The acoustic signature of fluid flow in complex porous media

Effective medium approximations for the frequency-dependent and complex-valued effective stiffness tensors of cracked/ porous rocks with multiple solid constituents are developed on the basis of the T-matrix approach (based on integral equation methods for quasi-static composites), the elastic - viscoelastic correspondence principle, and a unified treatment of the local and global flow mechanisms, which is consistent with the principle of fluid mass conservation. The main advantage of using the T-matrix approach, rather than the first-order approach of Eshelby or the second-order approach of Hudson, is that it produces physically plausible results even when the volume concentrations of inclusions or cavities are no longer small. The new formulae, which operates with an arbitrary homogeneous (anisotropic) reference medium and contains terms of all order in the volume concentrations of solid particles and communicating cavities, take explicitly account of inclusion shape and spatial distribution independently. We show analytically that an expansion of the T-matrix formulae to first order in the volume concentration of cavities (in agreement with the dilute estimate of Eshelby) has the correct dependence on the properties of the saturating fluid, in the sense that it is consistent with the Brown-Korringa relation, when the frequency is sufficiently low. We present numerical results for the (anisotropic) effective viscoelastic properties of a cracked permeable medium with finite storage porosity, indicating that the complete T-matrix formulae (including the higher-order terms) are generally consistent with the Brown-Korringa relation, at least if we assume the spatial distribution of cavities to be the same for all cavity pairs. We have found an efficient way to treat statistical correlations in the shapes and orientations of the communicating cavities, and also obtained a reasonable match between theoretical predictions (based on a dual porosity model for quartz-clay mixtures, involving relatively flat clay-related pores and more rounded quartz-related pores) and laboratory results for the ultrasonic velocity and attenuation spectra of a suite of typical reservoir rocks. (C) 2003 Elsevier B.V. All rights reserved.

Campanian crustacean burrow system from Israel with brood and nursery chambers representing communal organization

Phosphorite-filled crustacean burrows associated with a Campanian-age omission surface in the north-western Negev are described. The phosphatic burrow casts weather out displaying scratches (bioglyphs) and two types of local swellings (chambers), which are flattened normal to the course of the burrow. The more abundant chamber type is a flattened spheroid (diameter 45-50 mm) or a flattened, highly prolate ellipsoid of larger dimensions, with bioglyphs. The other type is a flattened spheroid (diameter 45 mm), gently rounded on the upper side and flat on the base. Rings of elevations on the cast (representing moats) form interconnected circlets, each capped by about eight rounded hemispherical tubercles (4 x 4 mm) (pits on original), the whole forming a discrete network. The first type of chamber may have hosted the young (nursery chamber) and/or stored food. The second type of cast replicates a chamber with a pitted floor, which may have formed a brood chamber for 60-70 spherical eggs, each about 3 mm in diameter. Brood chambers in crustacean burrow systems were previously suspected, but only at burrow terminations. The interpreted K-type breeding strategy, brood care and associated functions require a high degree of social organization, none of which has been observed in extant crustaceans, but all occur within social insects.

Remote sensing of intertidal morphological change in Morecambe Bay, U.K., between 1991 and 2007

Tidal Flats are important examples of extensive areas of natural environment that remain relatively unaffected by man. Monitoring of tidal flats is required for a variety of purposes. Remote sensing has become an established technique for the measurement of topography over tidal flats. A further requirement is to measure topographic changes in order to measure sediment budgets. To date there have been few attempts to make quantitative estimates of morphological change over tidal flat areas. This paper illustrates the use of remote sensing to measure quantitative and qualitative changes in the tidal flats of Morecambe Bay during the relatively long period 1991–2007. An understanding of the patterns of sediment transport within the Bay is of considerable interest for coastal management and defence purposes. Tidal asymmetry is considered to be the dominant cause of morphological change in the Bay, with the higher currents associated with the flood tide being the main agency moulding the channel system. Quantitative changes were measured by comparing a Digital Elevation Model (DEM) of the intertidal zone formed using the waterline technique applied to satellite Synthetic Aperture Radar (SAR) images from 1991–1994, to a second DEM constructed from airborne laser altimetry data acquired in 2005. Qualitative changes were studied using additional SAR images acquired since 2003. A significant movement of sediment from below Mean Sea Level (MSL) to above MSL was detected by comparing the two Digital Elevation Models, though the proportion of this change that could be ascribed to seasonal effects was not clear. Between 1991 and 2004 there was a migration of the Ulverston channel of the river Leven north-east by about 5 km, followed by the development of a straighter channel to the west, leaving the previous channel decoupled from the river. This is thought to be due to independent tidal and fluvial forcing mechanisms acting on the channel. The results demonstrate the effectiveness of remote sensing for measurement of long-term morphological change in tidal flat areas. An alternative use of waterlines as partial bathymetry for assimilation into a morphodynamic model of the coastal zone is also discussed.

A high-wavenumber boundary-element method for an acoustic scattering problem

In this paper we show stability and convergence for a novel Galerkin boundary element method approach to the impedance boundary value problem for the Helmholtz equation in a half-plane with piecewise constant boundary data. This problem models, for example, outdoor sound propagation over inhomogeneous flat terrain. To achieve a good approximation with a relatively low number of degrees of freedom we employ a graded mesh with smaller elements adjacent to discontinuities in impedance, and a special set of basis functions for the Galerkin method so that, on each element, the approximation space consists of polynomials (of degree $\nu$) multiplied by traces of plane waves on the boundary. In the case where the impedance is constant outside an interval $[a,b]$, which only requires the discretization of $[a,b]$, we show theoretically and experimentally that the $L_2$ error in computing the acoustic field on $[a,b]$ is ${\cal O}(\log^{\nu+3/2}|k(b-a)| M^{-(\nu+1)})$, where $M$ is the number of degrees of freedom and $k$ is the wavenumber. This indicates that the proposed method is especially commendable for large intervals or a high wavenumber. In a final section we sketch how the same methodology extends to more general scattering problems.

The influence of hilly terrain on canopy-atmosphere carbon dioxide exchange

Topography influences many aspects of forest-atmosphere carbon exchange; yet only a small number of studies have considered the role of topography on the structure of turbulence within and above vegetation and its effect on canopy photosynthesis and the measurement of net ecosystem exchange of CO2 (N-ee) using flux towers. Here, we focus on the interplay between radiative transfer, flow dynamics for neutral stratification, and ecophysiological controls on CO2 sources and sinks within a canopy on a gentle cosine hill. We examine how topography alters the forest-atmosphere CO2 exchange rate when compared to uniform flat terrain using a newly developed first-order closure model that explicitly accounts for the flow dynamics, radiative transfer, and nonlinear eco physiological processes within a plant canopy. We show that variation in radiation and airflow due to topography causes only a minor departure in horizontally averaged and vertically integrated photosynthesis from their flat terrain values. However, topography perturbs the airflow and concentration fields in and above plant canopies, leading to significant horizontal and vertical advection of CO2. Advection terms in the conservation equation may be neglected in flow over homogeneous, flat terrain, and then N-ee = F-c, the vertical turbulent flux of CO2. Model results suggest that vertical and horizontal advection terms are generally of opposite sign and of the same order as the biological sources and sinks. We show that, close to the hilltop, F-c departs by a factor of three compared to its flat terrain counterpart and that the horizontally averaged F-c-at canopy top differs by more than 20% compared to the flat-terrain case.

On the initiation of surface waves by turbulent shear flow

An analytical model is developed for the initial stage of surface wave generation at an air-water interface by a turbulent shear flow in either the air or in the water. The model treats the problem of wave growth departing from a flat interface and is relevant for small waves whose forcing is dominated by turbulent pressure fluctuations. The wave growth is predicted using the linearised and inviscid equations of motion, essentially following Phillips [Phillips, O.M., 1957. On the generation of waves by turbulent wind. J. Fluid Mech. 2, 417-445], but the pressure fluctuations that generate the waves are treated as unsteady and related to the turbulent velocity field using the rapid-distortion treatment of Durbin [Durbin, P.A., 1978. Rapid distortion theory of turbulent flows. PhD thesis, University of Cambridge]. This model, which assumes a constant mean shear rate F, can be viewed as the simplest representation of an oceanic or atmospheric boundary layer. For turbulent flows in the air and in the water producing pressure fluctuations of similar magnitude, the waves generated by turbulence in the water are found to be considerably steeper than those generated by turbulence in the air. For resonant waves, this is shown to be due to the shorter decorrelation time of turbulent pressure in the air (estimated as proportional to 1/Gamma), because of the higher shear rate existing in the air flow, and due to the smaller length scale of the turbulence in the water. Non-resonant waves generated by turbulence in the water, although being somewhat gentler, are still steeper than resonant waves generated by turbulence in the air. Hence, it is suggested that turbulence in the water may have a more important role than previously thought in the initiation of the surface waves that are subsequently amplified by feedback instability mechanisms.

Turbulent flow at 190 m height above London during 2006-2008: A climatology and the applicability of similarity theory

Flow and turbulence above urban terrain is more complex than above rural terrain, due to the different momentum and heat transfer characteristics that are affected by the presence of buildings (e.g. pressure variations around buildings). The applicability of similarity theory (as developed over rural terrain) is tested using observations of flow from a sonic anemometer located at 190.3 m height in London, U.K. using about 6500 h of data. Turbulence statistics—dimensionless wind speed and temperature, standard deviations and correlation coefficients for momentum and heat transfer—were analysed in three ways. First, turbulence statistics were plotted as a function only of a local stability parameter z/Λ (where Λ is the local Obukhov length and z is the height above ground); the σ_i/u_* values (i = u, v, w) for neutral conditions are 2.3, 1.85 and 1.35 respectively, similar to canonical values. Second, analysis of urban mixed-layer formulations during daytime convective conditions over London was undertaken, showing that atmospheric turbulence at high altitude over large cities might not behave dissimilarly from that over rural terrain. Third, correlation coefficients for heat and momentum were analyzed with respect to local stability. The results give confidence in using the framework of local similarity for turbulence measured over London, and perhaps other cities. However, the following caveats for our data are worth noting: (i) the terrain is reasonably flat, (ii) building heights vary little over a large area, and (iii) the sensor height is above the mean roughness sublayer depth.

Sonogashira coupling on an extended gold surface in vacuo: reaction of phenylacetylene with iodobenzene on Au(111)

Temperature-programmed reaction measurements supported by scanning tunneling microscopy have shown that phenylacetylene and iodobenzene react on smooth Au(111) under vacuum conditions to yield biphenyl and diphenyldiacetylene, the result of homocoupling of the reactant molecules. They also produce diphenylacetylene, the result of Sonogashira cross-coupling, prototypical of a class of reactions that are of paramount importance in synthetic organic chemistry and whose mechanism remains controversial. Roughened Au(111) is completely inert toward all three reactions, indicating that the availability of crystallographically well-defined adsorption sites is crucially important. High-resolution X-ray photoelectron spectroscopy and near-edge X-ray absorption fine structure spectroscopy show that the reactants are initially present as intact, essentially flat-lying molecules and that the temperature threshold for Sonogashira coupling coincides with that for C−I bond scission in the iodobenzene reactant. The fractional-order kinetics and low temperature associated with desorption of the Sonogashira product suggest that the reaction occurs at the boundaries of islands of adsorbed reactants and that its appearance in the gas phase is rate-limited by the surface reaction. These findings demonstrate unambiguously and for the first time that this heterogeneous cross-coupling chemistry is an intrinsic property of extended, metallic pure gold surfaces: no other species, including solvent molecules, basic or charged (ionic) species are necessary to mediate the process.

Histone H4 gene expression and morphological changes on shoot apices of strawberry (Fragaria x ananassa Duch.) during floral induction

To investigate flower induction in June-bearing strawberry plants, morphological changes in shoot apices and Historic H4 expression in the central zone during flower initiation were observed. Strawberry plants were placed under flower inducible, short-day conditions (23 degrees C/17 degrees C, 10 h day length) for differing number of days (8, 16, 20, 24 or 32 days) and then these plants were transferred to non-inducible, long-day conditions (25 degrees C/20 degrees C, 14 h day length). The shoot apices of plants placed under short-day conditions for 8 days were flat, similar to shoot apices of plants in the vegetative phase of development, and Histone H4 was not expressed in the central zone during the experimental period. On the other hand, the shoot apices of plants placed under short-day conditions for 16 days remained flat, similar to shoot apices of plants placed under short-day conditions for 8 days, but Histone H4 was expressed in the central zone at the end of the short-day treatment. Morphological changes in the shoot apices of these plants were observed 8 days after the change in day-length. These plants developed differentiated flower organs after they were grown for another 30 days under long-day conditions. These results indicate that changes in the expression pattern of the Histone H4 gene occur before morphological changes during flower induction and that the expression of the gene in the central zone can be used as one of the indicators of the flowering process in strawberries. (c) 2006 Elsevier B.V. All rights reserved.

Ecology of sponge assemblages (Porifera) in the Wakatobi region, south-east Sulawesi, Indonesia: richness and abundance

The influence of sedimentation, depth and substratum angle on sponge assemblages in the Wakatobi region, south-eastern Sulawesi, Indonesia was considered. Sponge assemblages were sampled from two reef localities. The first reef (Sampela) was highly impacted by high sedimentation rates with fine sediment particles that settle slowly, while the second (Hoga) experienced only fast settling coarse sediment with lower overall sedimentation rates. Sponge assemblages were sampled (area occupied and numbers) on the reef fiat (0 m) and at 5 (reef crest), 10 and 15 m (15 m at Hoga only). Some significant (P < 0.001) differences were observed in the area occupied and the number of sponge patches between surface angles and sites. Significantly lower (t > 4.61, df = 9, P < 0.001) sponge numbers, percentage cover and richness were associated with the reef flat at both sites compared with all other depths at each site, with the exception of abundance of sponges on the reef flat at Sampela, which was much greater than at any other depth sampled. Species richness increased with depth at both sites but differences between surface angles were only recorded at Sampela, with higher species richness being found on vertical, inclined and horizontal surfaces respectively A total of 100 sponge species (total area sampled 52.5 m(2)) was reported from the two sites, with 58 species found at Sampela and 71 species at Hoga (41% of species shared). Multi-dimensional scaling (MDS) indicated differences in assemblage structure between sites and most depth intervals, but not substratum angles. A number of biological (e.g. competition and predation) and physical (e.g. sedimentation and aerial exposure) factors were considered to control sponge abundance and richness. Unexpectedly a significant (F-1,F-169 = 148.98, P < 0.001) positive linear relationship was found between sponge density and area occupied. In areas of high sponge coverage, the number of patches was also high, possibly due to fragmentation of large sponges produced as a result of predation and physical disturbance. The MDS results were also the same whether sponge numbers or percentage cover estimates were used, suggesting that although these different approaches yield different sorts of information, the same assemblage structure can be identified.

PDBSprotEC: A web-accessible database linking PDB chains to EC numbers via SwissProt

A mapping between chains in the Protein Databank and Enzyme Classification numbers is invaluable for research into structure-function relationships. Mapping at the chain level is a non-trivial problem and we present an automatically updated Web-server, which provides this link in a queryable form and as a downloadable XML or flat file.

Analysis of the antigen combining site: Correlations between length and sequence composition of the hypervariable loops and the nature of the antigen

It has long been suggested that the overall shape of the antigen combining site (ACS) of antibodies is correlated with the nature of the antigen. For example, deep pockets are characteristic of antibodies that bind haptens, grooves indicate peptide binders, while antibodies that bind to proteins have relatively flat combining sites. In. 1996, MacCallum, Martin and Thornton used a fractal shape descriptor and showed a strong correlation of the shape of the binding region with the general nature of the antigen. However, the shape of the ACS is determined primarily by the lengths of the six complementarity-determining regions (CDRs). Here, we make a direct correlation between the lengths of the CDRs and the nature of the antigen. In addition, we show significant differences in the residue composition of the CDRs of antibodies that bind to different antigen classes. As well as helping us to understand the process of antigen recognition, autoimmune disease and cross-reactivity these results are of direct application in the design of antibody phage libraries and modification of affinity. (C) 2003 Elsevier Science Ltd. All rights reserved.

Computer modelling and estimation of recruitment patterns of non-branching coral colonies at three sites in Wakatobi Marine Park, S.E. Sulawesi, Indonesia; implications for coral reef conservation

We have studied growth and estimated recruitment of massive coral colonies at three sites, Kaledupa, Hoga and Sampela, separated by about 1.5 km in the Wakatobi Marine National Park, S.E. Sulawesi, Indonesia. There was significantly higher species richness (P<0.05), coral cover (P<0.05) and rugosity (P<0.01) at Kaledupa than at Sampela. A model for coral reef growth has been developed based on a rational polynomial function, where dx/dt is an index of coral growth with time; W is the variable (for example, coral weight, coral length or coral area), up to the power of n in the numerator and m in the denominator; a1……an and b1…bm are constants. The values for n and m represent the degree of the polynomial, and can relate to the morphology of the coral. The model was used to simulate typical coral growth curves, and tested using published data obtained by weighing coral colonies underwater in reefs on the south-west coast of Curaçao [‘Neth. J. Sea Res. 10 (1976) 285’]. The model proved an accurate fit to the data, and parameters were obtained for a number of coral species. Surface area data was obtained on over 1200 massive corals at three different sites in the Wakatobi Marine National Park, S.E. Sulawesi, Indonesia. The year of an individual's recruitment was calculated from knowledge of the growth rate modified by application of the rational polynomial model. The estimated pattern of recruitment was variable, with little numbers of massive corals settling and growing before 1950 at the heavily used site, Sampela, relative to the reef site with little or no human use, Kaledupa, and the intermediate site, Hoga. There was a significantly greater sedimentation rate at Sampela than at either Kaledupa (P<0.0001) or Hoga (P<0.0005). The relative mean abundance of fish families present at the reef crests at the three sites, determined using digital video photography, did not correlate with sedimentation rates, underwater visibility or lack of large non-branching coral colonies. Radial growth rates of three genera of non-branching corals were significantly lower at Sampela than at Kaledupa or at Hoga, and there was a high correlation (r=0.89) between radial growth rates and underwater visibility. Porites spp. was the most abundant coral over all the sites and at all depths followed by Favites (P<0.04) and Favia spp. (P<0.03). Colony ages of Porites corals were significantly lower at the 5 m reef flat on the Sampela reef than at the same depth on both other reefs (P<0.005). At Sampela, only 2.8% of corals on the 5 m reef crest are of a size to have survived from before 1950. The Scleractinian coral community of Sampela is severely impacted by depositing sediments which can lead to the suffocation of corals, whilst also decreasing light penetration resulting in decreased growth and calcification rates. The net loss of material from Sampela, if not checked, could result in the loss of this protective barrier which would be to the detriment of the sublittoral sand flats and hence the Sampela village.

The threading of [(CuCN)(2)(mu-4,4 '-bpy)] sheets by CuCN chains

Yellow (CuCN)(2)[(CuCN)(2)(mu-4,4'-bpy)], formed in the hydrothermal reaction of CuCN with 4,4'-bipyridine at 453 K, contains two types of infinite CuCN chains. One set of CuCN chains is linked by 4,4'-bpy ligands to form almost flat sheets of composition [(CuCN)(2)(mu-4,4'-bpy)]. Holes in these sheets are aligned to allow pairs of approximately linear, infinite -(CuCN)- chains to thread through them. The closest interatomic approach between copper atoms in the threading chains and host sheets (similar to2.74 Angstrom) does not appear to represent a significant covalent bond as it leads to only a small distortion of the -(CuCN)- chains from linearity The relationship of this material to the previously determined structures of the host [(CuCN)(2)(mu-4,4'-bpy)] sheets and (CuCN)(3)[(CuCN)(2)(mu-4,4'-bPY)](2), in which these sheets are threaded by single -(CuCN)- chains, is discussed.

Formation of fibrillar structures through self-assembly of designed peptide turns

Three tripeptides Boc-Phe-Aib-Val-OMe (1), Boc-Leu-Aib-p-NA-NO2 (2) and Boc-Pro-Aib-m-NA-NO2 (3) (Aib: alpha-aminoisobutyric acid; p- and m-NA: para- and meta-nitroaniline) have been designed by incorporating aromatic rings to study the self-assembly and fibril formation. Single crystal X-ray diffraction studies show that all the peptides adopt turn-like structures that are self-assembled through intermolecular hydrogen bonds and van der Waals interactions to create layers of beta-sheets. Solvent dependent NMR titration and CD studies show that the turn structures of the peptides also exist in the solution phase. The field emission scanning electron microscopic (FE-SEM) images of the peptides in the solid state reveal fibrillar structures of flat morphology that are formed through beta-sheet mediated self-assembly of the preorganized turn building blocks.