Three-dimensional models of mantle convection : influence of phase transitions and temperature-dependent viscosity

Two of the most important questions in mantle dynamics are investigated in three separate studies: the influence of phase transitions (studies 1 and 2), and the influence of temperature-dependent viscosity (study 3).

(1) Numerical modeling of mantle convection in a three-dimensional spherical shell incorporating the two major mantle phase transitions reveals an inherently three-dimensional flow pattern characterized by accumulation of cold downwellings above the 670 km discontinuity, and cylindrical 'avalanches' of upper mantle material into the lower mantle. The exothermic phase transition at 400 km depth reduces the degree of layering. A region of strongly-depressed temperature occurs at the base of the mantle. The temperature field is strongly modulated by this partial layering, both locally and in globally-averaged diagnostics. Flow penetration is strongly wavelength-dependent, with easy penetration at long wavelengths but strong inhibition at short wavelengths. The amplitude of the geoid is not significantly affected.

(2) Using a simple criterion for the deflection of an upwelling or downwelling by an endothermic phase transition, the scaling of the critical phase buoyancy parameter with the important lengthscales is obtained. The derived trends match those observed in numerical simulations, i.e., deflection is enhanced by (a) shorter wavelengths, (b) narrower up/downwellings (c) internal heating and (d) narrower phase loops.

(3) A systematic investigation into the effects of temperature-dependent viscosity on mantle convection has been performed in three-dimensional Cartesian geometry, with a factor of 1000-2500 viscosity variation, and Rayleigh numbers of 10^5-10^7. Enormous differences in model behavior are found, depending on the details of rheology, heating mode, compressibility and boundary conditions. Stress-free boundaries, compressibility, and temperature-dependent viscosity all favor long-wavelength flows, even in internally heated cases. However, small cells are obtained with some parameter combinations. Downwelling plumes and upwelling sheets are possible when viscosity is dependent solely on temperature. Viscous dissipation becomes important with temperature-dependent viscosity.

The sensitivity of mantle flow and structure to these various complexities illustrates the importance of performing mantle convection calculations with rheological and thermodynamic properties matching as closely as possible those of the Earth.

Structural and mechanistic motifs in membrane proteins: the three-dimensional modelling of rhodopsin, band 3, and the nicotinic acetylcholine receptor

Because so little is known about the structure of membrane proteins, an attempt has been made in this work to develop techniques by which to model them in three dimensions. The procedures devised rely heavily upon the availability of several sequences of a given protein. The modelling procedure is composed of two parts. The first identifies transmembrane regions within the protein sequence on the basis of hydrophobicity, β-turn potential, and the presence of certain amino acid types, specifically, proline and basic residues. The second part of the procedure arranges these transmembrane helices within the bilayer based upon the evolutionary conservation of their residues. Conserved residues are oriented toward other helices and variable residues are positioned to face the surrounding lipids. Available structural information concerning the protein's helical arrangement, including the lengths of interhelical loops, is also taken into account. Rhodopsin, band 3, and the nicotinic acetylcholine receptor have all been modelled using this methodology, and mechanisms of action could be proposed based upon the resulting structures.

Specific residues in the rhodopsin and iodopsin sequences were identified, which may regulate the proteins' wavelength selectivities. A hinge-like motion of helices M3, M4, and M5 with respect to the rest of the protein was proposed to result in the activation of transducin, the G-protein associated with rhodopsin. A similar mechanism is also proposed for signal transduction by the muscarinic acetylcholine and β-adrenergic receptors.

The nicotinic acetylcholine receptor was modelled with four trans-membrane helices per subunit and with the five homologous M2 helices forming the cation channel. Putative channel-lining residues were identified and a mechanism of channel-opening based upon the concerted, tangential rotation of the M2 helices was proposed.

Band 3, the anion exchange protein found in the erythrocyte membrane, was modelled with 14 transmembrane helices. In general the pathway of anion transport can be viewed as a channel composed of six helices that contains a single hydrophobic restriction. This hydrophobic region will not allow the passage of charged species, unless they are part of an ion-pair. An arginine residue located near this restriction is proposed to be responsible for anion transport. When ion-paired with a transportable anion it rotates across the barrier and releases the anion on the other side of the membrane. A similar process returns it to its original position. This proposed mechanism, based on the three-dimensional model, can account for the passive, electroneutral, anion exchange observed for band 3. Dianions can be transported through a similar mechanism with the additional participation of a histidine residue. Both residues are located on M10.

Shock / boundary-layer interaction control using three-dimensional bumps for transonic wings

Three-dimensional bumps have been developed and investigated, aiming at the two major objectives of shock-wave / boundary-layer interaction control, i.e. drag reduction and suppression of separation, simultaneously. An experimental investigation has been conducted for a default rounded bump in channel now at University of Cambridge and a computational study has been performed for a spanwise series of rounded bumps mounted on a transonic aerofoil at University of Stuttgart. Observed in both cases are wave drag reduction owing to A-shock structures produced by three-dimensional surface bumps and mild control effects on the boundary layer. The effects of rough surface and tall extension have been investigated as well as several geometric variations and multiple bump configurations. A double configuration of narrow rounded bumps has been found to best perform amongst the tested, considerably reducing wave drag through a well-established A-shock structure with little viscous penalty and thus achieving substantial overall drag reduction. Counter-rotating streamwise vortex pairs have been produced by some configurations as a result of local flow separation, but they have been observed to be confined in relatively narrow wake regions, expected to be beneficial in suppressing large-scale separation under off-design condition despite increase of viscous drag. On the whole a large potential of three-dimensional control with discrete rounded bumps has been demonstrated both experimentally and numerically, and experimental investigation of bumps fitted on a transonic aerofoil or wing is suggested toward practical application.

Behaviour of unsteady transonic shock / boundary layer interactions with three-dimensional effects

An experimental investigation into the response of transonic SBLIs to periodic down-stream pressure perturbations in a parallel walled duct has been conducted. Tests have been carried out with a shock strength of M ∞ = 1.5 for pressure perturbation frequencies in the range 16-90 Hz. Analysis of the steady interaction at M∞ = 1.5 has also been made. The principle measurement techniques were high speed schlieren photography and laser Doppler anemometry. The structure of the steady SBLI was found to be highly three-dimensional, with large corner flows and sidewall SBLIs. These aspects are thought to influence the upstream transmission of pressure information through the interaction by affecting the post-shock flow field, including the extent of regions of secondary supersonic flow. At low frequency, the dynamics of shock motion can be predicted using an inviscid analytical model. At increased frequencies, viscous effects become significant and the shock exhibits unexpected dynamic behaviour, due to a phase lag between the upstream transmission of pressure information in the core flow and in the viscous boundary layers. Flow control in the form of micro-vane vortex generators was found to have a small impact on shock dynamics, due to the effect it had on the post-shock flow field outside the viscous boundary layer region. The relationship between inviscid and viscous effects is developed and potential destabilising mechanisms for SBLIs in practical applications are suggested. Copyright © 2009 by Paul Bruce and Holger Babinsky.

Three-dimensional effects on sliding and waving wings

Like large insects, micro air vehicles operate at low Reynolds numbers O(1; 000 - 10; 000) in a regime characterized by separated flow and strong vortices. The leading-edge vortex has been identified as a significant source of high lift on insect wings, but the conditions required for the formation of a stably attached leading-edge vortex are not yet known. The waving wing is designed to model the translational phase of an insect wing stroke by preserving the unsteady starting and stopping motion as well as three-dimensionality in both wing geometry (via a finite-span wing) and kinematics (via wing rotation). The current study examines the effect of the spanwise velocity gradient on the development of the leading-edge vortex along the wing as well as the effects of increasing threedimensionalityby decreasing wing aspect ratio from four to two. Dye flow visualization and particle image velocimetry reveal that the leading-edge vortices that form on a sliding or waving wing have a very high aspect ratio. The structure of the flow is largely two-dimensional on both sliding and waving wings and there is minimal interaction between the leading-edge vortices and the tip vortex. Significant spanwise flow was observed on the waving wing but not on the sliding wing. Despite the increased three-dimensionality on the aspect ratio 2 waving wing, there is no evidence of an attached leading-edge vortex and the structure of the flow is very similar to that on the higher-aspect-ratio wing and sliding wing. © Copyright 2010.

Protein three-dimensional structural databases: Domains, structurally aligned homologues and superfamilies

This paper reports the availability of a database of protein structural domains (DDBASE), an alignment database of homologous proteins (HOMSTRAD) and a database of structurally aligned superfamilies (CAMPASS) on the World Wide Web (WWW). DDBASE contains information on the organization of structural domains and their boundaries; it includes only one representative domain from each of the homologous families. This database has been derived by identifying the presence of structural domains in proteins on the basis of inter-secondary structural distances using the program DIAL [Sowdhamini & Blundell (1995), Protein Sci. 4, 506-520]. The alignment of proteins in superfamilies has been performed on the basis of the structural features and relationships of individual residues using the program COMPARER [Sali & Blundell (1990), J. Mol. Biol. 212, 403-428]. The alignment databases contain information on the conserved structural features in homologous proteins and those belonging to superfamilies. Available data include the sequence alignments in structure-annotated formats and the provision for viewing superposed structures of proteins using a graphical interface. Such information, which is freely accessible on the WWW, should be of value to crystallographers in the comparison of newly determined protein structures with previously identified protein domains or existing families.

Experimental study into the flow physics of three-dimensional shock control bumps

This paper describes a fundamental experimental study of the flow structure around a single three-dimensional (3D) transonic shock control bump (SCB) mounted on a flat surface in a wind tunnel. Tests have been carried out with a Mach 1.3 normal shock wave located at a number of streamwise positions relative to the SCB. Details of the flow have been studied using the experimental techniques of schlieren photography, surface oil flow visualization, pressure sensitive paint, and laser Doppler anemometry. The results of the work build on the findings of previous researchers and shed new light on the flow physics of 3D SCBs. It is found that spanwise pressure gradients across the SCB ramp and the shape of the SCB sides affect the magnitude and uniformity of flow turning generated by the bump, which can impact on the spanwise propagation of the quasi-two-dimensional (2D) shock structure produced by a 3DSCB. At the bump crest, vortices can form if the pressure on the crest is significantly lower than at either side of the bump. The trajectories of these vortices, which are relatively weak, are strongly influenced by any spanwise pressure gradients across the bump tail. Asignificant difference between 2D and 3D SCBs highlighted by the study is the impact of spanwise pressure gradients on 3D SCB performance. The magnitude of these spanwise pressure gradients is determined largely by SCB geometry and shock position. Copyright © 2011 by the American Institute of Aeronautics and Astronautics, Inc.

Vortical structures on three-dimensional shock control bumps

The vortical wake structure produced by a three-dimensional shock control bump (SCB) is thought to be useful for controlling transonic buffet on airfoils. However, at present the vorticity produced is relatively weak and the production mechanism is not well understood. Using a combined experimental and computational approach, a preliminary investigation on the wake vorticity for different bump geometries has been carried out. The structure of the wake for on and off-design conditions are considered, and the effects on the downstream boundary layer demonstrated. Three main vortical structures are observed: a primary vortex pair, weak inter-bump vortices and shear flow in the lambda-shock region. The effect of pressure gradients on vortex strength is examined and it is found that spanwise pressure gradients on the front section of the bump are the most significant parameter influencing vortex strength. © 2013 by S.P. Colliss et al.

Binder free three-dimensional sulphur/few-layer graphene foam cathode with enhanced high-rate capability for rechargeable lithium sulphur batteries.

A novel ultra-lightweight three-dimensional (3-D) cathode system for lithium sulphur (Li-S) batteries has been synthesised by loading sulphur on to an interconnected 3-D network of few-layered graphene (FLG) via a sulphur solution infiltration method. A free-standing FLG monolithic network foam was formed as a negative of a Ni metallic foam template by CVD followed by etching away of Ni. The FLG foam offers excellent electrical conductivity, an appropriate hierarchical pore structure for containing the electro-active sulphur and facilitates rapid electron/ion transport. This cathode system does not require any additional binding agents, conductive additives or a separate metallic current collector thus decreasing the weight of the cathode by typically ∼20-30 wt%. A Li-S battery with the sulphur-FLG foam cathode shows good electrochemical stability and high rate discharge capacity retention for up to 400 discharge/charge cycles at a high current density of 3200 mA g(-1). Even after 400 cycles the capacity decay is only ∼0.064% per cycle relative to the early (e.g. the 5th cycle) discharge capacity, while yielding an average columbic efficiency of ∼96.2%. Our results indicate the potential suitability of graphene foam for efficient, ultra-light and high-performance batteries.

Syntheses, structures, and magnetic properties of two novel three-dimensional frameworks built from M4O4 cubanes and dicyanamide bridges

Two novel coordination polymers Ni-4(CH3O)(4)(CH3OH)(4)(dca)(4) (1) and Co-4(CH3O)(4)(CH3OH)(4)(dca)(4) (2) have been synthesized by solvethermal reaction. X-ray single-crystal analysis reveals that the two complexes are isostrutural and possess 3D frameworks that are built from the M4O4(M= Ni (1) and Co (2)) cubanelike building blocks linked by dicyanamide (dca) bridges. The temperature dependence of the magnetic susceptibility was measured and the DC experiment data were fitted using the Heisenberg spin Hamiltonian.

Supramolecular isomerism in zinc hydroxide coordination polymers with pyridine-2,4-dicarboxylic acid: Two polymorphs with centrosymmetric two-dimensional and acentric three-dimensional coordination networks

Reactions of Zn(BF4)(2) and pyridine-2,4-dicarboxylic acid (2,4-pydcH(2)) in the presence of 1,2-bis( 4-pyridyl) ethylene or 1,3-bis(4-pyridyl) propane under hydro(solvo) thermal conditions yielded two polymorphic metal-organic coordination polymers formulated as Zn-2(OH)(2)(2,4-pydc) (1 and 2). Polymorph 1 features a two-dimensional (2-D) layer-like structure that is constructed by 2,4-pydc ligands bridging between the Zn-OH-Zn double-chain units. Each single Zn-OH-Zn chain is composed of mu(2)-OH groups connecting trigonal bipyramidal and tetrahedral Zn centers. Polymorph 2 is a 3-D coordination polymer containing 2-D Zn-OH-Zn sheets that consist of mu(2)- and mu(3)-OH groups and trigonal bipyramidal Zn centers. The sheets are pillared by 2,4-pydc ligands to form an acentric structural architecture. 1 and 2 are rare examples that the two polymorphs exhibit a centrosymmetric 2-D coordination network and an acentric 3-D coordination network, respectively. The different structures lead to differences in photoluminescent properties and thermal stabilities for 1 and 2.

Three-dimensional structural features and the toxicity of aminobenzenes and phenols

For a QSAR of the toxicity of aminobenzenes in environment and their structures, the projection areas of the molecules in 3D space were calculated. The combinations of the projection areas and quantum chemical as well as topological parameters were performed for the methods of regression analysis and neural network, and much better results than that by using CoMFA were achieved.

Novel hydrogen-bonded three-dimensional networks encapsulating one-dimensional covalent chains: [M(4,4 '-bipy)(H2O)4](4-abs)2 center dot nH(2)O (4,4 '-bipy=4,4 '-Bipyridine; 4-abs=4-aminobenzenesulfonate) (M=Co, n=1; M=Mn, n=2)

Two novel compounds, [Co(4,4'-bipy)(H2O)(4)](4-abS)(2).H2O (1) and [Mn(4,4'-bipy)(H2O)(4)](4-abs)(2).2H(2)O (2) (4,4'-bipy = 4,4'-bipyridine; 4-abs = 4-aminobenzenesulfonate), have been synthesized in aqueous solution and characterized by single-crystal X-ray diffraction, elemental analyses, UV-vis and IR spectra, and TG analysis. X-ray structural analysis revealed that 1 and 2 both possess unusual hydrogen-bonded three-dimensional (3-D) networks encapsulating one-dimensional (1-D) covalently bonded infinite [M(4,4'-bipy)(H2O)(4)](2+) (M = Co, Mn) chains. The 4-abs anions in 1 form 1-D zigzag chains through hydrogen bonds. These chains are further extended through crystallization water molecules into 3-D hydrogen-bonded networks with 1-D channels, in which the [Co(4,4'-bipy)(H2O)(4)](2+) linear covalently bonded chains are located. Crystal data for 1: C22H30CoN4O11S2, monoclinic P2(1), a = 11.380(2) Angstrom, b = 8.0274(16) Angstrom, c = 15.670(3) Angstrom, alpha = gamma = 90degrees, beta = 92.82(3)degrees, Z = 2. Compound 2 contains interesting two-dimensional (2-D) honeycomb-like networks formed by 4-abs anions and lattice water molecules via hydrogen bonding, which are extended through other crystallization water molecules into three dimensions with 1-D hexagonal channels. The [Mn(4,4'-bipy)(H2O)(4)](2+) linear covalent chains exist in these channels. Crystal data for 2: C22H32WN4O12S2, monoclinic P2(1)/c, a = 15.0833(14) Angstrom, b = 8.2887(4) Angstrom, c = 23.2228(15) Angstrom, alpha = gamma = 90degrees, beta = 95.186(3)degrees, Z = 4.

The Three-Dimensional Interpretation of a Class of Simple Line-Drawings

We provide a theory of the three-dimensional interpretation of a class of line-drawings called p-images, which are interpreted by the human vision system as parallelepipeds ("boxes"). Despite their simplicity, p-images raise a number of interesting vision questions: *Why are p-images seen as three-dimensional objects? Why not just as flatimages? *What are the dimensions and pose of the perceived objects? *Why are some p-images interpreted as rectangular boxes, while others are seen as skewed, even though there is no obvious distinction between the images? *When p-images are rotated in three dimensions, why are the image-sequences perceived as distorting objects---even though structure-from-motion would predict that rigid objects would be seen? *Why are some three-dimensional parallelepipeds seen as radically different when viewed from different viewpoints? We show that these and related questions can be answered with the help of a single mathematical result and an associated perceptual principle. An interesting special case arises when there are right angles in the p-image. This case represents a singularity in the equations and is mystifying from the vision point of view. It would seem that (at least in this case) the vision system does not follow the ordinary rules of geometry but operates in accordance with other (and as yet unknown) principles.

Chondrogenesis and mineralization during in vitro culture of human mesenchymal stem cells on three-dimensional woven scaffolds.

Human mesenchymal stem cells (hMSCs) and three-dimensional (3D) woven poly(ɛ-caprolactone) (PCL) scaffolds are promising tools for skeletal tissue engineering. We hypothesized that in vitro culture duration and medium additives can individually and interactively influence the structure, composition, mechanical, and molecular properties of engineered tissues based on hMSCs and 3D poly(ɛ-caprolactone). Bone marrow hMSCs were suspended in collagen gel, seeded on scaffolds, and cultured for 1, 21, or 45 days under chondrogenic and/or osteogenic conditions. Structure, composition, biomechanics, and gene expression were analyzed. In chondrogenic medium, cartilaginous tissue formed by day 21, and hypertrophic mineralization was observed in the newly formed extracellular matrix at the interface with underlying scaffold by day 45. Glycosaminoglycan, hydroxyproline, and calcium contents, and alkaline phosphatase activity depended on culture duration and medium additives, with significant interactive effects (all p < 0.0001). The 45-day constructs exhibited mechanical properties on the order of magnitude of native articular cartilage (aggregate, Young's, and shear moduli of 0.15, 0.12, and 0.033 MPa, respectively). Gene expression was characteristic of chondrogenesis and endochondral bone formation, with sequential regulation of Sox-9, collagen type II, aggrecan, core binding factor alpha 1 (Cbfα1)/Runx2, bone sialoprotein, bone morphogenetic protein-2, and osteocalcin. In contrast, osteogenic medium produced limited osteogenesis. Long-term culture of hMSC on 3D scaffolds resulted in chondrogenesis and regional mineralization at the interface between soft, newly formed engineered cartilage, and stiffer underlying scaffold. These findings merit consideration when developing grafts for osteochondral defect repair.