Foliar micromorphology and anatomy of Ugni molinae Turcz. (Myrtaceae), with particular reference to schizogenous secretory cavities

Background Ugni molinae Turcz. is one of the most studied species of South American Myrtaceae due to its edible fruits and foliar medicinal compounds. However, there is no anatomical study of the leaves or secretory cavities. This paper seeks to describe the leaf micromorphology and anatomy of the species using standard protocols for light and scanning electron microscopy. Secretory cavities were anatomically characterized in young and mature leaves. Histochemical staining of the cavities was performed. Results The leaves of U. molinae are hypostomatic, have a wavy surface and possess scattered hairs. Leaf anatomical features include dorsiventral mesophyll, two to three layers of palisade parenchyma with abundant chloroplasts, calcium oxalate crystals and internal phloem in vascular bundles. Schizogenous secretory cavities are present on the abaxial surface and are mainly located on the margins of the leaves. Histochemical tests of these cavities suggest the presence of lipophilic substances. Conclusions This is the first study of secretory cavities in Chilean Myrtaceae. In general, micromorphological and anatomical characters are similar to other species of the family. The present findings could provide valuable anatomical information for future research in South American Myrtaceae.

Natural convection in rectangular cavities at high Rayleigh number

Natural convection in rectangular two-dimensional cavities with differentially heated side walls is a standard problem in numerical heat transfer. Most of the existing studies has considered the low Ra laminar regime. The general thrust of the present research is to investigate higher Ra flows extending into the unsteady and turbulent regimes where the physics is not fully understood and appropriate models for turbulence are not yet established. In the present study the Boussinesq approximation is being used, but the theoretical background and some preliminary results have been obtained[1] for flows with variable properties.

Laminar and turbulent natural convection in rectangular cavities

A computer program has been developed for the prediction of buoyancy-driven laminar and turbulent flow in rectangular air-filled two-dimensional cavities with differentially heated side walls. Laminar flow predictions for a square cavity and Rayleigh numbers from Ra = 10^3 up to the onset of unsteady flow have been obtained. Accurate solutions for Ra = 5 x 10^6, 10^7, 5 x 10^7 and 10^8 are presented and an estimate for the critical Rayleigh number at which the steady laminar flow becomes unsteady is given for this geometry. Numerical predictions of turbulent flow have been obtained for RaH~0(10^9 -10^11 ) and compared with existing experimental data. A previously developed second moment closure model (Behnia et al. 1987) has been used to model the turbulence. Results indicate that a second moment closure model is capable of predicting the observed flow features.

Laminar and turbulent natural convection in rectangular cavities

"This chapter discusses laminar and turbulent natural convection in rectangular cavities. Natural convection in rectangular two-dimensional cavities has become a standard problem in numerical heat transfer because of its relevance in understanding a number of problems in engineering. Current research identified a number of difficulties with regard to the numerical methods and the turbulence modeling for this class of flows. Obtaining numerical predictions at high Rayleigh numbers proved computationally expensive such that results beyond Ra ∼ 1014 are rarely reported. The chapter discusses a study in which it was found that turbulent computations in square cavities can't be extended beyond Ra ∼ O (1012) despite having developed a code that proved very efficient for the high Ra laminar regime. As the Rayleigh number increased, thin boundary layers began to form next to the vertical walls, and the central region became progressively more stagnant and highly stratified. Results obtained for the high Ra laminar regime were in good agreement with existing studies. Turbulence computations, although of a preliminary nature, indicated that a second moment closure model was capable of predicting the experimentally observed flow features."--Publisher Summary

Interfacial Regions Governing Internal Cavities of Dendrimers. Studies of Poly(alkyl aryl ether) Dendrimers Constituted with Linkers of Varying Alkyl Chain Length

This report deals with a study of the properties of internal cavities of dendritic macromolecules that are capable Of encapsulating and mediating photoreactions of guest molecules. The internal cavity structures of dendrimers are determined by the interfacial regions between the aqueous exterior and hydrocarbon like interior constituted by the linkers that connect symmetrically sited branch points constituting the dendrimer and head groups that cap the dendrimers. Phloroglucinol-based poly(alkyl aryl ether) dendrimers constituted with a homologous series of alkyl linkers were undertaken for the current study. Twelve dendrimers within first, second, and third generations, having ethyl, n-propyl, n-butyl, and n-pentyl groups as the linkers and hydroxyl groups at peripheries in each generation, were synthesized. Encapsulation of pyrene and coumarins by aqueous basic solutions of dendrimers were monitored-by UV-vis and fluorescence spectroscopies, which showed that a lower generation dendrimer with an optimal alkyl linker presented better encapsulation abilities than a higher generation dendrimer. Norrish type I photoreaction of dibenzyl ketone was carried out within the above: series of dendrimers to probe their abilities to hold guests and reactive inthermediate radical pairs within themselves. The extent of cage effect from the series of third generation dendrimers was observed to be higher with dendrimers having an n-pentyl group as the linker.

Nucleation and growth characteristics of cavities during the early stages of tensile creep deformation in a superplastic zirconia-20 wt% alumina composite

Constant-stress tensile creep experiments on a superplastic 3-mol%-yttria-stabilized tetragonal zirconia composite with 20 wt% alumina revealed that cavities nucleate relatively early during tensile deformation. The number of cavities nucleated increases with increasing imposed stress. The cavities nucleate at triple points associated largely with an alumina grain, and then grow rapidly in a cracklike manner to attain dimensions on the order of the grain facet size. It is suggested that coarser-grained superplastic ceramics exhibit lower ductility due to the ease in formation of such grain boundary facet-cracks and their interlinkage to form a macroscopic crack of critical dimensions.

DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins

Depth measures the extent of atom/residue burial within a protein. It correlates with properties such as protein stability, hydrogen exchange rate, protein-protein interaction hot spots, post-translational modification sites and sequence variability. Our server, DEPTH, accurately computes depth and solvent-accessible surface area (SASA) values. We show that depth can be used to predict small molecule ligand binding cavities in proteins. Often, some of the residues lining a ligand binding cavity are both deep and solvent exposed. Using the depth-SASA pair values for a residue, its likelihood to form part of a small molecule binding cavity is estimated. The parameters of the method were calibrated over a training set of 900 high-resolution X-ray crystal structures of single-domain proteins bound to small molecules (molecular weight < 1.5 KDa). The prediction accuracy of DEPTH is comparable to that of other geometry-based prediction methods including LIGSITE, SURFNET and Pocket-Finder (all with Matthew's correlation coefficient of similar to 0.4) over a testing set of 225 single and multi-chain protein structures. Users have the option of tuning several parameters to detect cavities of different sizes, for example, geometrically flat binding sites. The input to the server is a protein 3D structure in PDB format. The users have the option of tuning the values of four parameters associated with the computation of residue depth and the prediction of binding cavities. The computed depths, SASA and binding cavity predictions are displayed in 2D plots and mapped onto 3D representations of the protein structure using Jmol. Links are provided to download the outputs. Our server is useful for all structural analysis based on residue depth and SASA, such as guiding site-directed mutagenesis experiments and small molecule docking exercises, in the context of protein functional annotation and drug discovery.

Dynamic Internal Cavities of Dendrimers as Constrained Media. A Study of Photochemical Isomerizations of Stilbene and Azobenzene Using Poly(alkyl aryl ether) Dendrimers

Dendritic rnicroenvironments defined by dynamic internal cavities of a dendrimer were probed through geometric isomerization of stilbene and azobenzene. A third-generation poly(alkyl aryl ether) dendrimer with hydrophilic exterior and hydrophobic interior was used as a reaction cavity in aqueous medium. The dynamic inner cavity sizes were varied by utilizing alkyl linkers that connect the branch junctures from ethyl to n-pentyl moiety (C(2)G(3)-C(5)G(3)). Dendrimers constituted with n-pentyl linker were found to afford higher solubilities of stilbene and azobenzene. Direct irradiation of trans-stilbene showed that C(5)G(3) and C(4)G(3) dendrimers afforded considerable phenanthrene formation, in addition to cis-stilbene, whereas C(3)G(3) and C(2)G(3) gave only cis-stilbene. An electron-transfer sensitized trans-cis isomerization, using cresyl violet perchlorate as the sensitizer, also led to similar results. Thermal isomerization of cis-azobenzene to trans-azobenzene within dendritic microenvironments revealed that the activation energy of the cis- to trans-isomer was increasing in the series C(5)G(3) < C(4)G(3) < C(3)G(3)

Natural convection in a series of thermally interacting cavities with wall mounted heaters

Laminar natural convection in a series of thermally interacting cavities is numerically studied. Each cavity consists of a conducting bottom wall with a surface mounted heater. The side walls of the cavities are isothermally cooled. Each cavity thermally interacts with its adjacent cavities through the conducting walls. Flow and heat transfer characteristics are studied in detail for various Rayleigh numbers. The convection characteristics in multiple cavities are compared with those in single independent cavity. The thermal interaction between the cavities results in lower temperatures compared with those in independent cavities. While heat is rejected into the adjacent upper cavity through some portion of the conducting wall, heat is received from the adjacent cavity through the remaining portion of the wall. The influence of substrate conductivity on heat exchange between adjacent cavities are examined. Substrate conductivity shows strong effect on temperature distribution. When cooling at both vertical sides is changed to one side cooling, the heat transfer characteristics are changed drastically and many interesting flow features are observed. Effects of cavity aspect ratio is studied and higher heat transfer rates are observed at higher aspect ratios. Correlations for dimensionless temperature maximum and average Nusselt number are presented in terms of Rayleigh number.

Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pK(a) of ionizable residues in proteins

Residue depth accurately measures burial and parameterizes local protein environment. Depth is the distance of any atom/residue to the closest bulk water. We consider the non-bulk waters to occupy cavities, whose volumes are determined using a Voronoi procedure. Our estimation of cavity sizes is statistically superior to estimates made by CASTp and VOIDOO, and on par with McVol over a data set of 40 cavities. Our calculated cavity volumes correlated best with the experimentally determined destabilization of 34 mutants from five proteins. Some of the cavities identified are capable of binding small molecule ligands. In this study, we have enhanced our depth-based predictions of binding sites by including evolutionary information. We have demonstrated that on a database (LigASite) of similar to 200 proteins, we perform on par with ConCavity and better than MetaPocket 2.0. Our predictions, while less sensitive, are more specific and precise. Finally, we use depth (and other features) to predict pK(a)s of GLU, ASP, LYS and HIS residues. Our results produce an average error of just <1 pH unit over 60 predictions. Our simple empirical method is statistically on par with two and superior to three other methods while inferior to only one. The DEPTH server (http://mspc.bii.a-star.edu.sg/depth/) is an ideal tool for rapid yet accurate structural analyses of protein structures.

Numerical study of driven flows of shear thinning viscoelastic fluids in rectangular cavities

In this work, we present a numerical study of flow of shear thinning viscoelastic fluids in rectangular lid driven cavities for a wide range of aspect ratios (depth to width ratio) varying from 1/16 to 4. In particular, the effect of elasticity, inertia, model parameters and polymer concentration on flow features in rectangular driven cavity has been studied for two shear thinning viscoelastic fluids, namely, Giesekus and linear PTT. We perform numerical simulations using the symmetric square root representation of the conformation tensor to stabilize the numerical scheme against the high Weissenberg number problem. The variation in flow structures associated with merging and splitting of elongated vortices in shallow cavities and coalescence of corner eddies to yield a second primary vortex in deep cavities with respect to the variation in flow parameters is discussed. We discuss the effect of the dominant eigenvalues and the corresponding eigenvectors on the location of the primary eddy in the cavity. We also demonstrate, by performing numerical simulations for shallow and deep cavities, that where the Deborah number (based on convective time scale) characterizes the elastic behaviour of the fluid in deep cavities, Weissenberg number (based on shear rate) should be used for shallow cavities. (C) 2016 Elsevier B.V. All rights reserved.

The strength distribution of brittle materials with a high-concentration of cavities

The maximum stress concentration factor in brittle materials with a high concentration of cavities is obtained. The interaction between the nearest cavities, in addition to the far field interactions, is taken into account to evaluate the strength distribution based on the statistical analysis of the nearest distance distribution. Through this investigation, it is found that the interaction between the nearest neighbors is much more important than the far field interactions, and one has to consider it in calculating the strength of brittle materials even if the volume fraction of cavities it contains is small. The other important conclusion is that the maximum stress concentration factor has a wide scattered distribution.

Resonant mode analysis in toroidal cavities with elliptic cross-sections

Resonant cavity modes in a torus with elliptical cross section are studied by means of a direct variational method. The nonlinear effects of toroidicity and ellipticity on the frequency of the basic mode are analyzed simply and systematically without the restriction of linear theory. It is shown that the toroidicity effect on the m = 0 transverse magnetic mode is less-than-or-equal-to 11%. The frequency of the mode shifts approximately 11-29% when the elongation of the cross section changes from 1 to 2. The effects of toroidicity and ellipticity differ for each resonant mode.