bluuebunny/crossref_metadata_2025 huggingface dataset:
Rheological and flow characteristics of nanofluids: Influence of electroviscous effects and particle agglomeration
Authors: Anoop K. B. , Kabelac S. , Sundararajan T. , Das Sarit K.
Published: August 2009

Nanofluids have shown remarkable attraction in heat transfer community due to its reported enhanced thermal properties. One factor which can restrict nanofluids in heat transfer application is the increased viscosity value (compared to classical predictions). Particle aggregation occurring was the major reason for this observation. Even though majority of the aqueous nanofluids prepared in literature were stabilized electrostatically by adjusting the pH, studies on the effect of the electrical double layer thus created and its influence on viscosity increase has not been investigated for these nanofluids so far. Thus, in the present paper, rheological properties of alumina-water nanofluids, which are electrostatically stabilized, are measured and the increase in suspension viscosity due to presence of this electrical double layer causing additional electroviscous effects is brought out. Based on dynamic light scattering studies, particle agglomeration and its subsequent effect in increasing the viscosity of alumina-ethylene glycol nanofluid, where electroviscous effects are absent, are also considered. It is noted that the understanding of electroviscous effect is equally important as understanding the particle agglomeration effect and understanding both the effects is central to revealing the physics of nanofluid rheology. Further, hydrodynamic experiments are made, which show that nanofluids behaves almost like a homogeneous fluids under flow conditions, and by knowing their properties, such as viscosity and density, pressure drop can be predicted.
Thermal conductivity of cubic and hexagonal mesoporous silica thin films
Authors: Coquil Thomas , Richman Erik K. , Hutchinson Neal J. , Tolbert Sarah H. , Pilon Laurent
Published: August 2009

This paper reports the cross-plane thermal conductivity of highly ordered cubic and hexagonal templated mesoporous amorphous silica thin films synthesized by evaporation-induced self-assembly process. Cubic and hexagonal films featured spherical and cylindrical pores and average porosities of 25% and 45%, respectively. The pore diameters ranged from 3 to 18 nm and film thickness from 80 to 540 nm, while the average wall thickness varied from 3 to 12 nm. The thermal conductivity was measured at room temperature using the 3ω method. The experimental setup and the associated analysis were validated by comparing the thermal conductivity measurements with the data reported in literature for the silicon substrate and for high quality thermal oxide thin films with thicknesses ranging from 100 to 500 nm. The cross-plane thermal conductivity of the synthesized mesoporous silica thin films does not show strong dependence on pore size, wall thickness, or film thickness. This is due to the fact that heat is mainly carried by very localized nonpropagating vibrational modes. The average thermal conductivity for the cubic mesoporous silica films was 0.30±0.02 W/m K, while it was 0.20±0.01 W/m K for the hexagonal films. This corresponds to reductions of 79% and 86% from bulk fused silica at room temperature.
The modified model of the dielectric characteristics for porous Ba0.6Sr0.4TiO3 ceramics
Authors: Zhang Guangzu , Jiang Shenglin , Zeng Yike , Zhang Yangyang , Zhang Qingfeng , Yu Yan
Published: August 2009

The effect of direct-current (dc) biasing on the dielectric properties of porous Ba0.6Sr0.4TiO3 with various porosities, pore sizes, and different pore shapes has been studied in the paraelectric state. The existing model did not consider the effect of the change in grain size and pore shape, lead to the theory fitting the fine grained or nonspherical pore ceramics less well. The bias equation used in this literature to predict the electric field dependence of permittivity is modified by introducing a coefficient α. α is the microstructure parameter introduced to depict the influence of grain size and pore shape effect. Taking high porosity samples and nonspherical pore ceramic samples, for example, the modified bias equation gives a better fit to the experimental result in this study.
Origin of the butterfly-shaped magnetoresistance in reactive sputtered epitaxial Fe3O4 films
Authors: Li P. , Zhang L. T. , Mi W. B. , Jiang E. Y. , Bai H. L.
Published: August 2009

Epitaxial Fe3O4 thin films were synthesized by facing-target reactive sputtering Fe targets. The epitaxy of the Fe3O4 film on MgO (100) was examined macroscopically using x-ray diffraction, including conventional θ-2θ scan, tilting 2θ scan, φ scan, and pole figure. The observed low-field butterfly-shaped magnetoresistance (MR) are explained by the primary fast rotation of the spins far away from antiphase boundaries and the high-field MR changing linearly with magnetic field can be understood by the gradual rotation of the spins near the antiphase boundaries. It is magnetocrystalline anisotropy that causes an increase in MR below Verwey transition temperature.
Charge constrained density functional molecular dynamics for simulation of condensed phase electron transfer reactions
Authors: Oberhofer Harald , Blumberger Jochen
Published: August 2009

We present a plane-wave basis set implementation of charge constrained density functional molecular dynamics (CDFT-MD) for simulation of electron transfer reactions in condensed phase systems. Following the earlier work of Wu and Van Voorhis [Phys. Rev. A 72, 024502 (2005)], the density functional is minimized under the constraint that the charge difference between donor and acceptor is equal to a given value. The classical ion dynamics is propagated on the Born–Oppenheimer surface of the charge constrained state. We investigate the dependence of the constrained energy and of the energy gap on the definition of the charge and present expressions for the constraint forces. The method is applied to the Ru2+–Ru3+ electron self-exchange reaction in aqueous solution. Sampling the vertical energy gap along CDFT-MD trajectories and correcting for finite size effects, a reorganization free energy of 1.6 eV is obtained. This is 0.1−0.2 eV lower than a previous estimate based on a continuum model for solvation. The smaller value for the reorganization free energy can be explained by the fact that the Ru–O distances of the divalent and trivalent Ru hexahydrates are predicted to be more similar in the electron transfer complex than for the separated aqua ions.
A compact apparatus for studies of element and phase-resolved ferromagnetic resonance
Authors: Arena D. A. , Ding Y. , Vescovo E. , Zohar S. , Guan Y. , Bailey W. E.
Published: August 2009

We present a compact sample holder equipped with electromagnets and high frequency transmission lines; the sample holder is intended for combined x-ray magnetic circular dichroism (XMCD) and ferromagnetic resonance measurements (FMR). Time-resolved measurements of resonant x-ray detected FMR during forced precession are enabled by use of a rf excitation that is phase-locked to the storage ring bunch clock. Several applications of the combined XMCD+FMR technique are presented, demonstrating the flexibility of the experimental design.
Diffusion under temperature gradient: A phase-field model study
Authors: Mohanty R. R. , Guyer J. E. , Sohn Y. H.
Published: August 2009

A diffuse interface model was devised and employed to investigate the effect of thermotransport (a.k.a., thermomigration) process in single-phase and two-phase alloys of a binary system. Simulation results show that an applied temperature gradient can cause significant redistribution of constituent elements and phases in the alloy. The magnitude and the direction of the redistribution depend on the initial composition, the atomic mobility and the heat of transport of the respective elements. In two-phase alloys, the thermomigration effect can cause the formation of single-element rich phases at the cold and hot ends of the alloy (i.e., demixing).
Unambiguous determination of carrier concentration and mobility for InAs/GaSb superlattice photodiode optimization
Authors: Cervera C. , Rodriguez J. B. , Perez J. P. , Aït-Kaci H. , Chaghi R. , Konczewicz L. , Contreras S. , Christol P.
Published: August 2009

In this communication we report on electrical properties of nonintentionally doped (nid) type II InAs/GaSb superlattice grown by molecular beam epitaxy. We present a simple technological process which, thanks to the suppression of substrate, allows direct Hall measurement on superlattice structures grown on conductive GaSb substrate. Two samples were used to characterize the transport: one grown on a semi-insulating GaAs substrate and another grown on n-GaSb substrate where a etch stop layer was inserted to remove the conductive substrate. Mobilities and carrier concentrations have been measured as a function of temperature (77–300 K), and compared with capacitance-voltage characteristic at 80 K of a photodiode comprising a similar nid superlattice.
Theoretical investigation of 1.3 μm dots-under-a-well and dots-in-a-well InAs/GaAs quantum dot vertical-cavity surface-emitting lasers
Authors: Tong C. Z. , Xu D. W. , Yoon S. F.
Published: August 2009

The threshold characteristic and output power of 1.3 μm quantum dot (QD) vertical-cavity surface-emitting laser (VCSEL) with dots-under-a-well and dots-in-a-well InAs/GaAs QD structures are investigated by using rate equation model and output power model. The influence of VCSEL and QD structures on the modal gain of VCSEL is analyzed. Threshold current density, quantum efficiency, and characteristic temperature are simulated for different QD structures. The dependence of output power of 1.3 μm QD VCSEL on the QD structure, threshold current, quantum efficiency, and oxide-aperture size is investigated in detail.
Temperature dependence of piezoelectric properties of high-TC Bi(Mg1/2Ti1/2)O3–PbTiO3
Authors: Chen Jun , Tan Xiaoli , Jo Wook , Rödel Jürgen
Published: August 2009

The temperature dependence of both polarization and electric-field induced strain was investigated for (1−x)Bi(Mg1/2Ti1/2)O3–xPbTiO3 (x=0.36, 0.37, and 0.38), with the morphotropic phase boundary located at x=0.37. Remanent polarization (Pr) and maximum polarization (Pmax) of all compositions are enhanced with increasing temperature up to 175 °C, which is rationalized as improved domain switching due to reduced tetragonality (c/a). The hysteresis during unipolar electric cycling tends to decrease with increase in the fraction of tetragonal phase. Temperature dependent x-ray diffraction demonstrates that switched non-180° domains are stable against thermal depoling above 200 °C, which indicates that the currently investigated materials are suitable for high temperature applications. This promising high-TC piezoelectric is further discussed with reference to oxygen octahedron of the tilted R3c and untilted R3m space groups and the tolerance factor (t).
Rayleigh wave reflection from single surface imperfections on isotropic substrates
Authors: Darinskii A. N. , Weihnacht M. , Schmidt H.
Published: August 2009

The specific features of the Rayleigh wave reflection from single surface imperfections of an isotropic substrate are studied by the finite element method. Six types of the imperfections are considered, namely, upstep and downstep, projection and groove, and strip of foreign material coating the substrate and buried into it. The dependence is found and analyzed of the absolute value and the phase of the reflection coefficients on the geometrical parameters of defects and the angle of incidence. Numerical results are compared to analytical predictions based on a development of the reflection coefficient in powers of the defect height to wavelength ratio h/λ and limited to the first-order term. In particular, this comparison reveals that in some cases approximate expressions are able to provide a good precision. At the same time situations are met when the linear approximation fails to describe the behavior of the reflection coefficient even at fairly small h/λ.
External cavity quantum cascade laser tunable from 7.6 to 11.4 μm
Authors: Hugi Andreas , Terazzi Romain , Bonetti Yargo , Wittmann Andreas , Fischer Milan , Beck Mattias , Faist Jérôme , Gini Emilio
Published: August 2009

We present the development of a broad gain quantum cascade active region. By appropriate cascade design and using a symmetric active region arrangement, we engineer a flat gain and increase the total modal gain in the desired spectral range. Grating-coupled external cavity quantum cascade lasers using this symmetric active region are tunable from 7.6 to 11.4 μm with a peak optical output power of 1 W and an average output power of 15 mW at room-temperature. With a tuning of over 432 cm−1, this single source covers an emission range of over 39% around the center frequency.
Molecular beam epitaxy of SrTiO3 on Si (001): Early stages of the growth and strain relaxation
Authors: Niu G. , Saint-Girons G. , Vilquin B. , Delhaye G. , Maurice J.-L. , Botella C. , Robach Y. , Hollinger G.
Published: August 2009

The molecular beam epitaxy of SrTiO3 (STO) layers on Si (001) is studied, focusing on the early stages of the growth and on the strain relaxation process. Evidence is given that even for optimized growth conditions, STO grows initially amorphous on silicon and recrystallizes, leading to the formation of an atomically abrupt heterointerface with silicon. Just after recrystallization, STO is partially strained. Further increase in its thickness leads to the onset of a progressive plastic relaxation mechanism. STO recovers its bulk lattice parameter for thicknesses of the order of 30 ML.
Normal forms and gauge symmetry of local dynamics
Authors: Lyakhovich S. L. , Sharapov A. A.
Published: August 2009

A systematic procedure is proposed for deriving all the gauge symmetries of the general, not necessarily variational, equations of motion. For the variational equations, this procedure reduces to the Dirac–Bergmann algorithm for the constrained Hamiltonian systems with certain extension: it remains applicable beyond the scope of Dirac’s conjecture. Even though no pairing exists between the constraints and the gauge symmetry generators in general nonvariational dynamics, certain counterparts still can be identified of the first- and second-class constraints without appealing to any Poisson structure. It is shown that the general local gauge dynamics can be equivalently reformulated in an involutive normal form. The last form of dynamics always admits the BRST embedding, which does not require the classical equations to follow from any variational principle.
Effect of self-focusing on third harmonic generation by a Gaussian beam in a collisional plasma
Authors: Sodha Mahendra Singh , Faisal Mohammad , Verma M. P.
Published: August 2009

In this paper the third harmonic generation caused by the self-focusing of a Gaussian electromagnetic beam in collisional plasmas has been investigated. The wave equations for the fundamental and the third harmonic fields have been solved in the paraxial approximation. The wave frequency has been assumed to be much larger than the electron collision frequency. The generation of the third harmonic considering self-focusing has been investigated and graphically presented. It is seen that the self-focusing of the fundamental beam enhances the power of the third harmonic output indicating that the region of third harmonic generation is localized near the axis of the beam. The dependence of the third harmonic power on the distance of propagation for different values of initial fundamental power, beam width, and plasma density has also been plotted and discussed.
Experimental investigation of transition from Fowler–Nordheim field emission to space-charge-limited flows in a nanogap
Authors: Bhattacharjee Sudeep , Chowdhury Tathagata
Published: August 2009

An experimental investigation of the transition from Fowler–Nordheim (FN) field emission to space-charge-limited (SCL) flows in a nanogap is presented. Electrodes with gap size D∼30–70 nm corresponding to D/λo up to a maximum of ∼2×103, where λo is the de Broglie wavelength of the space-charge-electrons, are experimented. The transition from the FN field emission to the classical SCL flow is a function of the applied bias and lies in the range 5–15 V. The equilibrium transmitted current density for the 50 nm sample indicates a transition from the FN to the quantum SCL flow at ∼0.4 V with D/λo of ∼35 and then gradually to the classical SCL behavior as the voltage is increased beyond ∼9 V. The experiments indicate no sharp demarcation between the different regimes.
Flow control around a circular cylinder using pulsed dielectric barrier discharge surface plasma
Authors: Jukes Timothy N. , Choi Kwing-So
Published: August 2009

Dielectric barrier discharge (DBD) plasma actuators have been used to control the flow around a circular cylinder at Re=15 000, where the near-wake structure was studied using time-resolved particle image velocimetry with simultaneous measurements of the dynamic lift and drag forces. It was shown that the vortex shedding was suppressed when the surface plasma placed near the natural separation point was activated in a pulsed mode at nondimensional frequency, fp+, above 0.6 with a force coefficient, Cp, greater than 0.05%. Plasma actuator performance on flow control was summarized by mapping the changes in drag and lift fluctuations as a function of the forcing frequency and the force coefficient. They showed that more than 70% reduction in lift fluctuations was obtained with up to 32% drag reduction at fp+=2.0 and Cp=0.32%. Here, narrowing of the wake was observed as the plasma promoted shear-layer roll-ups at the forcing frequency. This, however, did not affect the shear layer on the opposite side of the wake. At nondimensional forcing frequencies less than 0.6, the vortex shedding locked onto a multiple of the plasma frequency to amplify the wake oscillations. This caused more than 85% increase in lift fluctuations with 8% drag increase at fp+=0.2 and Cp=0.01%. The efficiency of flow control using DBD plasma was found to be 1%–2% for drag reduction while around 6% for drag increase.
Anomalous specific heat of charge-ordered La0.5Ca0.5MnO3
Authors: Xian-Sheng Cao , Chang-Le Chen , Tong-Li Wei , Guo-Mian Gao
Published: August 2009

An exact treatment of the double exchange-Holstein model with an electron-phonon interaction γ coupled to magnetism is used to compute the heat capacity. The model is performed combining a mean-field approximation for the double exchange interaction and the Lang–Firsov transformation for the electron-phonon interaction. The calculated results of heat capacity point to the dominance of the lattice contribution, especially in the ferromagnetic regime. This behavior is in qualitative agreement with experimental findings.
Time-reversible molecular dynamics algorithms with bond constraints
Authors: Toxvaerd Søren , Heilmann Ole J. , Ingebrigtsen Trond , Schrøder Thomas B. , Dyre Jeppe C.
Published: August 2009

Time-reversible molecular dynamics algorithms with bond constraints are derived. The algorithms are stable with and without a thermostat and in double precision as well as in single-precision arithmetic. Time reversibility is achieved by applying a central-difference expression for the velocities in the expression for Gauss’ principle of least constraint. The imposed time symmetry results in a quadratic expression for the Lagrange multiplier. For a system of complex molecules with connected constraints the corresponding set of coupled quadratic equations is easily solved by a consecutive iteration scheme. The algorithms were tested on two models. One is a dumbbell model of Toluene, the other system consists of molecules with four connected constraints forming a triangle and a branch point of constraints. The equilibrium particle distributions and the mean-square particle displacements for the dumbbell model were compared to the corresponding functions obtained by GROMACS. The agreement is perfect within statistical error.
Thermoluminescence properties of carbon doped Y3Al5O12 (YAG) crystal
Authors: Yang Xin-Bo , Xu Jun , Li Hong-Jun , Bi Qun-Yu , Su Liang-Bi , Cheng Yan , Tang Qiang
Published: August 2009

In this work, carbon doped yttrium aluminum garnet (YAG) (YAG:C) crystal was grown by the temperature gradient technique in a reducing atmosphere. The optical and thermoluminescence (TL) properties of the as-grown YAG:C crystal were investigated. Four absorption bands at 235, 255, 298, and 370 nm and a main blue emission peak at 400 nm are observed in the YAG:C crystal. The absorption coefficients of the bands at 235 and 370 nm, which are associated with the F+-center, increase sharply in YAG crystal by the introduction of carbon. As-grown YAG:C crystal shows high TL sensitivity, and three main glow peaks at 390 K (P1), 465 K (P2), 524 K (P3) and two weak glow peaks at 580 and 625 K are found. The TL dose responses of the three main glow peaks show linear-supralinear characteristic, and wide linearity dose response are found in P1 and P2 glow peaks. The temperature position and TL intensity of three main glow peaks show a strong dependence of heating rate in YAG:C crystal.
Analytical solutions to the Navier–Stokes equations with density-dependent viscosity and with pressure
Authors: Yeung Ling Hei , Manwai Yuen
Published: August 2009

This article is the continued version of the analytical solutions for the pressureless Navier–Stokes equations with density-dependent viscosity [Yuen, M. W., “Analytical solutions to the Navier-Stokes equations,” J. Math. Phys. 49, 113102 (2008)]. We are able to extend the similar solution structure to the case with pressure under some restriction to the constants γ and θ.
Magnetohydrodynamic dissipation range spectra for isotropic viscosity and resistivity
Authors: Terry P. W. , Tangri V.
Published: August 2009

Dissipation range spectra for incompressible magnetohydrodynamic turbulence are derived for isotropic viscosity μ and resistivity η. The spectra are obtained from heuristic closures of spectral transfer correlations for cases with Pm=μ/η≤1, where Pm is the magnetic Prandtl number. Familiar inertial range power laws are modified by exponential factors that dominate spectral falloff in the dissipation range. Spectral forms are sensitive to alignment between flow and magnetic field. There are as many as four Kolmogorov wavenumbers that parametrize the transition between inertial and dissipative behavior and enter corresponding spectral forms. They depend on the values of the viscosity and resistivity and on the nature of alignment in inertial and dissipation ranges.
Accurate determination of the magnetic anisotropy in cluster-assembled nanostructures
Authors: Tamion Alexandre , Hillenkamp Matthias , Tournus Florent , Bonet Edgar , Dupuis Véronique
Published: August 2009

The simultaneous triple adjustment of experimental magnetization curves under different conditions is shown to allow the unambiguous and consistent determination of both the magnetic particle size distribution and anisotropy for granular nanostructures of Co clusters embedded in protective matrices. The importance of interface effects resulting in magnetically dead layers is demonstrated.
Complex emission dynamics of type-II GaSb/GaAs quantum dots
Authors: Gradkowski Kamil , Pavarelli Nicola , Ochalski Tomasz J. , Williams David P. , Tatebayashi Jun , Huyet Guillaume , O’Reilly Eoin P. , Huffaker Diana L.
Published: August 2009

Optical properties of the GaSb/GaAs quantum dot system are investigated using a time-resolved photoluminescence technique. In this type-II heterostructure the carriers of different species are spatially separated and, as a consequence, a smooth evolution of both the emission wavelength and decay timescale is observed. A wavelength shift of 170 nm is measured simultaneously with the progressive timescale change from 100 ps to 23 ns. These phenomena are explained by the evolution of the carrier density, which brings a modification to the optical transition probability as well as the shift in the emission toward the higher energies.
Shock-induced melting of (100)-oriented nitromethane: Structural relaxation
Authors: Siavosh-Haghighi Ali , Dawes Richard , Sewell Thomas D. , Thompson Donald L.
Published: August 2009

Molecules subjected to shock waves will, in general, undergo significant intramolecular distortion and exhibit large amplitude orientational and translational displacements relative to the unshocked material. The analysis of molecular dynamics simulations of strongly perturbed materials is complicated, particularly when the goal is to express time-dependent molecular-scale properties in terms of structural or geometric descriptors/properties defined for molecules in the equilibrium geometry. We illustrate the use of the Eckart–Sayvetz condition in a molecular dynamics study of the response of crystalline nitromethane subjected to supported shock waves propagating normal to (100). The simulations were performed with the nonreactive but vibrationally accurate force field due to Sorescu et al. [J. Phys. Chem. B 104, 8406 (2000)]. Shocks were initiated with impact velocities of Up=0.5, 1.0, 2.0, and 3.0 km s−1 in crystals at initial temperatures of T0=50 and 200 K. Statistical precision in the analysis was enhanced through the use of a spatiotemporal reference frame centered on the advancing shock front, which was located as a function of time using the gradient of the kinetic energy along the shock direction. The Eckart–Sayvetz condition provides a rigorous approach by which the alignment can be obtained between a coordinate frame for a perturbed molecule and one in a convenient reference frame (e.g., one based on the equilibrium crystal structure) for analyses of the molecules in the material as the system evolves toward equilibrium. Structural and dynamic properties of the material corresponding to orientation in the lattice, translational symmetry, and mass transport (orientational order parameters, two dimensional radial distribution functions, and self-diffusion coefficients, respectively) were computed as functions of time with 4 fs resolution. The results provide clear evidence of melting for shocks initiated by impacts of at least Up=2.0 km s−1 and provide insights into the evolution of changes at the molecular-mode level associated with the onset of the melting instability in shocked crystal.
Size dependent thermoelectric properties of silicon nanowires
Authors: Shi Lihong , Yao Donglai , Zhang Gang , Li Baowen
Published: August 2009

By using first-principles tight-binding electronic structure calculation and Boltzmann transport equation, we investigate the size dependence of thermoelectric properties of silicon nanowires (SiNWs). With cross section area increasing, the electrical conductivity increases slowly, while the Seebeck coefficient reduces remarkably. This leads to a quick reduction of cooling power factor with diameter. Moreover, the figure of merit also decreases with transverse size. Our results demonstrate that in thermoelectric application, NW with small diameter is preferred. We also predict that isotopic doping can increase the value of ZT significantly. With 50% S29i doping (S28i0.5 S29i0.5 NW), the ZT can be increased by 31%.
Formation of long-range ordered quantum dots arrays in amorphous matrix by ion beam irradiation
Authors: Buljan M. , Bogdanović-Radović I. , Karlušić M. , Desnica U. V. , Dražić G. , Radić N. , Dubček P. , Salamon K. , Bernstorff S. , Holý V.
Published: August 2009

We demonstrate the production of a well ordered three-dimensional array of Ge quantum dots in amorphous silica matrix. The ordering is achieved by ion beam irradiation and annealing of a multilayer film. Structural analysis shows that quantum dots nucleate along the direction of the ion beam used for irradiation, while the mutual distance of the quantum dots is determined by the diffusion properties of the multilayer material rather than the distances between traces of ions that are used for irradiation.
Full-configuration-interaction calculation of three-body nonadditive contribution to helium interaction potential
Authors: Cencek Wojciech , Patkowski Konrad , Szalewicz Krzysztof
Published: August 2009

The three-body nonadditive interaction energy between helium atoms was calculated at 253 trimer configurations using the full-configuration-interaction (FCI) method. The analytic potential fitted to these energies is the best current representation of the three-body nonadditive interactions between helium atoms. At the equilateral triangle configuration with R=5.6 bohr, near the minimum of the total potential, the nonadditive three-body energy calculated at the FCI level amounts to −88.5 mK, compared to −98.5 mK at the coupled cluster with single, double, and noniterative triple excitations [CCSD(T)] level. The uncertainty of the former result resulting from basis set incompleteness is estimated to be 1.5 mK. The relative uncertainty of our present complete three-body fit, including the uncertainties resulting from the fitting procedure, is estimated at 2%, a fivefold improvement over the previous best potential. Overall, the FCI contribution beyond CCSD(T) is rather important, being of the same order of magnitude as the uncertainty of the sum of two-body interactions. The inclusion of this contribution makes uncertainties of the total trimer interaction energies dominated by the uncertainties of the two-body component.
Autophagy genes protect against
Salmonella typhimurium
infection and mediate insulin signaling-regulated pathogen resistance
Authors: Jia Kailiang , Thomas Collin , Akbar Muhammad , Sun Qihua , Adams-Huet Beverley , Gilpin Christopher , Levine Beth
Published: August 2009

A conserved insulin-like pathway modulates both aging and pathogen resistance in
Caenorhabditis elegans
. However, the specific innate effector functions that mediate this pathogen resistance are largely unknown. Autophagy, a lysosomal degradation pathway, plays a role in controlling intracellular bacterial pathogen infections in cultured cells, but less is known about its role at the organismal level. We examined the effects of autophagy gene inactivation on
Salmonella enterica
Serovar Typhimurium (
Salmonella typhimurium
) infection in 2 model organisms,
Caenorhabditis elegans
and
Dictyostelium discoideum
. In both organisms, genetic inactivation of the autophagy pathway increases bacterial intracellular replication, decreases animal lifespan, and results in apoptotic-independent death. In
C. elegans
, genetic knockdown of autophagy genes abrogates pathogen resistance conferred by a loss-of-function mutation,
daf-2(e1370)
, in the insulin-like tyrosine kinase receptor or by over-expression of the DAF-16 FOXO transcription factor. Thus, autophagy genes play an essential role in host defense in vivo against an intracellular bacterial pathogen and mediate pathogen resistance in long-lived mutant nematodes.
Highly pathogenic H5N1 influenza virus can enter the central nervous system and induce neuroinflammation and neurodegeneration
Authors: Jang Haeman , Boltz David , Sturm-Ramirez Katharine , Shepherd Kennie R. , Jiao Yun , Webster Robert , Smeyne Richard J.
Published: August 2009

One of the greatest influenza pandemic threats at this time is posed by the highly pathogenic H5N1 avian influenza viruses. To date, 61% of the 433 known human cases of H5N1 infection have proved fatal. Animals infected by H5N1 viruses have demonstrated acute neurological signs ranging from mild encephalitis to motor disturbances to coma. However, no studies have examined the longer-term neurologic consequences of H5N1 infection among surviving hosts. Using the C57BL/6J mouse, a mouse strain that can be infected by the A/Vietnam/1203/04 H5N1 virus without adaptation, we show that this virus travels from the peripheral nervous system into the CNS to higher levels of the neuroaxis. In regions infected by H5N1 virus, we observe activation of microglia and alpha-synuclein phosphorylation and aggregation that persists long after resolution of the infection. We also observe a significant loss of dopaminergic neurons in the substantia nigra pars compacta 60 days after infection. Our results suggest that a pandemic H5N1 pathogen, or other neurotropic influenza virus, could initiate CNS disorders of protein aggregation including Parkinson's and Alzheimer's diseases.
Chromosome 14 transfer and functional studies identify a candidate tumor suppressor gene,
Mirror image polydactyly 1
, in nasopharyngeal carcinoma
Authors: Cheung Arthur Kwok Leung , Lung Hong Lok , Ko Josephine Mun Yee , Cheng Yue , Stanbridge Eric J. , Zabarovsky Eugene R. , Nicholls John M. , Chua Daniel , Tsao Sai Wah , Guan Xin-Yuan , Lung Maria Li
Published: August 2009

Chromosome 14 allelic loss is common in nasopharyngeal carcinoma (NPC) and may reflect essential tumor suppressor gene loss in tumorigenesis. An intact chromosome 14 was transferred to an NPC cell line using a microcell-mediated chromosome transfer approach. Microcell hybrids (MCHs) containing intact exogenously transferred chromosome 14 were tumor suppressive in athymic mice, demonstrating that intact chromosome 14 NPC MCHs are able to suppress tumor growth in mice. Comparative analysis of these MCHs and their derived tumor segregants identified 4 commonly eliminated tumor-suppressive CRs. Here we provide functional evidence that a gene,
Mirror-Image POLydactyly 1 (MIPOL1)
, which maps within a single 14q13.1–13.3 CR and that hitherto has been reported to be associated only with a developmental disorder, specifically suppresses in vivo tumor formation.
MIPOL1
gene expression is down-regulated in all NPC cell lines and in ≈63% of NPC tumors via promoter hypermethylation and allelic loss.
SLC25A21
and
FOXA1
, 2 neighboring genes mapping to this region, did not show this frequent down-regulated gene expression or promoter hypermethylation, precluding possible global methylation effects and providing further evidence that
MIPOL1
plays a unique role in NPC. The protein localizes mainly to the nucleus. Re-expression of
MIPOL1
in the stable transfectants induces cell cycle arrest.
MIPOL1
tumor suppression is related to up-regulation of the p21(WAF1/CIP1) and p27(KIP1) protein pathways. This study provides compelling evidence that chromosome 14 harbors tumor suppressor genes associated with NPC and that a candidate gene,
MIPOL1
, is associated with tumor development.
Folded biomimetic oligomers for enantioselective catalysis
Authors: Maayan Galia , Ward Michael D. , Kirshenbaum Kent
Published: August 2009

Many naturally occurring biopolymers (i.e., proteins, RNA, DNA) owe their unique properties to their well-defined three-dimensional structures. These attributes have inspired the design and synthesis of folded architectures with functions ranging from molecular recognition to asymmetric catalysis. Among these are synthetic oligomeric peptide (“foldamer”) mimics, which can display conformational ordering at short chain lengths. Foldamers, however, have not been explored as platforms for asymmetric catalysis. This report describes a library of synthetic helical “peptoid” oligomers that enable enantioselective transformations at an embedded achiral catalytic center, as illustrated by the oxidative kinetic resolution of 1-phenylethanol. In an investigation aimed at elucidating key structure–function relationships, we have discovered that the enantioselectivity of the catalytic peptoids depends on the handedness of the asymmetric environment derived from the helical scaffold, the position of the catalytic center along the peptoid backbone, and the degree of conformational ordering of the peptoid scaffold. The transfer of chiral information from a folded scaffold can enable the use of a diverse assortment of embedded achiral catalytic centers, promising a generation of synthetic foldamer catalysts for enantioselective transformations that can be performed under a broad range of reaction environments.
Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism
Authors: Clayton T. Andrew , Baker David , Lindon John C. , Everett Jeremy R. , Nicholson Jeremy K.
Published: August 2009

We provide a demonstration in humans of the principle of pharmacometabonomics by showing a clear connection between an individual's metabolic phenotype, in the form of a predose urinary metabolite profile, and the metabolic fate of a standard dose of the widely used analgesic acetaminophen. Predose and postdose urinary metabolite profiles were determined by1H NMR spectroscopy. The predose spectra were statistically analyzed in relation to drug metabolite excretion to detect predose biomarkers of drug fate and a human-gut microbiome cometabolite predictor was identified. Thus, we found that individuals having high predose urinary levels ofp-cresol sulfate had low postdose urinary ratios of acetaminophen sulfate to acetaminophen glucuronide. We conclude that, in individuals with high bacterially mediatedp-cresol generation, competitive O-sulfonation ofp-cresol reduces the effective systemic capacity to sulfonate acetaminophen. Given that acetaminophen is such a widely used and seemingly well-understood drug, this finding provides a clear demonstration of the immense potential and power of the pharmacometabonomic approach. However, we expect many other sulfonation reactions to be similarly affected by competition withp-cresol and our finding also has important implications for certain diseases as well as for the variable responses induced by many different drugs and xenobiotics. We propose that assessing the effects of microbiome activity should be an integral part of pharmaceutical development and of personalized health care. Furthermore, we envisage that gut bacterial populations might be deliberately manipulated to improve drug efficacy and to reduce adverse drug reactions.
Sexual development in the industrial workhorse
Trichoderma reesei
Authors: Seidl Verena , Seibel Christian , Kubicek Christian P. , Schmoll Monika
Published: August 2009

Filamentous fungi are indispensable biotechnological tools for the production of organic chemicals, enzymes, and antibiotics. Most of the strains used for industrial applications have been—and still are—screened and improved by classical mutagenesis. Sexual crossing approaches would yield considerable advantages for research and industrial strain improvement, but interestingly, industrially applied filamentous fungal species have so far been considered to be largely asexual. This is also true for the ascomycete
Trichoderma reesei
(anamorph of
Hypocrea jecorina
), which is used for production of cellulolytic and hemicellulolytic enzymes. In this study, we report that
T. reesei
QM6a has a
MAT1-2
mating type locus, and the identification of its respective mating type counterpart,
MAT1-1
, in natural isolates of
H. jecorina
, thus proving that this is a heterothallic species. After being considered asexual since its discovery more than 50 years ago, we were now able to induce sexual reproduction of
T. reesei
QM6a and obtained fertilized stromata and mature ascospores. This sexual crossing approach therefore opens up perspectives for biotechnologically important fungi. Our findings provide a tool for fast and efficient industrial strain improvement in
T. reesei
, thus boosting research toward economically feasible biofuel production. In addition, knowledge of
MAT
-loci and sexual crossing techniques will facilitate research with other
Trichoderma
spp. relevant for agriculture and human health.
XIAP mediates NOD signaling via interaction with RIP2
Authors: Krieg Andreas , Correa Ricardo G. , Garrison Jason B. , Le Negrate Gaëlle , Welsh Kate , Huang Ziwei , Knoefel Wolfram T. , Reed John C.
Published: August 2009

NOD1 and NOD2 are members of the NOD-like receptor (NLR) protein family that are involved in sensing the presence of pathogens and are a component of the innate immune system. Upon activation by specific bacterial peptides derived from peptidoglycans, NODs interact via a CARD-CARD interaction with the receptor-interacting protein kinase RIP2, an inducer of NF-κB activation. In this report, we show that NOD signaling is dependent on XIAP, a member of the inhibitor of apoptosis protein (IAP) family. Cells deficient in XIAP exhibit a marked reduction in NF-κB activation induced by microbial NOD ligands and by over-expression of NOD1 or NOD2. Moreover, we show that XIAP interacts with RIP2 via its BIR2 domain, which could be disrupted by XIAP antagonists SMAC and SMAC-mimicking compounds. Both NOD1 and NOD2 associated with XIAP in a RIP2-dependent manner, providing evidence that XIAP associates with the NOD signalosome. Taken together, our data suggest a role for XIAP in regulating innate immune responses by interacting with NOD1 and NOD2 through interaction with RIP2.
Restriction of dopamine signaling to the dorsolateral striatum is sufficient for many cognitive behaviors
Authors: Darvas Martin , Palmiter Richard D.
Published: August 2009

The striatum is a vital substrate for performance, procedural memory, and learning. The ventral and medial striatum are thought to be critical for acquisition of tasks while the dorsolateral striatum is important for performance and habitual enactment of skills. Evidence based on cortical, thalamic, and amygdaloid inputs to the striatum suggests a medio-lateral zonation imposed on the classical dorso-ventral distinction. We therefore investigated the functional significance of dopaminergic signaling in cognitive tasks by studying dopamine-deficient (DD) mice and mice with dopamine signaling restored to only the dorsolateral (DL) striatum by viral rescue (vrDD-DL mice). Whereas DD mice failed in all of the tasks examined here, vrDD-DL mice displayed intact discriminatory learning, object recognition, visuospatial learning and spatial memory. Acquisition of operant behavior for food rewards was delayed in vrDD-DL mice and their motivation in a progressive ratio experiments was reduced. Therefore, dopaminergic signaling in the dorsolateral striatum is sufficient for mice to learn several different cognitive tasks although the rate of learning some of them was reduced. These results indicate that dopaminergic signaling in the ventromedial striatum is not absolutely necessary for mastery of these behaviors, but may facilitate them.
Neural encoding of auditory discrimination in ventral premotor cortex
Authors: Lemus Luis , Hernández Adrián , Romo Ranulfo
Published: August 2009

Monkeys have the capacity to accurately discriminate the difference between two acoustic flutter stimuli. In this task, monkeys must compare information about the second stimulus to the memory trace of the first stimulus, and must postpone the decision report until a sensory cue triggers the beginning of the decision motor report. The neuronal processes associated with the different components of this task have been investigated in the primary auditory cortex (A1); but, A1 seems exclusively associated with the sensory and not with the working memory and decision components of this task. Here, we show that ventral premotor cortex (VPC) neurons reflect in their activities the current and remembered acoustic stimulus, their comparison, and the result of the animal's decision report. These results provide evidence that the neural dynamics of VPC is involved in the processing steps that link sensation and decision-making during auditory discrimination.
Spectro-temporal modulation transfer function of single voxels in the human auditory cortex measured with high-resolution fMRI
Authors: Schönwiesner Marc , Zatorre Robert J.
Published: August 2009

Are visual and auditory stimuli processed by similar mechanisms in the human cerebral cortex? Images can be thought of as light energy modulations over two spatial dimensions, and low-level visual areas analyze images by decomposition into spatial frequencies. Similarly, sounds are energy modulations over time and frequency, and they can be identified and discriminated by the content of such modulations. An obvious question is therefore whether human auditory areas, in direct analogy to visual areas, represent the spectro-temporal modulation content of acoustic stimuli. To answer this question, we measured spectro-temporal modulation transfer functions of single voxels in the human auditory cortex with functional magnetic resonance imaging. We presented dynamic ripples, complex broadband stimuli with a drifting sinusoidal spectral envelope. Dynamic ripples are the auditory equivalent of the gratings often used in studies of the visual system. We demonstrate selective tuning to combined spectro-temporal modulations in the primary and secondary auditory cortex. We describe several types of modulation transfer functions, extracting different spectro-temporal features, with a high degree of interaction between spectral and temporal parameters. The overall low-pass modulation rate preference of the cortex matches the modulation content of natural sounds. These results demonstrate that combined spectro-temporal modulations are represented in the human auditory cortex, and suggest that complex signals are decomposed and processed according to their modulation content, the same transformation used by the visual system.
Postischemic PKC activation rescues retrograde and anterograde long-term memory
Authors: Sun Miao-Kun , Hongpaisan Jarin , Alkon Daniel L.
Published: August 2009

Therapeutics for cerebral ischemia/hypoxia, which often results in ischemic stroke in humans, are a global unmet medical need. Here, we report that bryostatin-1, a highly potent protein kinase C (PKC) activator, interrupts pathophysiological molecular cascades and apoptosis triggered by cerebral ischemia/hypoxia, enhances neurotrophic activity, and induces synaptogenesis in rats. This postischemic therapeutic approach is further shown to preserve learning and memory capacity even 4 months later as well as long-term memory induced before the ischemic event. Our results of electromicroscopic and immunohistochemical analyses of neuronal and synaptic ultra-structure are consistent with a PKC-mediated synaptic remodeling and repair process that confers long-lasting preservation of spatial learning and memory before and after the cerebral ischemic/hypoxic event, suggesting a previously undescribed therapeutic modality for cerebral ischemia/hypoxia and ischemic stroke.
Feedback control of regulatory T cell homeostasis by dendritic cells in vivo
Authors: Darrasse-Jèze Guillaume , Deroubaix Stephanie , Mouquet Hugo , Victora Gabriel D. , Eisenreich Thomas , Yao Kai-hui , Masilamani Revati F. , Dustin Michael L. , Rudensky Alexander , Liu Kang , Nussenzweig Michel C.
Published: August 2009

CD4+CD25+Foxp3+ natural regulatory T cells (T reg cells) maintain self-tolerance and suppress autoimmune diseases such as type 1 diabetes and inflammatory bowel disease (IBD). In addition to their effects on T cells, T reg cells are essential for maintaining normal numbers of dendritic cells (DCs): when T reg cells are depleted, there is a compensatory Flt3-dependent increase in DCs. However, little is known about how T reg cell homeostasis is maintained in vivo. We demonstrate the existence of a feedback regulatory loop between DCs and T reg cells. We find that loss of DCs leads to a loss of T reg cells, and that the remaining T reg cells exhibit decreased Foxp3 expression. The DC-dependent loss in T reg cells leads to an increase in the number of T cells producing inflammatory cytokines, such as interferon γ and interleukin 17. Conversely, increasing the number of DCs leads to increased T reg cell division and accumulation by a mechanism that requires major histocompatibility complex II expression on DCs. The increase in T reg cells induced by DC expansion is sufficient to prevent type 1 autoimmune diabetes and IBD, which suggests that interference with this feedback loop will create new opportunities for immune-based therapies.