bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting turbulence in flows with strong stable stratification
Authors: Hebert David A. , de Bruyn Kops Stephen M.
Published: July 2006

High resolution direct numerical simulations are used to understand how turbulence can be predicted in flows subject to strong stable stratification. It is observed that shear instabilities are the predominant cause of turbulence in the simulations, which supports the derivation of a Froude-Reynolds number scaling to predict turbulence in this flow regime. It is found that when the autocorrelation length of the horizontal velocities is used as the length scale for the Froude and Reynolds number then that length scale, the Froude number, and the Reynolds number all evolve, as theory suggests. An advection length scale based on the kinetic energy and its dissipation rate is found not to be of practical use for characterizing the flow. Finally, it is observed the Froude-Reynolds number parameter of Riley and de Bruyn Kops is very similar to the commonly used buoyancy Reynolds number. This suggests that a shear-based approach to parametrizing turbulence under stable stratification, rather than the ratio-of-length-scales approach that is often used as the physical justification for the buoyancy Reynolds number, might be appropriate. While the Froude-Reynolds parameter and the buoyancy Reynolds number are closely related, the former may be the more useful when configuring laboratory experiments or numerical simulations since it can be estimated a priori.
On the extension of the Boussinesq approximation for inertia dominated flows
Authors: Shirgaonkar Anup A. , Lele Sanjiva K.
Published: July 2006

We examine the validity of the Boussinesq approximation for shallow flows with stratification where the atmosphere can be incompressible or compressible, with possible existence of strong base flow motion and externally imposed small initial density perturbations. It is known that the “incompressible fluid” Boussinesq approximation when applied to a compressible atmosphere predicts an incorrect Brunt-Väisälä frequency. We deduce a nondimensional parameter for selecting the appropriate equations depending on the compressibility of the medium. An asymptotic reduction of the compressible Navier-Stokes equations is used to elucidate various physical aspects such as small entropy perturbations in the initial conditions, stratification, and the existence of a time-varying, three-dimensional base flow for a general (compressible or incompressible) fluid. The final equations are uniformly valid for combinations of these effects. An extension to the Boussinesq approximation is proposed to take into account the interaction of density perturbations and flow inertia. It is shown that only a minimal modification to the traditional Boussinesq algorithm is required for efficient and accurate numerical solution of the extended equations for many practical flows.
Simulating flow of DNA suspension using dissipative particle dynamics
Authors: Fan Xijun , Phan-Thien Nhan , Chen Shuo , Wu Xuhong , Yong Ng Teng
Published: July 2006

We simulate DNA suspension microchannel flows using the dissipative particle dynamics (DPD) method. Two developments make this simulation more realistic. One is to improve the dynamic characteristics of a DPD system by modifying the weighting function of the dissipative force and increasing its cutoff radius, so that the Schmidt number can be increased to a practical level. Another is to set up a wormlike chain model in the DPD framework, according to the measured extension properties of a DNA molecule in uniform flows. This chain model is then used to study flows of a DNA suspension through microchannels. Interesting results on the conformation evolution of DNA molecules passing through the microchannels, including periodic contraction-diffusion microchannels, are reported.
Evolution of a compound droplet attached to a core-shell nozzle under the action of a strong electric field
Authors: Reznik S. N. , Yarin A. L. , Zussman E. , Bercovici L.
Published: July 2006

The shape evolution of small compound droplets at the exit of a core-shell system in the presence of a sufficiently strong electric field is studied both experimentally and theoretically. It is shown that the jetting effect at the tip of the shell nozzle does not necessarily cause entrainment of the core fluid, in which case the co-electrospinning process fails to produce core-shell nanofibers. The remedy lies in extending the core nozzle outside its shell counterpart by about half the radius of the latter. The results also show that the free charges migrate very rapidly from both fluids and their interface to the free surface of the shell. This reflects the fact that most of the prejetting evolution of the droplet can be effectively described in terms of the perfect conductor model, even though the fluids can be characterized as leaky dielectrics. The stress level at the core-shell interface is of the order of 5×103g∕(cms2), the relevant value in assessing the viability of viruses, bacteria, DNA molecules, drugs, enzymes, chromophores, and proteins to be encapsulated in nanofibers via co-electrospinning.
Spin coating of thin liquid films on an axisymmetrically heated disk
Authors: Wu Lin
Published: July 2006

Spin coating of nonvolatile thin liquid films on an axisymmetrically heated disk is studied numerically under lubrication and zero Biot number assumptions. Important effects such as viscosity, centrifugal force, external air shearing, surface tension, disjoining pressure, thermocapillarity (temperature dependent surface tension), and thermoviscosity (temperature dependent viscosity) are included in the simulation. Both thermocapillarity and thermoviscosity effects are shown to be able to significantly enhance the film depletion rate when the disk center is at a higher temperature than the disk outer edge. The enhancing effect of thermoviscosity on the film depletion is not sensitive to the film thickness change and is larger than that of the external air shearing even at a moderate radial temperature difference applied to the disk. The thermocapillarity effect on the film depletion is negligible at the earlier stage of spin coating when the film thickness is relatively large, but its significance increases and eventually becomes dominant when the film thickness is further reduced. When the applied disk temperature profile has a steep change, a double shock structure for the liquid film is generated. Measurement of the anchored shock profile may provide an alternative mechanism to determine the viscosity change with temperature of wall bounded thin liquid films.
Mean and turbulence structures of Couette-Poiseuille flows at different mean shear rates in a square duct
Authors: Lo Wei , Lin Chao-An
Published: July 2006

Turbulent Couette-Poiseuille flows inside a square duct at bulk Reynolds number 9700 are investigated using the large eddy simulation technique. Suppression of turbulence intensities and a tendency towards rod-like axisymmetric turbulence state at the wall bisector near the moving wall are identified. The turbulence generated secondary flow is modified by the presence of the top moving wall, where the symmetric vortex pattern vanishes. The angle between the two top vortices is found to correlate with the ratio of moving wall velocity to duct bulk velocity.
Secondary circulations in Holmboe waves
Authors: Smyth William D.
Published: July 2006

A sequence of direct simulations is used to study mechanisms for the growth of secondary circulations and turbulence in stratified shear flows. Five cases are examined, of which four deliver Holmboe waves as the primary instability and the fifth generates Kelvin-Helmholtz billows. Secondary circulations range in strength from weak, laminar motions to turbulence that destroys the parent wave. Processes that drive disturbance growth include shear production via the Orr mechanism, sheared convection in overturned regions, and sloping convection in stably stratified wave crests. Results are compared with previous predictions based on normal mode stability analysis.
Steady solutions of the Navier-Stokes equations by selective frequency damping
Authors: Åkervik Espen , Brandt Luca , Henningson Dan S. , Hœpffner Jérôme , Marxen Olaf , Schlatter Philipp
Published: July 2006

A new method, enabling the computation of steady solutions of the Navier-Stokes equations in globally unstable configurations, is presented. We show that it is possible to reach a steady state by damping the unstable (temporal) frequencies. This is achieved by adding a dissipative relaxation term proportional to the high-frequency content of the velocity fluctuations. Results are presented for cavity-driven boundary-layer separation and a separation bubble induced by an external pressure gradient.
Taylor dispersion in cyclic electric field-flow fractionation
Authors: Chen Zhi , Chauhan Anuj
Published: July 2006

Electric field-flow fractionation (EFFF), which combines a constant lateral electric field with an axial pressure-driven flow, can separate polyelectrolytes of different sizes in free solution. In large EFFF devices, fields are required to accomplish sharp resolution and such large fields can effectively immobilize the colloidal particles at the wall [Caldwell et al., Science 176, 269 (1972)]. Furthermore, particles with the same values of D∕uye cannot be separated by EFFF, where D is the molecular diffusivity and uye is the electric field driven velocity on the lateral direction. It has been suggested that some of the difficulties associated with EFFF could be eliminated by using a cyclic transverse electric field [J. C. Giddings, Anal. Chem. 58, 2052 (1986)]. This technique in which a transverse cyclic electric field is combined with axial Poiseuille flow is called cyclic electric field-flow fractionation (CEFFF). In this paper, a multiple time scale analysis and regular expansions in the aspect ratio are used to determine the mean velocity and the dispersion coefficient of molecules in CEFFF. This problem was first studied for the case of large Peclet number and square wave electric fields by Shapiro and Brenner [M. Shapiro and H. Brenner, Phys. Fluids A 2, 1731 (1990)]. We extend the results of their study by developing results for both square wave and sinusoidal fields that are valid for all Peclet numbers. The dimensionless mean velocity (U¯*) depends on the dimensionless frequency (Ω) and the product of the Peclet number (Pe) and the dimensionless amplitude of the lateral velocity driven by the applied field (R). The convective contribution to the dispersion coefficient is of the form Pe2f(PeR,Ω). We also obtain the expressions for the mean velocity and the dispersion coefficient in the limit of small Ω. In this limit the results are essentially the time average of the unidirectional-EFFF results. Also, the mean velocities and dispersion are calculated for the case of square wave electric field and these results are compared with the large Peclet asymptotic results that were obtained by Shapiro and Brenner [M. Shapiro and H. Brenner, Phys. Fluids A 2, 1744 (1990)]. The results of mean velocity and dispersion coefficient for the square wave are also compared with those for sinusoidal fields.
Effect of initial conditions on interaction between a boundary layer and a wall-mounted finite-length-cylinder wake
Authors: Wang H. F. , Zhou Y. , Chan C. K. , Lam K. S.
Published: July 2006

The effects of initial conditions on interaction between a boundary layer over a flat plate and flow around a wall-mounted finite-length cylinder were experimentally investigated. A square cylinder with a characteristic width (d) of 20mm and a length of H=5d was vertically mounted on a horizontal flat plate. Three different boundary layers were investigated, their momentum thickness being 0.07d, 0.13d, and 0.245d, respectively, measured at the cylinder axis in the absence of the cylinder. All the experiments were carried out in a closed-loop water tunnel at a Reynolds numbers of 11 500 based on d and the free-stream velocity U∞. It is found that initial boundary layer conditions have a profound effect on the near wake, including the flow near the cylinder free end that is well beyond the boundary layer. With increasing boundary layer thickness, the base vortex is enhanced, inducing a stronger upwash flow from the cylinder base, which acts to weaken the downwash free-end shear layer and the tip vortex. Consequently, spanwise vortices gain strength near the free end but impair near the wall, causing the ratio of symmetrically to antisymmetrically arranged vortices to vary and subsequently the Reynolds stresses to increase significantly in magnitude near the free end but to decrease near the wall.
Hole dynamics in polymer Langmuir films
Authors: Alexander James C. , Bernoff Andrew J. , Mann Elizabeth K. , Mann J. Adin , Zou Lu
Published: July 2006

This article develops a model for the closing of a gaseous hole in a liquid domain within a two-dimensional fluid layer coupled to a Stokesian subfluid substrate, and compares this model to experiments following hole dynamics in a polymer Langmuir monolayer. Closure of such a hole in a fluid layer is driven by the line tension at the hole boundary and the difference in surface pressure within the hole and far outside it. The observed rate of hole closing is close to that predicted by our model using estimates of the line tension obtained by other means, assuming that the surface pressure in the gas is negligible. This result both supports the model and suggests an independent means of determining the line tension. Unlike most previous hydrodynamics models of Langmuir films, the closing of a hole necessarily involves vertical motion of the underlying incompressible fluid. Fluid is dragged along with the liquid monolayer towards the center of the hole, and must plunge away from the surface. An explicit expression is found for this vertical fluid flow in the bulk substrate.
Properties of the particle velocity field in gas-solid turbulent channel flow
Authors: Vance Marion W. , Squires Kyle D. , Simonin Olivier
Published: July 2006

Spatial characteristics of the particle velocity field are investigated using numerical simulations of gas-solid turbulent channel flow. The carrier phase is resolved using large eddy simulation (LES) of the incompressible Navier-Stokes equations. The dispersed phase is computed using Lagrangian tracking in which particle motion is governed by the drag force. Predictions of dispersed phase transport are obtained for three particle response times in simulations with and without interparticle collisions. Spatial correlations of the particle velocity field are measured in planes parallel to the wall and exhibit a discontinuity at the origin. The discontinuity in the spatial correlations is consistent with recent work by Fevrier et al. [J. Fluid Mech., 533, 1 (2005)] that shows the velocity of a particle is comprised of a contribution from a continuous field, shared by all the particles, and a random velocity component that is not spatially correlated. Analysis of the simulation database shows that the random component of the particle velocity increases with increasing particle response time. The influence of interparticle collisions leads to a changes in the partitioning of the particle velocity, with a greater fraction residing in the uncorrelated component compared to the correlated part.
Accumulation of heavy particles in N-vortex flow on a disk
Authors: IJzermans Rutger H.A. , Hagmeijer Rob
Published: July 2006

The motion of heavy particles in potential vortex flows on the unit disk is investigated theoretically and numerically. Configurations with one vortex and with two vortices are considered. In both cases, each vortex follows a regular path on the disk. In the one-vortex case, it is shown that small, heavy particles may accumulate in elliptic regions of the flow, counter-rotating with respect to the vortex. When the particle Stokes number exceeds a threshold depending on the vortex configuration, all particles are expelled from the circular domain. A stability criterion for particle accumulation is derived analytically and verified by numerical results. In the two-vortex case, heavy particles are shown to accumulate in elliptic islands of regular motion. Again, this result is explained by a stability analysis. The results may be useful in the design of gas-particle separators containing a helical vortex filament.
Influence of variable Froude number on waves generated by ships in shallow water
Authors: Torsvik Tomas , Dysthe Kristian , Pedersen Geir
Published: July 2006

Passage through the transcritical speed region of a moving disturbance in a shallow channel, is examined using numerical simulations based on a set of forced Boussinesq equations. The transition is accomplished either by accelerating the wave generating disturbance in a region of constant depth or by moving the disturbance with constant speed over a sloping bottom topography. A series of test cases are examined where the transcritical region is traversed both from subcritical to supercritical speed and vice versa. Results show that the generation of upstream solitary waves depends on the time required for the transition, with large waves being generated for long transition times. It is also apparent that the shape of the wave pattern, and the maximum amplitude of the waves, differ significantly depending on whether the Froude number increase or decrease during the transition of the transcritical region. However, the wave pattern is not determined simply in terms of the Froude number. The strength of the forcing term as well as the underlying process which cause the Froude number to vary, i.e., acceleration and depth variation, influence the wave pattern in different ways. The Froude number is none the less a useful indicator for the problem, as all cases with similar Froude number variations share some common characteristic features.
Linear and nonlinear Rayleigh-Taylor growth at strongly convergent spherical interfaces
Authors: Clark Daniel S. , Tabak Max
Published: July 2006

Recent attention has focused on the effect of spherical convergence on the nonlinear phase of Rayleigh-Taylor growth. For instability growth on spherically converging interfaces, modifications to the predictions of the Layzer model for the secular growth of a single, nonlinear mode have been reported [D. S. Clark and M. Tabak, Phys. Rev. E 72, 056308 (2005)]. However, this model is limited in assuming a self-similar background implosion history as well as only addressing growth from a perturbation of already nonlinearly large amplitude. Additionally, only the case of single mode growth was considered and not the multimode growth of interest in applications. Here, these deficiencies are remedied. First, the connection of the recent nonlinear results (including convergence) to the well-known results for the linear regime of growth is demonstrated. Second, the applicability of the model to more general implosion histories (i.e., not self-similar) is shown. Finally, to address the case of multimode growth with convergence, the recent nonlinear single mode results are combined with the Haan model formulation for weakly nonlinear multimode growth. Remarkably, convergence in the nonlinear regime is found not to modify substantially the multimode predictions of Haan’s original model.
Shear-flow and thermocapillary interfacial instabilities in a two-layer viscous flow
Authors: Wei Hsien-Hung
Published: July 2006

Combined effects of shear-flow and thermocapillary instabilities in a two-layer Couette flow are asymptotically examined in the thin-layer limit. The basic features of the system instability are revealed by first analyzing the two-dimensional stability problem. A scaling analysis is devised to identify dominant mechanisms in various parameter regimes. With an appropriate scaling, the leading order linear stability is reduced to a one-dimensional evolution equation containing a nonlocal contribution from viscosity stratification. Viscosity stratification destabilizes (stabilizes) the system with a more (less) viscous film, but the effect can be compromised by thermocapillary stabilization (destabilization) as the film is cooled (heated). Thermocapillary effects dominate over viscosity stratification effects for short-wave perturbations albeit the latter could be stronger than the former for long waves. The competition between these two effects gives rise to the critical Reynolds number for the onset of stability/instability. A nontrivial interplay is found within a window in the weak interfacial-tension regime. It demonstrates a possibility of the existence of two neutral states in the wavenumber space. The three-dimensional problem is also examined. For the first time, a two-dimensional film evolution equation with the inclusion of a nonlocal term is systematically derived for the corresponding stability. It can be shown analytically that three-dimensional perturbations can be more unstable than two-dimensional ones due to thermocapillarity in line with the nonexistence of Squires’ theorem. The three-dimensional problem has the critical Reynolds number larger than the two-dimensional problem, but an instability in the latter does not necessarily suggest an instability in the former. An extension of each problem to the weakly nonlinear regime is also discussed in the context of the Kuramoto-Sivashinsky equation.
Experimental study of liquid metal channel flow under the influence of a nonuniform magnetic field
Authors: Andreev O. , Kolesnikov Yu. , Thess A.
Published: July 2006

We present an experimental study of a liquid metal flow in a rectangular channel under the influence of an inhomogeneous magnetic field. This is a fundamental problem of liquid metal magnetohydrodynamics that is relevant to the technique of electromagnetic braking in the process of continuous casting of steel as well as for Lorentz force velocimetry. Based on local velocity and electric potential measurements we identify three distinct flow regions; namely (i) a turbulence suppression region, (ii) a vortical region, and (iii) a wall jet region. It is shown that in region (i) the applied inhomogeneous magnetic field brakes the incoming flow in its central part and transforms the velocity profile, which is initially flat, into an M-shaped form. In the central part of the flow, the intensity of the velocity fluctuations is found to decrease strongly. In region (ii) where the magnetic field is strongest, the flow is characterized by large-scale vortical structures which are time dependent for certain values of the control parameters. In region (iii), downstream of the magnetic system, two sidewall boundary layers are observed which generate velocity fluctuations with intensity up to 25% of the mean flow. These boundary layers bear close resemblance to wall jets known from ordinary hydrodynamics. Our experimental data provide a comprehensive database against which numerical simulations and turbulence models can be tested.
Effect of particle distribution on the compaction behavior of granular beds
Authors: Lowe C. A. , Longbottom A. W.
Published: July 2006

This research determines how particle size and particle distribution affects the compaction of granular beds. A modelling and experimental effort was recently designed to compare the compaction behavior of two types of granular HMX: prepressed conventional (coarse) HMX material (mean diameter of 40μm) and microfine HMX (mean diameter <5μm) [M. Greenaway, Journal of Applied Physics 97, 093521 (2005)]. The microfine material demonstrated higher levels of granular bed strength. Mesoscale modelling of granular beds that are of fixed initial solid volume fraction but vary in particle size and distribution have been undertaken that include a simple elastic-plastic strength model. These suggest that it is not inherently the “size” of a particle that controls the bed strength but the morphology and distribution of particle grains. These solutions are compared with the behavior predicted from continuum scale models of material compaction.
Direct numerical simulations of the double scalar mixing layer. Part I: Passive scalar mixing and dissipation
Authors: Cha Chong M. , de Bruyn Kops Stephen M. , Mortensen Mikael
Published: July 2006

The double scalar mixing layer (DSML) is a canonical problem for studying the mixing of multiple streams and, with reaction, combustion of the partially premixed type. In a DSML, a third stream consisting of a premixture of the reactants is introduced in between the pure fuel and air streams of the classic twin-feed or binary mixing problem. The well-known presumed probability density function (PDF), such as the β-PDF, can adequately model passive scalar mixing for the binary mixing problem on which state-of-the-art turbulent combustion models such as conditional moment closure and flamelet approaches rely. However, the β-PDF model, now a standard in CFD simulation, cannot describe turbulent mixing involving multiple streams; e.g., the asymmetric three-stream mixing characterizing the DSML. In this paper, direct numerical simulations of the DSML are performed to make available a high-fidelity database for developing more general, fine-scale mixing models required to compute turbulent combustion problems of practical engineering interest, which usually involve mixing between multiple streams. In this first part of two investigations, nonreacting numerical experiments are presented with emphasis on the nontrivial distributions of the passive scalar and its dissipation rate. Mapping closure modeling is applied to describe the PDFs and conditional dissipation rates of a single mixture fraction.
Low-gravity sideways double-diffusive instabilities: Small wave number asymptotics
Authors: Kerr Oliver S. , Zebib Abdelfattah
Published: July 2006

When a stable salinity gradient in a vertical slot undergoes lateral heating, instabilities can arise. The level of heating required for instability can be several orders of magnitude smaller than is required in the absence of a salinity gradient. Previously it has been found that the portion of the stability boundary corresponding to this most unstable region could be derived using small wave number asymptotics. Although the leading order asymptotics are unaffected by consideration of vibration or g-jitter, it has been observed that the region of the stability boundary given by these asymptotics could be reduced or eliminated by increasing the level of vibration. Here we look at the higher order asymptotics and determine how vibration affects the stability boundary in the region of maximum instability.
A refined interpretation of the logarithmic structure function law in wall layer turbulence
Authors: Davidson P. A. , Krogstad P.-Å. , Nickels T. B.
Published: July 2006

It has been shown recently that the real-space equivalent of the k−1 law for near-wall turbulence is a logarithmic law for the second-order longitudinal structure function, ⟨(Δu)2⟩(r)=u*2(A+Bln(r∕y)). Here y is the distance from the wall, u* is the shear velocity, A and B are coefficients of order unity and r is measured in the streamwise direction. In this paper we provide theoretical arguments to suggest that, in the limit of large Reynolds number, B is a universal constant while A is of the form A=A′−Bln(P∕ϵ), where A′ is a universal constant and P and ϵ are the rates of production and dissipation of energy, respectively. Hence A is a weak, universal, function of y. Two independent sets of data are examined and it is shown that, to within experimental error, our predictions are consistent with the data.
Generalized hydrodynamic model for fluid flows: From nanoscale to macroscale
Authors: Guo Zhaoli , Zhao T. S. , Shi Yong
Published: July 2006

At the macroscale, the hydrodynamics of a fluid can be well described by conventional hydrodynamic models such as the Navier-Stokes equations. However, as the flow passage is shrunk down to the nanometer size, the micro-interaction between the fluid and the confined solid walls becomes significant, and the conventional hydrodynamic model will become insufficient for describing such a flow system. In this work, we propose a generalized hydrodynamic model that is derived from a recently developed kinetic model for strong inhomogeneous fluid systems [Guo, Zhao, and Shi, Phys. Rev. E 71, 035301(R) (2005)]. We show that the present model can reduce to other hydrodynamic models in certain limits, and can be used for flows ranging from nanoscale to macroscale. Based on this generalized model, the static and dynamic behaviors of several simple fluid systems are studied. It is shown that at a small scale, the results predicted by the generalized hydrodynamic model are in agreement with those simulated by the molecular dynamic and the Monte Carlo methods, while for flow systems at a large scale, the results agree with those by the Navier-Stokes equations.
Internal wave generation from rough topography
Authors: Aguilar D. A. , Sutherland B. R.
Published: July 2006

Through laboratory experiments we examine internal wave generation above and in the lee of finite-amplitude periodic topography having various degrees of roughness. We show that internal waves are generated not only by flow over the hills but also by flow over “boundary-trapped” lee waves and by vigorous turbulence created in the lee of sharp-crested hills. For low values of the excitation frequency, linear theory well predicts the internal wave frequencies but significantly overestimates the wave amplitudes because it neglects processes associated with boundary layer separation. When the excitation frequency exceeds the buoyancy frequency, turbulence results in the excitation of internal waves with frequencies approximately 0.72±0.05 of the buoyancy frequency and vertical displacement amplitudes ranging between 1.5% and 2% of the horizontal wavelength.
Growth of crack-free, carbon-doped GaN and AlGaN∕GaN high electron mobility transistor structures on Si (111) substrates by ammonia molecular beam epitaxy
Authors: Haffouz S. , Tang H. , Rolfe S. , Bardwell J. A.
Published: July 2006

The growth of C-doped GaN epilayers on p-Si (111) substrates by ammonia molecular beam epitaxy is reported. Highly insulating and crack-free 1.5-μm-thick C-doped GaN layers have been prepared using ionized methane as the dopant source. Using such a template, AlGaN∕GaN two-dimensional electron gas structures with a mobility of 1260cm2∕Vs for a sheet carrier density of 1.24×1013cm−2 have been achieved at room temperature. Fabricated devices demonstrated an excellent pinch-off characteristic as revealed by an on-to-off ratio higher than four orders of magnitudes and by very low leakage current (10μA∕mm at VDS=20V).
Dissipation mechanisms for convection in rapidly rotating spheres and the formation of banded structures
Authors: Morin Vincent , Dormy Emmanuel
Published: July 2006

We report banded zonal structures in numerical simulations of weakly nonlinear rapidly rotating convection. A quasigeostrophic model of convection is used to demonstrate how, in the presence of Ekman pumping, banded structures can develop immediately above the onset of convection, and in the absence of developed turbulence. We argue that these bands necessarily correspond to a regime in which both Ekman pumping and bulk viscosity equally affect the zonal flow and that their width scales with the Ekman number E as E1∕4.
Temperature dependent characteristics of λ∼3.8μm room-temperature continuous-wave quantum-cascade lasers
Authors: Yu J. S. , Evans A. , Slivken S. , Darvish S. R. , Razeghi M.
Published: July 2006

Temperature dependent characteristics of λ∼3.8μm quantum-cascade lasers (QCLs) operating up to 318K in continuous-wave (cw) mode are reported. A high-reflectivity coated 11.5-μm-wide and 4-mm-long epilayer-down bonded QCL using a diamond submount shows a considerable improved cw operation with an output power of 143mW and a threshold current density of 1.51kA∕cm2 at 298K. The temperature dependence on optical and electrical performances of the QCLs with respect to the output power, slope efficiency, threshold current/voltage, turn-on voltage, differential series resistance, and emission wavelength are investigated systematically above liquid nitrogen temperature.
Fabrication of stable Pd nanowire assisted by hydrogen in solution
Authors: Kiguchi Manabu , Murakoshi Kei
Published: July 2006

We have mechanically fabricated a Pd nanowire in solution under electrochemical potential control. A clear feature appeared in the conductance histogram when the electrochemical potential of the Pd wire was kept at the hydrogen evolution potential. Conductance traces showed the Pd wire was stretched 0.4nm in length just before breaking, suggesting that at least two Pd atoms might contribute to the formation of the Pd wire. The results indicate that a certain atomic configuration of the Pd nanowire is stabilized by hydrogen. We discuss the stabilization mechanism due to changes in bond strengths caused by hydrogen adsorption or incorporation.
Effects of n-type doping on active Fe sites in ion implanted Fe in InP
Authors: Amore Bonapasta A. , Filippone F. , Gasparotto A. , Cesca T.
Published: July 2006

An n-type doping significantly increases the number of active Fe atoms substituting In (FeIn) in Fe-implanted InP. We address the origin of this doping effect by investigating the relative stability of neutral and charged FeIn states with first-principles theoretical methods. The present results show that donor-acceptor pairs have direct stabilizing effects on FeIn related to charge rearrangements strongly localized at the Fe site and involving d orbitals. The resulting microscopic description of the doping effects accounts for the experimental findings and provides a significant guideline for tuning electronic and optical properties of Fe implanted InP and InP-based compounds.
Influence of inertia and gravity on the stability of filament jet flow
Authors: German Radoslav , Khayat Roger E. , Cui Jing Kai
Published: July 2006

The interplay between inertia and gravity is examined for a filament jet flow. The velocity is imposed at the tube exit and jet tip downstream. Both linear and nonlinear stability analyses are carried out. The loss of stability coincides with the onset of a Hopf bifurcation. While both inertia and gravity enhance the stability of steady flow, inertia plays a more dominant role regarding critical parameters. In contrast, the disturbance frequency is more sensitive to the effect of gravity. Above criticality, finite-amplitude disturbances are amplified, and sustained oscillation is achieved. It is found that the growth rate increases with velocity ratio, but decreases with inertia and gravity, which suggests that initial transients tend to take longer to die out for a fluid with stronger inertia and gravity. Transient postcritical calculations show that the nonlinearity can be effectively halted by inertia and gravity. The oscillation frequency (jet radius) decreases (increases) with velocity ratio. However, the jet oscillates more frequently but less fiercely with stronger inertia and gravity effects. The rupture of the jet is also examined, and is found to be delayed by inertia and gravity. Although the oscillation amplitude is found to be weakest at the jet tip, it is at this location that the jet tends to rupture first. Finally, comparison is carried out between theory and experiment, leading to good agreement.
Relation between native ensembles and experimental structures of proteins
Authors: Best Robert B. , Lindorff-Larsen Kresten , DePristo Mark A. , Vendruscolo Michele
Published: July 2006

Different experimental structures of the same protein or of proteins with high sequence similarity contain many small variations. Here we construct ensembles of “high-sequence similarity Protein Data Bank” (HSP) structures and consider the extent to which such ensembles represent the structural heterogeneity of the native state in solution. We find that different NMR measurements probing structure and dynamics of given proteins in solution, including order parameters, scalar couplings, and residual dipolar couplings, are remarkably well reproduced by their respective high-sequence similarity Protein Data Bank ensembles; moreover, we show that the effects of uncertainties in structure determination are insufficient to explain the results. These results highlight the importance of accounting for native-state protein dynamics in making comparisons with ensemble-averaged experimental data and suggest that even a modest number of structures of a protein determined under different conditions, or with small variations in sequence, capture a representative subset of the true native-state ensemble.
Whirlin complexes with p55 at the stereocilia tip during hair cell development
Authors: Mburu Philomena , Kikkawa Yoshiaki , Townsend Stuart , Romero Rosario , Yonekawa Hiromichi , Brown Steve D. M.
Published: July 2006

Hearing in mammals depends upon the proper development of actin-filled stereocilia at the hair cell surface in the inner ear. Whirlin, a PDZ domain-containing protein, is expressed at stereocilia tips and, by virtue of mutations in the whirlin gene, is known to play a key role in stereocilia development. We show that whirlin interacts with the membrane-associated guanylate kinase (MAGUK) protein, erythrocyte protein p55 (p55). p55 is expressed in outer hair cells in long stereocilia that make up the stereocilia bundle as well as surrounding shorter stereocilia structures. p55 interacts with protein 4.1R in erythrocytes, and we find that 4.1R is also expressed in stereocilia structures with an identical pattern to p55. Mutations in the whirlin gene (whirler) and in the myosin XVa gene (shaker2) affect stereocilia development and lead to early ablation of p55 and 4.1R labeling of stereocilia. The related MAGUK protein Ca
2+
-calmodulin serine kinase (CASK) is also expressed in stereocilia in both outer and inner hair cells, where it is confined to the stereocilia bundle. CASK interacts with protein 4.1N in neuronal tissue, and we find that 4.1N is expressed in stereocilia with an identical pattern to CASK. Unlike p55, CASK labeling shows little diminution of labeling in the whirler mutant and is unaffected in the shaker2 mutant. Similarly, expression of 4.1N in stereocilia is unaltered in whirler and shaker2 mutants. p55 and protein 4.1R form complexes critical for actin cytoskeletal assembly in erythrocytes, and the interaction of whirlin with p55 indicates it plays a similar role in hair cell stereocilia.
Monoamine oxidase A and repressor R1 are involved in apoptotic signaling pathway
Authors: Ou Xiao-Ming , Chen Kevin , Shih Jean C.
Published: July 2006

Monoamine oxidase A (MAO A) degrades serotonin, norepinephrine, and dopamine and produces reactive oxygen that may cause neuronal cell death. We have previously reported that a novel transcription factor R1 (RAM2/CDCA7L/JPO2) inhibits the MAO A promoter and enzymatic activities. This study reports the roles of MAO A and R1 in apoptosis and proliferation. We have found that in serum starvation-induced apoptosis, p38 kinase, MAO A, and caspase-3 were increased, whereas Bcl-2 and R1 were reduced. Using a p38 kinase inhibitor, R1 overexpression, and MAO A inhibitor, we have shown that MAO A and R1 are downstream of p38 kinase and Bcl-2, but upstream of caspase-3. Inhibition of MAO A prevents cell apoptosis. This notion was further supported by the finding that serum starvation-induced apoptosis is reduced in cortical brain cells from MAO A-deficient mice compared with WT. In addition, we found that MAO A and R1 are involved in the c-Myc-induced proliferative signaling pathway in the presence of serum. Immunoprecipitation and immunohistochemistry experiments indicate that the oncogene c-Myc colocalizes with R1 and induces R1 gene expression. Using R1 overexpression, R1 small interfering RNA, and a MAO A inhibitor, we found that R1 and MAO A act upstream of cyclin D1 and E2F1. In summary, this study demonstrates the functions of MAO A and its repressor R1 in apoptotic signaling pathways.
Evolution of cooperation by multilevel selection
Authors: Traulsen Arne , Nowak Martin A.
Published: July 2006

We propose a minimalist stochastic model of multilevel (or group) selection. A population is subdivided into groups. Individuals interact with other members of the group in an evolutionary game that determines their fitness. Individuals reproduce, and offspring are added to the same group. If a group reaches a certain size, it can split into two. Faster reproducing individuals lead to larger groups that split more often. In our model, higher-level selection emerges as a byproduct of individual reproduction and population structure. We derive a fundamental condition for the evolution of cooperation by group selection: if
b
/
c
> 1 +
n
/
m
, then group selection favors cooperation. The parameters
b
and
c
denote the benefit and cost of the altruistic act, whereas
n
and
m
denote the maximum group size and the number of groups. The model can be extended to more than two levels of selection and to include migration.
Functionally diverging molecular quasi-species evolve by crossing two enzymes
Authors: Emrén Lars O. , Kurtovic Sanela , Runarsdottir Arna , Larsson Anna-Karin , Mannervik Bengt
Published: July 2006

Molecular evolution is frequently portrayed by structural relationships, but delineation of separate functional species is more elusive. We have generated enzyme variants by stochastic recombinations of DNA encoding two homologous detoxication enzymes, human glutathione transferases M1–1 and M2–2, and explored their catalytic versatilities. Sampled mutants were screened for activities with eight alternative substrates, and the activity fingerprints were subjected to principal component analysis. This phenotype characterization clearly identified at least three distributions of substrate selectivity, where one was orthogonal to those of the parent-like distributions. This approach to evolutionary data mining serves to identify emerging molecular quasi-species and indicates potential trajectories available for further protein evolution.
Minimal model of spiky oscillations in NF-κB signaling
Authors: Krishna Sandeep , Jensen Mogens H. , Sneppen Kim
Published: July 2006

The NF-κB signaling system is involved in a variety of cellular processes including immune response, inflammation, and apoptosis. Recent experiments have found oscillations in the nuclear-cytoplasmic translocation of the NF-κB transcription factor [Hoffmann, A.,
et al.
(2002)
Science
298, 1241–1245; Nelson, D. E.,
et al.
(2004)
Science
306, 704–708.] How the cell uses the oscillations to differentiate input conditions and send specific signals to downstream genes is an open problem. We shed light on this issue by examining the small core network driving the oscillations, which we show is designed to produce periodic spikes in nuclear NF-κB concentration. The presence of oscillations is extremely robust to variation of parameters, depending mainly on the saturation of the active degradation rate of IκB, an inhibitor of NF-κB. The oscillations can be used to regulate downstream genes in a variety of ways. In particular, we show that genes to whose operator sites NF-κB binds and dissociates fast can respond very sensitively to changes in the input signal, with effective Hill coefficients of >20.
Functional foods: concepts and application to inulin and oligofructose
Authors: Roberfroid Marcel B.
Published: July 2006

A food can be regarded as functional if it is satisfactorily demonstrated to affect beneficially one or more target functions in the body, beyond adequate nutritional effects, in a way which is relevant to either the state of well-being and health or the reduction of the risk of a disease. Health claims are expected to be authorized for functional foods based either on enhanced function (type A claim) or disease risk reduction (type B claim). Their development is a unique opportunity to contribute to the improvement of the quality of the food offered to consumer's choice for the benefit of his well-being and health. But only a rigorous scientific approach producing sound data will garantee its success. The functional food components that are discussed in the proceedings of the 3rd ORAFTI Research Conference are the inulin-type fructans, natural food components found in miscellaneous edible plants. They are non-digestible oligosaccharides that are classified as dietary fiber. The targets for their functional effects are the colonic microflora that use them as selective ‘fertilizers’; the gastrointestinal physiology; the immune functions; the bioavailability of minerals; and the metabolism of lipids. Potential health benefits may also concern reduction of the risk of some diseases like intestinal infections, constipation, non-insulin dependent diabetes, obesity, osteoporosis or colon cancer. The present proceedings review the scientific data available and, by reference to the concepts in functional food science, they assess the scientific evidence which will be used to substantiate health claims.
Inulin, oligofructose and mineral metabolism — experimental data and mechanism
Authors: Scholz-Ahrens Katharina E. , Schrezenmeir J.
Published: July 2006

Numerous investigations performed in animal models in the past 10 years have shown repeatedly that non-digestible oligosaccharides (NDO), such as inulin, oligofructose or transgalacto-oligosaccharides (TOS), stimulate mineral absorption, mainly calcium and magnesium. Long-term beneficial effects on bone health have been indicated by accumulation of bone mineral content in growing rats or prevention of bone loss in ovariectomized rats. However, bone mineral content or density are not necessarily associated with bone quality. In recent studies both oligofructose and calcium prevented loss of trabecular bone area induced by oestrogen deficiency, this, however, occurred at different trabecular shapes. The effects of NDO on mineral metabolism may be based on the enhancement of passive and active mineral transport across the intestinal epithelium, mediated by an increase in certain metabolites of the intestinal flora and a reduction of pH. The possible impact of short-chain fatty acids, butyrate in particular, and of polyamines on the stimulation of mineral absorption capacity, and the interaction of oligofructose and antibiotics is discussed.
Prebiotic effects of inulin and oligofructose
Authors: Kolida S. , Tuohy K. , Gibson G. R.
Published: July 2006

Prebiotics are non-digestible food ingredients that target certain components within the microbiota of the human large intestine. Efficient prebiotics need to have a specific fermentation therein and thereby have the ability to alter the faecal microflora composition towards a more ‘beneficial’ community structure. This should occur by the stimulation of benign or potentially health promoting genera but not the harmful groups. Because of their positive attributes bifidobacteria and lactobacilli are the most frequent target organisms. Both inulin and oligofructose have been demonstrated to be effective prebiotics. This has been shown through both in vitro and in vivo assessments in different laboratories. Because of their recognised prebiotic properties, principally the selective stimulation of colonic bifidobacteria, both inulin and oligofructose are increasingly used in new food product developments. Examples include drinks, yoghurts, biscuits and table spreads. Because of the recognised inhibitory effects that bifidobacteria can exert against gut pathogens, one of the most important aspects of prebiotic ingestion is fortification of the gut flora to resist acute infections.