bluuebunny/crossref_metadata_2025 huggingface dataset:
Cofactor assisted gating mechanism in the active site of NADH oxidase from Thermus thermophilus
Authors: Hritz Jozef , Žoldák Gabriel , Sedlák Erik
Published: April 2006

NADH oxidase (NOX) from Thermus thermophilus is a member of a structurally homologous flavoprotein family of nitroreductases and flavin reductases. The importance of local conformational dynamics in the active site of NOX has been recently demonstrated. The enzyme activity was increased by 250% in the presence of 1 M urea with no apparent perturbation of the native structure of the protein. The present in silico results correlate with the in vitro data and suggest the possible explanation about the effect of urea on NOX activity at the molecular level. Both, X‐ray structure and molecular dynamics (MD) simulations, show open conformation of the active site represented by −f0.9 nm distance between the indole ring of Trp47 and the isoalloxazine ring of FMN412. In this conformation, the substrate molecule can bind in the active site without sterical restraints. MD simulations also indicate more stable conformation of the active site called “closed” conformation. In this conformation, Trp47 and the isoalloxazine ring of FMN412 are so close to each other (−f0.5 nm) that the substrate molecule is unable to bind between them without perturbing this conformation. The open/close transition of the active site between Trp47 and the flavin ring is accompanied by release of the “tightly” bound water molecule from the active site—cofactor assisted gating mechanism. The presence of urea in aqueous solutions of NOX prohibits closing of the active site and even unlocks the closed active site because of the concomitant binding of a urea molecule in the active site cavity. The binding of urea in the active site is stabilized by formation of one/two persistent hydrogen bonds involving the carbonyl group of the urea molecule. Our report represents the first MD study of an enzyme from the novel flavoprotein family of nitroreductases and flavin reductases. The common occurrence of aromatic residues covering the active sites in homologous enzymes suggests the possibility of a general gating mechanism and the importance of local dynamics within this flavoprotein family. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Association of calcineurin with mitochondrial proteins
Authors: Tokheim Abigail M. , Martin Bruce L.
Published: April 2006

Using mouse hearts from Swiss Webster mice, calcineurin was immunoprecipitated using commercially available anti‐calcineurin antibody and the resulting complex analyzed by using sodium dodecyl sulfate‐gel electrophoresis with silver staining. Distinct proteins were observed and subjected to in situ trypsin digestion followed by extraction of the resulting peptides. Peptides from each protein band were loaded onto a target for matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry and analyzed. The resulting peptide mass spectrum was compared with the Mascot and Protein Prospector databases and resulted in the specific identification of heart mitochondrial proteins, specifically Mn‐superoxide dismutase (SOD), aconitase (ACN), and malate dehydrogenase (MDH). Each of the three mitochondrial enzymes was identified with approximately 15–25% sequence coverage and all with statistical significance (P < 0.05) according to the Mascot database search engine. Tandem mass spectrometry analysis of the peptide fragmentation spectra confirmed the identification of these protein partners and also yielded the identification of mitochondrial isocitrate dehydrogenase (ICDH) as another protein in the immunoprecipitated complex. Using antibody preparations against Mn‐SOD, ACN, and ICDH showed the presence of calcineurin and each of the three proteins in the immunoprecipitated complex by Western slot blotting. The activity of ACN, but not MDH or ICDH, was enhanced after incubation with calcineurin indicating one possible regulatory function for the complex. The mitochondrial forms of Mn‐SOD, ACN, MDH, and ICDH were identified as partner proteins of calcineurin with all the proteins present in a single multiprotein complex. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Revisiting DIERS' two‐phase methodology for reactive systems twenty years later
Authors: Fauske Hans K.
Published: April 2006

Building on the original DIERS methodology presented 20 years ago, an easy to use design methodology for reactive vapor, gassy, and hybrid systems has resulted that properly accounts for two‐phase flow effects. The methodology is shown to be consistent with available experimental and incident information and examples of bad and good design practices are provided for vapor, gassy, and hybrid systems. The latest methods for calculating the area of reliefs for vapor, gassy, and hybrid systems are given in this article. © 2006 American Institute of Chemical Engineers Process Saf Prog, 2006
Rural population growth in Sweden in the 1990s: unexpected reality or spatial–statistical chimera?
Authors: Amcoff Jan
Published: April 2006

Although estimating rural population change at first glance seems simple, it in fact involves methodological difficulties and requires the accommodation of definitional ambiguities. This article addresses the matter of urban spillover in rural population development. Simply stated, ‘urban spillover’ here refers to how urban localities tend to push a ring of diffuse urban growth outwards as they expand in area. If constant delimitations of urban localities and rural areas are employed, their definitions will de facto change, and what is actually diffuse urban growth will be treated as rural. The effect of urban spillover in different methods of estimating rural population change are illustrated here using Swedish data, which are suitable for this purpose given their high spatial resolution. The data do not support the existence of any actual rural population growth in Sweden in the 1990s, apart from the effects of urban spillover. Copyright © 2006 John Wiley & Sons, Ltd.
Bacterial entry into cells: A role for the endocytic machinery
Authors: Bonazzi Matteo , Cossart Pascale
Published: April 2006

Increasing evidence indicates that pathogens have evolved highly efficient strategies to induce their internalization within host cells. Viruses and bacteria express and expose on their surface, molecules that mimic endogenous ligands to cell receptors, thereby inducing specific intracellular signalling cascades. More recently it has become clear that, as most viruses, bacteria can enter cells via the clathrin‐mediated pathway, indicating a key role for endocytosis in pathogens entry into cells. Here we review the pathways followed by Listeria monocytogenes to enter into non‐phagocytic cells, as a model for the subversion of cellular functions to induce pathogens internalization.
The metabolic syndrome and adipocytokines
Authors: Matsuzawa Yuji
Published: April 2006

Visceral fat accumulation has been shown to play crucial roles in the development of cardiovascular disease as well as the development of obesity‐related disorders such as diabetes mellitus, hyperlipidemia and hypertension and the so‐called metabolic syndrome. Given these clinical findings, adipocytes functions have been intensively investigated in the past 10 years, and have been revealed to act as endocrine cells that have been termed adipocytokines, which secrete various bioactive substances. Among adipocytokines, tumor necrosis factor‐α, plasminogen activator inhibitor type 1 and heparin binding epidermal growth factor‐like growth factor are produced in adipocytes as well as other organs, and may contribute to the development of vascular diseases. Visfatin has been identified as a visceral‐fat‐specific protein that might be involved in the development of obesity‐related diseases, such as diabetes mellitus and cardiovascular disease. On the contrary to these adipocytokines, adiponectin, an adipose‐tissue‐specific, collagen‐like protein, has been noted as an important antiatherogenic and antidiabetic protein, or as an anti‐inflammatory protein. The functions of adipocytokine secretion might be regulated dynamically by nutritional state. Visceral fat accumulation causes dysregulation of adipocyte functions, including oversecretion of tumor necrosis factor‐α, plasminogen activator inhibitor type 1 and heparin binding epidermal growth factor‐like growth and hyposecretion of adiponectin, which results in the development of a variety of metabolic and circulatory diseases. In this review, the importance of adipocytokines, especially focusing on adiponectin is discussed with respect to cardiovascular diseases.
Escherichia coli engineered to produce eicosapentaenoic acid becomes resistant against oxidative damages
Authors: Nishida Takanori , Orikasa Yoshitake , Ito Yukiya , Yu Reiko , Yamada Akiko , Watanabe Kazuo , Okuyama Hidetoshi
Published: April 2006

The colony‐forming ability of Escherichia coli genetically engineered to produce eicosapentaenoic acid (EPA) grown in 3 mM hydrogen peroxide (H2O2) was similar to that of untreated cells. It was rapidly lost in the absence of EPA. H2O2‐induced protein carbonylation was enhanced in cells lacking EPA. The fatty acid composition of the transformants was unaffected by H2O2 treatment, but the amount of fatty acids decreased in cultures of cells lacking EPA and increased in cultures of cells producing EPA, suggesting that cellular EPA is stable in the presence of H2O2 in vivo and may protect cells directly against oxidative damage. We discuss the possible role of EPA in partially blocking the penetration of H2O2 into cells through membranes containing EPA.
Do investors overreact to earnings warnings?
Authors: Tawatnuntachai Oranee , Yaman Devrim
Published: April 2006

This study shows that contrary to what many managers argue, there is no overreaction to earnings warnings. Our sample consists of 986 firms that had significantly lower fourth‐quarter earnings than analysts' forecasts during the period of 1983 to 1998. About 9% of these firms released quantitative earnings information while 6.5% of the firms disclosed qualitative earnings information prior to the formal earnings report dates. We find that although these firms experience significant stock price declines during the warning period, their share prices are still higher than the economic values, calculated using Ohlson's residual income model. Further, long‐run operating and stock performance of these firms are not more positive than the performance of firms that do not warn. We also find that investor reaction to both warning and non‐warning firms is positively related to the firms' long‐run stock and operating performance. These findings support the argument that investors do not overreact to the warnings but base their reaction on anticipated long‐term performance of the firms.
Linearized dynamics of spherical bubble clouds
Authors: D'Agostino Luca , Brennen Christopher E.
Published: April 2006

The present work investigates the dynamics of the one-dimensional, unsteady flow of a spherical bubble cloud subject to harmonic far-field pressure excitation. Bubble dynamics effects and energy dissipation due to viscosity, heat transfer, liquid compressibility and relative motion of the two phases are included. The equations of motion for the average flow and the bubble radius are linearized and a closed-form solution is obtained. The results are then generalized by means of Fourier synthesis to the case of arbitrary far-field pressure excitation. The flow displays various regimes (sub-resonant, trans-resonant and super-resonant) with different properties depending on the value of the relevant flow parameters. Examples are discussed in order to show the effects of the inclusion of the various energy dissipation mechanisms. Finally the results for the case of Gaussian-shaped far-field pressure change are presented and the most important limitations of the theory are briefly discussed. The simple linearized dynamical analysis developed so far clearly demonstrates the importance of the complex phenomena connected to the interaction of the dynamics of the bubbles with the flow and provides an introduction to the more realistic study of the same flows with nonlinear bubble dynamics.
The effect of order on dispersion in porous media
Authors: Koch Donald L. , Cox Raymond G. , Brenner Howard , Brady John F.
Published: April 2006

The effect of spatial periodicity in grain structure on the average transport properties resulting from flow through porous media are derived from the basic conservation equations. At high Péclet number, the mechanical dispersion that is induced by the stochastic fluid velocity field in disordered media and is independent of the molecular diffusivity is absent in periodic media where the velocity field is deterministic. Instead, the fluid motion enhances diffusion by an amount proportional to U2l2/D when the bulk flow is in certain directions (of which there are an infinite number), and to D otherwise. The non-mechanical dispersion mechanisms associated with the zero velocity of the fixed grains is qualitatively similar in ordered and disordered media.
The complete second-order diffraction solution for an axisymmetric body Part 1. Monochromatic incident waves
Authors: Kim Moo-Hyun , Yue Dick K. P.
Published: April 2006

We study the diffraction, to second order, of plane monochromatic incident gravity waves by a vertically axisymmetric body. The second-order double-frequency diffraction potential is obtained explicitly. A sequence of one-dimensional integral equations along the generator of the body involving free-surface ring sources of general order are formulated and solved for the circumferential components of the second-order potential. The solution is expedited by analytic integration in the entire local-wave-free outer field of a requisite free-surface integral. The method is validated by extensive convergence tests and comparisons to semi-analytic results for the second-order forces and moments on a uniform vertical circular cylinder. Complete second-order forces, moments, surface pressures and run-up on the vertical cylinder as well as a truncated vertical cone are presented. A summary of the important findings is given in §5.
Direct numerical simulation of stratified homogeneous turbulent shear flows
Authors: Gerz T. , Schumann U. , Elghobashi S. E.
Published: April 2006

The exact time-dependent three-dimensional Navier-Stokes and temperature equations are integrated numerically to simulate stably stratified homogeneous turbulent shear flows at moderate Reynolds numbers whose horizontal mean velocity and mean temperature have uniform vertical gradients. The method uses shear-periodic boundary conditions and a combination of finite-difference and pseudospectral approximations. The gradient Richardson number Ri is varied between 0 and 1. The simulations start from isotropic Gaussian fields for velocity and temperature both having the same variances.

The simulations represent approximately the conditions of the experiment by Komori et al. (1983) who studied stably stratified flows in a water channel (molecular Prandtl number Pr = 5). In these flows internal gravity waves build up, superposed by hot cells leading to a persistent counter-gradient heat-flux (CGHF) in the vertical direction, i.e. heat is transported from lower-temperature to higher-temperature regions. Further, simulations with Pr = 0.7 for air have been carried out in order to investigate the influence of the molecular Prandtl number. In these cases, no persistent CGHF occurred. This confirms our general conclusion that the counter-gradient heat flux develops for strongly stable flows (Ri ≈ 0.5–1.0) at sufficiently large Prandtl numbers (Pr = 5). The flux is carried by hot ascending, as well as cold descending turbulent cells which form at places where the highest positive and negative temperature fluctuations initially existed. Buoyancy forces suppress vertical motions so that the cells degenerate to two-dimensional fossil turbulence. The counter-gradient heat flux acts to enforce a quasi-static equilibrium between potential and kinetic energy.

Previously derived turbulence closure models for the pressure-strain and pressure-temperature gradients in the equations for the Reynolds stress and turbulent heat flux are tested for moderate-Reynolds-number flows with strongly stable stratification (Ri = 1). These models overestimate the turbulent interactions and underestimate the buoyancy contributions. The dissipative timescale ratio for stably stratified turbulence is a strong function of the Richardson number and is inversely proportional to the molecular Prandtl number of the fluid.
Measurements of heat diffusion from a continuous line source in a uniformly sheared turbulent flow
Authors: Karnik U. , Tavoularis S.
Published: April 2006

The diffusion of a passive scalar (heat) from a continuous line source placed in a uniformly sheared, nearly homogeneous, turbulent shear flow is examined. Measurements indicate that the mean temperature profile is approximately Gaussian near the source but, further downstream, it becomes asymmetric and its peak shifts towards the region of lower velocity. The r.m.s. temperature fluctuation profile is double peaked close to the source, it is single peaked at intermediate distances and it demonstrates a re-emergence of double peaks which grow in relative magnitude far away from the source. In comparison to similar experiments in isotropic turbulence, the centreline mean temperature appears to have a comparable decay rate, whereas the centreline mean-square temperature fluctuations appear to decay at a faster rate. The spread of the plume is faster than that in isotropic turbulence. The measured turbulent heat fluxes and triple temperature-velocity correlations demonstrate self-similar features. The development of temperature integral lengthscales and microscales is comparable to that in other heated, uniformly sheared flows, while the temperature p.d.f. and the temperature-velocity joint p.d.f. are distinctly non-Gaussian, especially away from the centreline. The relative magnitudes of the two measured components of the turbulent diffusivity tensor are in agreement with earlier measurements.
A natural low-frequency oscillation of the flow over an airfoil near stalling conditions
Authors: Zaman K. B. M. Q. , Mckinzie D. J. , Rumsey C. L.
Published: April 2006

An unusually low-frequency oscillation in the flow over an airfoil is studied experimentally as well as computationally. Wind-tunnel measurements are carried out with two-dimensional airfoil models in the chord Reynolds number (Rc) range of 0.15 × 105−3.0 × 105. During deep stall, at α [gsim ] 18°, the usual ‘bluff-body shedding’ occurs at a Strouhal number, Sts ≈ 0.2. But at the onset of static stall around α = 15°, a low-frequency periodic oscillation is observed, the corresponding Sts being an order of magnitude lower. The phenomenon apparently takes place only with a transitional state of the separating boundary layer. Thus, on the one hand, it is not readily observed with a smooth airfoil in a clean wind tunnel, while on the other, it is easily removed by appropriate ‘acoustic tripping’. Details of the flow field for a typical case are compared with a case of bluff-body shedding. The flow field is different in many ways from the latter case and does not involve a Kármán Vortex street. The origin of the flow fluctuations traces to the upper surface of the airfoil and is associated with a periodic switching between stalled and unstalled states. The mechanism of the frequency selection remains unresolved, but any connection to blower instabilities, acoustic standing waves or structural resonances has been ruled out.

A similar result has been encountered computationally using a two-dimensional Navier–Stokes code. While with the assumption of laminar flow, wake oscillation akin to the bluff-body shedding has been observed previously, the Sts is found to drop to about 0.03 when a ‘turbulent’ boundary layer is assumed. Details of the flow field and unsteady forces, computed for the same conditions as in the experiment, compare reasonably well with the experimental data.

The phenomenon produces intense flow fluctuations imparting much larger unsteady forces to the airfoil than that experienced in bluff-body shedding, and may represent the primary aerodynamics of stall flutter of blades and wings.
Three-dimensional marginal separation
Authors: Duck P. W.
Published: April 2006

The three-dimensional marginal separation of a boundary layer along a line of symmetry is considered. The key equation governing the displacement function is derived, and found to be a nonlinear integral equation in two space variables. This is solved iteratively using a pseudospectral approach, based partly in double Fourier space, and partly in physical space. Qualitatively the results are similar to previously reported two-dimensional results (which are also computed to test the accuracy of the numerical scheme); however quantitatively the three-dimensional results are much different.
The effect of geometry on the gravitational instability of a buoyant region of viscous fluid
Authors: Lister John R. , Kerr Ross C.
Published: April 2006

The low-Reynolds-number stability of a region of buoyant fluid surrounded by denser fluid is analysed in two situations. In the first study, the buoyant fluid lies in a thin layer sandwiched between two denser and much deeper layers. The growth rate and wavelength of the most unstable sinusoidal perturbation are calculated and the effects of the viscosity ratios and density differences between the fluids are investigated. It is found that if the buoyant fluid is much less viscous than the overlying fluid then, in quite general circumstances, both the most unstable wavelength and the corresponding growth rate are inversely proportional to the cube root of the viscosity of the buoyant fluid. A physical explanation of this result is given by scaling analysis of the total dissipation. In the second study, the buoyant fluid takes the form of a cylinder rising through a uniform environment. The eigenmodes of small perturbation about this state of motion are found for each axial wavenumber in terms of Fourier series of separable solutions to the Stokes equations. In contrast to the first study, it is found that the most unstable wavelength and growth rate are asymptotically independent of the viscosity of the buoyant fluid when this viscosity is small.

The difference between the results of the two studies is of importance, particularly for geophysical applications in which viscosity ratios are very large. Previous models of linear regions of volcanism at mid-ocean ridges and at island arcs have assumed that results obtained in simple two-layered systems can be generalized to other geometries. The conclusions of these models are discussed in the light of the stability results for a cylindrical (and hence linea.
The transition to baroclinic chaos on the β-plane
Authors: Ohlsen Daniel R. , Hart John E.
Published: April 2006

Experiments on two-layer β-plane flows are described. The regime diagrams for both easterly and westerly forcing indicate complex scenarios by which baroclinically unstable flows can become chaotic as the forcing is increased. The transition sequence can involve as many as three different vacillation mechanisms, but also exhibits the periodic window phenomena prevalent in many model dynamical systems. The fractal dimension of the chaos at low rotational Froude number F is measurable and is somewhat less than 3. The dimension increases as F is raised. A six-wave low-order model, while successfully predicting some of the observed vacillations, gives a relatively poor description of the chaos.
One-dimensional adiabatic flow of equilibrium gas–particle mixtures in long vertical ducts with friction
Authors: Buresti Guido , Casarosa Claudio
Published: April 2006

The equations of the steady, adiabatic, one-dimensional flow of an equilibrium mixture of a perfect gas and incompressible particles, in constant-area ducts with friction, are derived taking into account the effects of gravity and of the finite volume of the particles. As is the case for a pure gas, the mixture is shown to be subject to the phenomenon of choking, and the possibility of an adiabatic heating of the mixture in a subsonic expansion is also theoretically predicted for certain flow inlet conditions. The model may be used to approximately describe the conditions existing in portions of volcanic conduits during the Plinian phases of explosive eruptions. Some results of the numerical integration of the equations for a typical application of this type are briefly discussed, thus showing the potential of the model for carrying out rapid analyses of the influence of the main geometrical and flow parameters describing the problem. A non-volcanological application is also analysed to illustrate the possibility of the adiabatic heating of the mixture.
The Dean equations extended to a helical pipe flow
Authors: Germano M.
Published: April 2006

In this paper the Dean (1928) equations are extended to the case of a helical pipe flow, and it is shown that they depend not only on the Dean number K but also on a new parameter λ/[Rscr ] where λ is the ratio of the torsion τ to the curvature κ of the pipe axis and [Rscr ] the Reynolds number referred in the usual way to the pipe radius a and to the equivalent maximum speed in a straight pipe under the same axial pressure gradient. The fact that the torsion has no first-order effect on the flow is confirmed, but it is shown that this is peculiar to a circular cross-section. In the case of an elliptical cross-section there is a first-order effect of the torsion on the secondary flow, and in the limit λ/[Rscr ] → ∞ (twisted pipes, provided only with torsion), the first-order ‘displacement’ effect of the walls on the secondary flow, analysed in detail by Choi (1988), is recovered.

Different systems of coordinates and different orders of approximations have recently been adopted in the study of the flow in a helical pipe. Thus comparisons between the equations and the results presented in different reports are in some cases difficult and uneasy. In this paper the extended Dean equations for a helical pipe flow recently derived by Kao (1987) are converted to a simpler form by introducing an appropriate modified stream function, and their equivalence with the present set of equations is recovered. Finally, the first-order equivalence of this set of equations with the equations obtained by Murata et al. (1981) is discussed.
The squeezing of red blood cells through capillaries with near-minimal diameters
Authors: Halpern D. , Secomb T. W.
Published: April 2006

An analysis is presented of the mechanics of red blood cells flowing in very narrow tubes. Mammalian red cells are highly flexible, but their deformations satisfy two significant constraints. They must deform at constant volume, because the contents of the cell are incompressible, and also at nearly constant surface area, because the red cell membrane strongly resists dilation. Consequently, there exists a minimal tube diameter below which passage of intact cells is not possible. A cell in a tube with this diameter has its critical shape: a cylinder with hemispherical ends. Here, flow of red cells in tubes with near-minimal diameters is analysed using lubrication theory. When the tube diameter is slightly larger than the minimal value, the cell shape is close to its shape in the critical case. However, the rear end of the cell becomes flattened and then concave with a relatively small further increase in the diameter. The changes in cell shape and the resulting rheological parameters are analysed using matched asymptotic expansions for the high-velocity limit and using numerical solutions. Predictions of rheological parameters are also obtained using the assumption that the cell is effectively rigid with its critical shape, yielding very similar results. A rapid decrease in the apparent viscosity of red cell suspensions with increasing tube diameter is predicted over the range of diameters considered. The red cell velocity is found to exceed the mean bulk velocity by an amount that increases with increasing tube diameter.
Steady compressible flow in collapsible tubes: application to forced expiration
Authors: Elad David , Kamm Roger D. , Shapiro Ascher H.
Published: April 2006

Steady, one-dimensional flow of a compressible fluid through a collapsible tube is analysed. A general model is employed, incorporating axial variations in the parameters of the conducting system, such as the tube unstressed cross-section area and wall stiffness, the external pressure and energy exchange with the environment. The flow variables are described in differential form as functions of the conduit system parameters. A coupled set of equations for the dependent flow variables is summarized in a table of influence coefficients, which provides a clear and simple description of the effects produced by the system parameters. Examples of the effects of fluid compressibility in the respiratory system are presented for forced expiration manoeuvres. The effects are found to be generally small, but are most accentuated when breathing heavy gases and when the airways are pathologically stiffened.
Flow in a partially filled, rotating, tapered cylinder
Authors: Ribando R. J. , Palmer J. L. , Scott J. E.
Published: April 2006

The secondary flow patterns induced by a differentially rotating lid in a partially filled, rapidly rotating, tapered cylinder have been investigated. Using a new laser-Doppler velocimeter system capable of making measurements in the rotor frame of reference, the radial dependence of the azimuthal and axial velocity components was measured at two axial positions in the rotor. A linear, asymptotic analysis and a finite-difference simulation were made for comparison. The latter was performed on a boundary-fitted computational mesh so that the slanted rotor wall and the sagging free surface could be accommodated in the model. The agreement between the experimental and numerical results was excellent for the azimuthal velocity component and good for the axial component. Of particular interest is the modified E½ boundary layer on the slanted wall, a feature which is not present with a vertical sidewall.
Oblique and parallel modes of vortex shedding in the wake of a circular cylinder at low Reynolds numbers
Authors: Williamson C. H. K.
Published: April 2006

Two fundamental characteristics of the low-Reynolds-number cylinder wake, which have involved considerable debate, are first the existence of discontinuities in the Strouhal-Reynolds number relationship, and secondly the phenomenon of oblique vortex shedding. The present paper shows that both of these characteristics of the wake are directly related to each other, and that both are influenced by the boundary conditions at the ends of the cylinder, even for spans of hundreds of diameters in length. It is found that a Strouhal discontinuity exists, which is not due to any of the previously proposed mechanisms, but instead is caused by a transition from one oblique shedding mode to another oblique mode. This transition is explained by a change from one mode where the central flow over the span matches the end boundary conditions to one where the central flow is unable to match the end conditions. In the latter case, quasi-periodic spectra of the velocity fluctuations appear; these are due to the presence of spanwise cells of different frequency. During periods when vortices in neighbouring cells move out of phase with each other, ‘vortex dislocations’ are observed, and are associated with rather complex vortex linking between the cells. However, by manipulating the end boundary conditions, parallel shedding can be induced, which then results in a completely continuous Strouhal curve. It is also universal in the sense that the oblique-shedding Strouhal data (Sθ) can be collapsed onto the parallel-shedding Strouhal curve (S0) by the transformation, S0 = Sθ/cosθ, where θ is the angle of oblique shedding. Close agreement between measurements in two distinctly different facilities confirms the continuous and universal nature of this Strouhal curve. It is believed that the case of parallel shedding represents truly two-dimensional shedding, and a comparison of Strouhal frequency data is made with several two-dimensional numerical simulations, yielding a large disparity which is not clearly understood. The oblique and parallel modes of vortex shedding are both intrinsic to the flow over a cylinder, and are simply solutions to different problems, because the boundary conditions are different in each case.
Combined buoyant-thermocapillary flow in a cavity
Authors: Carpenter Bradley M. , Homsy G. M.
Published: April 2006

We treat the problem of combined buoyancy-thermocapillary convection in a cavity with a free surface heated differentially in the horizontal. Attention is focused on the structure and strength of the flow for large ΔT, i.e. large Marangoni and Rayleigh numbers. In the combined problem, the boundary-layer scalings for buoyant and thermocapillary convection suggest that in the limit of large ΔT, thermocapillarity will dominate the large-scale flow. Accurate numerical solutions are used to study this question at fixed cavity aspect ratio and Prandtl number, with G = Ra/Ma as a parameter. For G = 1, the flow evolves toward its boundary-layer limit in a fashion identical to that for G = 0, i.e. pure thermocapillary flow. For G = 10, the evolution is from a buoyancy-dominated structure, through a transition, to a thermocapillary-dominated structure. We infer that thermocapillarity will ultimately dominate all such flows at sufficiently large ΔT, for any fixed values of G, the aspect ratio, and the Prandtl number.
The effect of barotropic instability on the nonlinear evolution of a Rossby-wave critical layer
Authors: Haynes Peter H.
Published: April 2006

A study of the flow within the critical layer of a forced Rossby-wave is made, using a high-resolution numerical model. The possibility of growth of disturbances through barotropic instability and the extent to which these disturbances modify the subsequent time evolution is of particular interest. The flow is characterized by a parameter μ, equal to the cross-stream lengthscale divided by a downstream wavelength. In the long-wavelength case, μ [Lt ] 1, where there is a clear conceptual division between the instability and the basic flow, the results of the simulation confirm the importance of the growing and saturating disturbances in rearranging the vorticity within the critical layer. When the wavelength is not so long, the distinction between the instability and the straightforward time evolution of the basic flow is less clear. Nonetheless for μ < 0.25 the ultimate evolution is still sensitive to the details of the initial perturbations and in this sense the flow may be regarded as being unstable. The time-integrated absorptivity of the critical layer may be considerably increased by the effects of the instability, sometimes to three or four times that predicted by the Stewartson-Warn-Warn solution. The nature of the flow, at least during the period in which the dynamics are essentially inviscid, does not seem to change when higher harmonics to the forced wave are resonant. The behaviour seen in Béland's (1976) numerical model is re-examined in the light of these findings. A simple model of the redistribution of vorticity by the unstable disturbances is formulated, and its predictions are shown to agree well with the numerical simulations.
Flow development in a model airway bronchus
Authors: Snyder B. , Olson D. E.
Published: April 2006

Three-dimensional laminar flow profiles were measured at each of three axial stations downstream from the inlet of a slowly tapering tube of constant flow cross-section. It was found that strong inlet wall shear induces significant secondary swirl, whose downstream growth is initially consistent with an inviscid model of vorticity transfer. This secondary flow may act to retard the onset of local flow separation by convecting axial momentum into the boundary layer adjacent to the diverging wall of the tube. These observations could account for the similar geometric shape of major bronchial airways: the suppression of flow separation in pulmonary bifurcations would promote moire effective airway ventilation in the human lung.
Buoyancy-driven motion of a deformable drop through a quiescent liquid at intermediate Reynolds numbers
Authors: Dandy David S. , Leal L. Gary
Published: April 2006

Numerical solutions have been obtained for steady streaming flow past an axisymmetric drop over a wide range of Reynolds numbers (0.005 [les ] Re [les ] 250), Weber numbers (0.005 [les ] We [les ] 14), viscosity ratios (0.001 [les ] λ [les ] 1000), and density ratios (0.001 [les ] ζ [les ] 1000). Our results indicate that at lower Reynolds numbers the shape of the drop tends toward a spherical cap with increasing We, but at higher Re the body becomes more disk shaped with increasing We. Unlike the recirculating wake behind an inviscid bubble or solid particle, the eddy behind a drop is detached from the interface. The size of the eddy and the separation distance from the drop depend on the four dimensionless parameters of the problem. The motion of the fluid inside the drop appears to control the behaviour of the external flow near the body, and even for cases when λ and ζ [Lt ] 1 (a ‘real’ bubble), a recirculating wake remains unattached.
Upper bounds on functions of the dissipation rate in turbulent shear flow
Authors: Malkus W. V. R. , Smith L. M.
Published: April 2006

The search for a statistical stability criterion characterizing steady-state turbulent shear flows ‘has led us to the study of a function proportional to the ratio of the fluctuation dissipation rate and the dissipation rate of the mean. The first Euler–Lagrange equations for an upper bound of this function have optimal solutions with the observed scaling laws and an asymptotic velocity defect for turbulent channel flow. As in the case of maximum transport, the optimal solution for the model equations is a discrete spectrum of streamwise vortices. It is shown how these solutions can be brought closer to the realized flow with additional constraints on the smallest vortex.
Inviscid spatial stability of a compressible mixing layer
Authors: Jackson T. L. , Grosch C. E.
Published: April 2006

We present the results of the inviscid spatial stability of a parallel compressible mixing layer. The parameters of this study are the Mach number of the moving stream, the ratio of the temperature of the stationary stream to that of the moving stream, the frequency, and the direction of propagation of the disturbance wave. Stability characteristics of the flow as a function of these parameters are given. It is shown that if the Mach number exceeds a critical value there are always two groups of unstable waves. One of these groups is fast with phase speeds greater than ½ and is supersonic with respect to the stationary stream. The other is slow with phase speeds less than ½ and supersonic with respect to the moving stream. Phase speeds for the neutral and unstable modes are given, as well as growth rates for the unstable modes. Finally, we show that three-dimensional modes have the same general behaviour as the two-dimensional modes but with higher growth rates over some range of propagation direction.
The axisymmetric deformation of a red blood cell in uniaxial straining Stokes flow
Authors: Pozrikidis C.
Published: April 2006

The axisymmetric deformation of a red blood cell placed in a uniaxial straining Stokes flow is considered. The cell is modelled as a fluid capsule that contains a Newtonian fluid, and is bounded by an area-preserving membrane with negligible resistance to bending. First, it is theoretically demonstrated that spheroidal cells with isotropic membrane tension constitute stationary configurations. To compute transient cell deformations, a numerical procedure is developed based on the boundary-integral method for Stokes flow. Calculations show that initially prolate or oblate cells with isotropic membrane tension deform into stationary spheroids. Cells with a highly oblate initial shape may develop a persistent small pocket along their axis during the deformation. The shear elasticity of the membrane prevents folding, but may cause the formation of sharp corners and concave regions along the cell contour. A decrease in the membrane shear elasticity results in substantial increase in the magnitude of the transient and asymptotic membrane tensions. The maximum strain rate below which a red blood cell remains intact is estimated to be ex = 105 s−1.
Large-amplitude wavetrains and solitary waves in vortices
Authors: Leibovich S. , Kribus A.
Published: April 2006

Large-amplitude axisymmetric waves on columnar vortices, thought to be related to flow structures observed in vortex breakdown, are found as static bifurcations of the Bragg–Hawthorne equation. Solutions of this equation satisfy the steady, axisymmetric, Euler equations. Non-trivial solution branches bifurcate as the swirl ratio (the ratio of azimuthal to axial velocity) changes, and are followed into strongly nonlinear regimes using a numerical continuation method. Four types of solutions are found: multiple columnar solutions, corresponding to Benjamin's ‘conjugate flows’, with subcritical–supercritical pairing of wave characteristics; solitary waves, extending previously known weakly nonlinear solutions to amplitudes large enough to produce flow reversals similar to the breakdown transition; periodic wavetrains; and solitary waves superimposed on the conjugate flow that emerge from the periodic wavetrain as the wavelength or amplitude becomes sufficiently large. Weakly nonlinear soliton solutions are found to be accurate even when the perturbations they cause are fairly strong.
Structure of turbulence at high shear rate
Authors: Lee Moon Joo , Kim John , Moin Parviz
Published: April 2006

The structure of homogeneous turbulence subject to high shear rate has been investigated by using three-dimensional, time-dependent numerical simulations of the Navier–Stokes equations. The instantaneous velocity fields reveal that a high shear rate produces structures in homogeneous turbulence similar to the ‘streaks’ that are present in the sublayer of wall-bounded turbulent shear flows. Statistical quantities such as the Reynolds stresses are compared with those in the sublayer of a turbulent channel flow at a comparable shear rate made dimensionless by turbulent kinetic energy and its dissipation rate. This study indicates that high shear rate alone is sufficient for generation of the streaky structures, and that the presence of a solid boundary is not necessary.

Evolution of the statistical correlations is examined to determine the effect of high shear rate on the development of anisotropy in turbulence. It is shown that the streamwise fluctuating motions are enhanced so profoundly that a highly anisotropic turbulence state with a ‘one-component’ velocity field and ‘two-component’ vorticity field develops asymptotically as total shear increases. Because of high shear rate, rapid distortion theory predicts remarkably well the anisotropic behaviour of the structural quantities.
Flow over a leading edge with distributed roughness
Authors: Floryan J. M. , Dallmann U.
Published: April 2006

An analysis of the flow over a leading edge with distributed roughness is presented. The analysis is focused on a small neighbourhood of the stagnation line. The roughness is assumed to have a small amplitude and to be symmetric with respect to the stagnation line. Results show that roughness acts as a source of streamwise vorticity. The existence of a universal form of the flow field for long-wavelength roughness is demonstrated. It is shown that surface stresses tend to eliminate roughness if erosion or wall flexibility are admitted. The heat flow tends to concentrate at the tips of the roughness and this may lead to the generation of large thermal stresses along the surface of the leading edge.
Solidification of an alloy cooled from above Part 2. Non-equilibrium interfacial kinetics
Authors: Kerr Ross C. , Woods Andrew W. , Worster M. Grae , Huppert Herbert E.
Published: April 2006

The model developed in Part 1 for the solidification and convection that occurs when an alloy is cooled from above is extended to investigate the role of disequilibrium at the mush–liquid interface. Small departures from equilibrium are important because in a convecting system an interfacial temperature below its equilibrium value can drive the bulk temperature of the melt below its liquidus. This behaviour is observed in experiments and can result in crystallization within and at the base of the convecting melt. The additional crystals formed in the interior can settle to the base of the fluid and continue to grow, causing the composition of the melt to change. This ultimately affects the solidification at the roof. The effects of disequilibrium are explored in this paper by replacing the condition of marginal equilibrium at the interface used in the model of Part 1 with a kinetic growth law of the form $\dot{h}_1 = {\cal G}\delta T$, where $\dot{h}_1$ is the rate of advance of the mush–liquid interface, δT is the amount by which the interfacial temperature is below the liquidus temperature of the melt and [Gscr ] is an empirical constant. This modification enables the model to predict very accurately both the growth of the mushy layer and the development of supersaturation in the isopropanol experiments described in Part 1. An additional series of experiments, using aqueous solutions of sodium sulphate, is presented in which the development of supersaturation leads to the internal nucleation and growth of crystals. A further extension of the model is introduced which successfully accounts for this internal crystal growth and the changing composition of the melt. We discuss the implications of this work for geologists studying the formation of igneous rocks. Important conclusions include the facts that cooling the roof of a magma chamber can lead to crystallization at its floor and that vigorous convection can occur in a magma chamber even when there is no initial superheat.
Wave interactions in a three-dimensional attachment-line boundary layer
Authors: Hall Philip , Seddougui Sharon O.
Published: April 2006

The three-dimensional boundary layer on a swept wing can support different types of hydrodynamic instability. Here attention is focused on the so-called ‘spanwise instability’ problem which occurs when the attachment-line boundary layer on the leading edge becomes unstable to Tollmien–Schlichting waves. In order to gain insight into the interactions that are important in that problem a simplified basic state is considered. This simplified flow corresponds to the swept attachment-line boundary layer on an infinite flat plate. The basic flow here is an exact solution of the Navier–Stokes equations and its stability to two-dimensional waves propagating along the attachment line can be considered exactly at finite Reynolds number. This has been done in the linear and weakly nonlinear regimes by Hall, Malik & Poll (1984) and Hall & Malik (1986). Here the corresponding problem is studied for oblique waves and their interaction with two-dimensional waves is investigated. In fact oblique modes cannot be described exactly at finite Reynolds number so it is necessary to make a high-Reynolds-number approximation and use triple-deck theory. It is shown that there are two types of oblique wave which, if excited, cause the destabilization of the two-dimensional mode and the breakdown of the disturbed flow at a finite distance from the leading edge. First a low-frequency mode closely related to the viscous stationary crossflow mode discussed by Hall (1986) and MacKerrell (1987) is a possible cause of breakdown. Secondly a class of oblique wave with frequency comparable with that of the two-dimensional mode is another cause of breakdown. It is shown that the relative importance of the modes depends on the distance from the attachment line.