show that the Ser319Thr320 motif in PS1 is an important JNK phosphorylation site that is critical for the TNF-α–elicited regulation of γ-secretase. This JNK phosphorylation of PS1 at Ser319Thr320 enhances the stability of the PS1 C-terminal fragment that is necessary for γ-secretase activity. Together, our findings strongly suggest that JNK is a critical intracellular mediator of TNF-α–elicited regulation of γ-secretase and governs the pivotal step in the assembly of functional γ-secretase.
Microtubules Have Opposite Orientation in Axons and Dendrites of Drosophila Neurons
Authors: Stone Michelle C. , Roegiers Fabrice , Rolls Melissa M.
Published: July 2008

In vertebrate neurons, axons have a uniform arrangement of microtubules with plus ends distal to the cell body (plus-end-out), and dendrites have equal numbers of plus- and minus-end-out microtubules. To determine whether microtubule orientation is a conserved feature of axons and dendrites, we analyzed microtubule orientation in invertebrate neurons. Using microtubule plus end dynamics, we mapped microtubule orientation in Drosophila sensory neurons, interneurons, and motor neurons. As expected, all axonal microtubules have plus-end-out orientation. However, in proximal dendrites of all classes of neuron, ∼90% of dendritic microtubules were oriented with minus ends distal to the cell body. This result suggests that minus-end-out, rather than mixed orientation, microtubules are the signature of the dendritic microtubule cytoskeleton. Surprisingly, our map of microtubule orientation predicts that there are no tracks for direct cargo transport between the cell body and dendrites in unipolar neurons. We confirm this prediction, and validate the completeness of our map, by imaging endosome movements in motor neurons. As predicted by our map, endosomes travel smoothly between the cell body and axon, but they cannot move directly between the cell body and dendrites.
Genetic and Structural Analysis of Hmg2p-induced Endoplasmic Reticulum Remodeling inSaccharomyces cerevisiae
Authors: Federovitch Christine M. , Jones Ying Z. , Tong Amy H. , Boone Charles , Prinz William A. , Hampton Randolph Y.
Published: July 2008

The endoplasmic reticulum (ER) is highly plastic, and increased expression of distinct single ER-resident membrane proteins, such as HMG-CoA reductase (HMGR), can induce a dramatic restructuring of ER membranes into highly organized arrays. Studies on the ER-remodeling behavior of the two yeast HMGR isozymes, Hmg1p and Hmg2p, suggest that they could be mechanistically distinct. We examined the features of Hmg2p required to generate its characteristic structures, and we found that the molecular requirements are similar to those of Hmg1p. However, the structures generated by Hmg1p and Hmg2p have distinct cell biological features determined by the transmembrane regions of the proteins. In parallel, we conducted a genetic screen to identify HER genes (required for Hmg2p-induced ER Remodeling), further confirming that the mechanisms of membrane reorganization by these two proteins are distinct because most of the HER genes were required for Hmg2p but not Hmg1p-induced ER remodeling. One of the HER genes identified was PSD1, which encodes the phospholipid biosynthetic enzyme phosphatidylserine decarboxylase. This direct connection to phospholipid biosynthesis prompted a more detailed examination of the effects of Hmg2p on phospholipid mutants and composition. Our analysis revealed that overexpression of Hmg2p caused significant and specific growth defects in nulls of the methylation pathway for phosphatidylcholine biosynthesis that includes the Psd1p enzyme. Furthermore, increased expression of Hmg2p altered the composition of cellular phospholipids in a manner that implied a role for PSD1. These phospholipid effects, unlike Hmg2p-induced ER remodeling, required the enzymatic activity of Hmg2p. Together, our results indicate that, although related, Hmg2p- and Hmg1p-induced ER remodeling are mechanistically distinct.
Activation of the DNA Damage Checkpoint in Mutants Defective in DNA Replication Initiation
Authors: Yin Ling , Locovei Alexandra Monica , D'Urso Gennaro
Published: July 2008

In the fission yeast, Schizosaccharomyces pombe, blocks to DNA replication elongation trigger the intra-S phase checkpoint that leads to the activation of the Cds1 kinase. Cds1 is required to both prevent premature entry into mitosis and to stabilize paused replication forks. Interestingly, although Cds1 is essential to maintain the viability of mutants defective in DNA replication elongation, mutants defective in DNA replication initiation require the Chk1 kinase. This suggests that defects in DNA replication initiation can lead to activation of the DNA damage checkpoint independent of the intra-S phase checkpoint. This might result from reduced origin firing that leads to an increase in replication fork stalling or replication fork collapse that activates the G2 DNA damage checkpoint. We refer to the Chk1-dependent, Cds1-independent phenotype as the rid phenotype (for replication initiation defective). Chk1 is active in rid mutants, and rid mutant viability is dependent on the DNA damage checkpoint, and surprisingly Mrc1, a protein required for activation of Cds1. Mutations in Mrc1 that prevent activation of Cds1 have no effect on its ability to support rid mutant viability, suggesting that Mrc1 has a checkpoint-independent role in maintaining the viability of mutants defective in DNA replication initiation.
Prominent Actin Fiber Arrays inDrosophilaTendon Cells Represent Architectural Elements Different from Stress Fibers
Authors: Alves-Silva Juliana , Hahn Ines , Huber Olga , Mende Michael , Reissaus Andre , Prokop Andreas
Published: July 2008

Tendon cells are specialized cells of the insect epidermis that connect basally attached muscle tips to the cuticle on their apical surface via prominent arrays of microtubules. Tendon cells of Drosophila have become a useful genetic model system to address questions with relevance to cell and developmental biology. Here, we use light, confocal, and electron microscopy to present a refined model of the subcellular organization of tendon cells. We show that prominent arrays of F-actin exist in tendon cells that fully overlap with the microtubule arrays, and that type II myosin accumulates in the same area. The F-actin arrays in tendon cells seem to represent a new kind of actin structure, clearly distinct from stress fibers. They are highly resistant to F-actin–destabilizing drugs, to the application of myosin blockers, and to loss of integrin, Rho1, or mechanical force. They seem to represent an important architectural element of tendon cells, because they maintain a connection between apical and basal surfaces even when microtubule arrays of tendon cells are dysfunctional. Features reported here and elsewhere for tendon cells are reminiscent of the structural and molecular features of support cells in the inner ear of vertebrates, and they might have potential translational value.
The THP1-SAC3-SUS1-CDC31 Complex Works in Transcription Elongation-mRNA Export Preventing RNA-mediated Genome Instability
Authors: González-Aguilera Cristina , Tous Cristina , Gómez-González Belén , Huertas Pablo , Luna Rosa , Aguilera Andrés
Published: July 2008

The eukaryotic THO/TREX complex, involved in mRNP biogenesis, plays a key role in the maintenance of genome integrity in yeast. mRNA export factors such as Thp1-Sac3 also affect genome integrity, but their mutations have other phenotypes different from those of THO/TREX. Sus1 is a novel component of SAGA transcription factor that also associates with Thp1-Sac3, but little is known about its effect on genome instability and transcription. Here we show that Thp1, Sac3, and Sus1 form a functional unit with a role in mRNP biogenesis and maintenance of genome integrity that is independent of SAGA. Importantly, the effects of ribozyme-containing transcription units, RNase H, and the action of human activation-induced cytidine deaminase on transcription and genome instability are consistent with the possibility that R-loops are formed in Thp1-Sac3-Sus1-Cdc31 as in THO mutants. Our data reveal that Thp1-Sac3-Sus1-Cdc31, together with THO/TREX, define a specific pathway connecting transcription elongation with export via an RNA-dependent dynamic process that provides a feedback mechanism for the control of transcription and the preservation of genetic integrity of transcribed DNA regions.
Exon Loss Accounts for Differential Sorting of Na-K-Cl Cotransporters in Polarized Epithelial Cells
Authors: Carmosino Monica , Giménez Ignacio , Caplan Michael , Forbush Biff
Published: July 2008

The renal Na-K-Cl cotransporter (NKCC2) is selectively expressed in the apical membranes of cells of the mammalian kidney, where it is the target of the clinically important loop diuretics. In contrast, the “secretory” NKCC1 cotransporter is localized in the basolateral membranes of many epithelia. To identify the sorting signal(s) that direct trafficking of NKCCs, we generated chimeras between the two isoforms and expressed these constructs in polarized renal epithelial cell lines. This analysis revealed an amino acid stretch in NKCC2 containing apical sorting information. The NKCC1 C terminus contains a dileucine motif that constitutes the smallest essential component of its basolateral sorting signal. NKCC1 lacking this motif behaves as an apical protein. Examination of the NKCC gene structure reveals that this dileucine motif is encoded by an additional exon in NKCC1 absent in NKCC2. Phylogenetic analysis of this exon suggests that the evolutionary loss of this exon from the gene encoding the basolateral NKCC1 constitutes a novel mechanism that accounts for the apical sorting of the protein encoded by the NKCC2 gene.