Travel time tomographic studies of seismic structures around subducted lithospheric slabs

The nature of the subducted lithospheric slab is investigated seismologically by tomographic inversions of ISC residual travel times. The slab, in which nearly all deep earthquakes occur, is fast in the seismic images because it is much cooler than the ambient mantle. High resolution three-dimensional P and S wave models in the NW Pacific are obtained using regional data, while inversion for the SW Pacific slabs includes teleseismic arrivals. Resolution and noise estimations show the models are generally well-resolved.

The slab anomalies in these models, as inferred from the seismicity, are generally coherent in the upper mantle and become contorted and decrease in amplitude with depth. Fast slabs are surrounded by slow regions shallower than 350 km depth. Slab fingering, including segmentation and spreading, is indicated near the bottom of the upper mantle. The fast anomalies associated with the Japan, Izu-Bonin, Mariana and Kermadec subduction zones tend to flatten to sub-horizontal at depth, while downward spreading may occur under parts of the Mariana and Kuril arcs. The Tonga slab appears to end around 550 km depth, but is underlain by a fast band at 750-1000 km depths.

The NW Pacific model combined with the Clayton-Comer mantle model predicts many observed residual sphere patterns. The predictions indicate that the near-source anomalies affect the residual spheres less than the teleseismic contributions. The teleseismic contributions may be removed either by using a mantle model, or using teleseismic station averages of residuals from only regional events. The slab-like fast bands in the corrected residual spheres are are consistent with seismicity trends under the Mariana Tzu-Bonin and Japan trenches, but are inconsistent for the Kuril events.

The comparison of the tomographic models with earthquake focal mechanisms shows that deep compression axes and fast velocity slab anomalies are in consistent alignment, even when the slab is contorted or flattened. Abnormal stress patterns are seen at major junctions of the arcs. The depth boundary between tension and compression in the central parts of these arcs appears to depend on the dip and topology of the slab.

Computational Predictions of G Protein-Coupled Receptor Structures and Binding Sites

G protein-coupled receptors (GPCRs) are the largest family of proteins within the human genome. They consist of seven transmembrane (TM) helices, with a N-terminal region of varying length and structure on the extracellular side, and a C-terminus on the intracellular side. GPCRs are involved in transmitting extracellular signals to cells, and as such are crucial drug targets. Designing pharmaceuticals to target GPCRs is greatly aided by full-atom structural information of the proteins. In particular, the TM region of GPCRs is where small molecule ligands (much more bioavailable than peptide ligands) typically bind to the receptors. In recent years nearly thirty distinct GPCR TM regions have been crystallized. However, there are more than 1,000 GPCRs, leaving the vast majority of GPCRs with limited structural information. Additionally, GPCRs are known to exist in a myriad of conformational states in the body, rendering the static x-ray crystal structures an incomplete reflection of GPCR structures. In order to obtain an ensemble of GPCR structures, we have developed the GEnSeMBLE procedure to rapidly sample a large number of variations of GPCR helix rotations and tilts. The lowest energy GEnSeMBLE structures are then docked to small molecule ligands and optimized. The GPCR family consists of five subfamilies with little to no sequence homology between them: class A, B1, B2, C, and Frizzled/Taste2. Almost all of the GPCR crystal structures have been of class A GPCRs, and much is known about their conserved interactions and binding sites. In this work we particularly focus on class B1 GPCRs, and aim to understand that family’s interactions and binding sites both to small molecules and their native peptide ligands. Specifically, we predict the full atom structure and peptide binding site of the glucagon-like peptide receptor and the TM region and small molecule binding sites for eight other class B1 GPCRs: CALRL, CRFR1, GIPR, GLR, PACR, PTH1R, VIPR1, and VIPR2. Our class B1 work reveals multiple conserved interactions across the B1 subfamily as well as a consistent small molecule binding site centrally located in the TM bundle. Both the interactions and the binding sites are distinct from those seen in the more well-characterized class A GPCRs, and as such our work provides a strong starting point for drug design targeting class B1 proteins. We also predict the full structure of CXCR4 bound to a small molecule, a class A GPCR that was not closely related to any of the class A GPCRs at the time of the work.

Fish pass design - criteria for the design and approval of fish passes and other structures to facilitate the passage of migratory fish in rivers

Many of British rivers hold stocks of salmon (Salmo salar L.) and sea trout (Salmo trutta L.) and during most of the year some of the adult fish migrate upstream to the head waters where, with the advent of winter, they will eventually spawn. For a variety of reasons, including the generation of power for milling, improving navigation and measuring water flow, man has put obstacles in the way of migratory fish which have added to those already provided by nature in the shape of rapids and waterfalls. While both salmon and sea trout, particularly the former, are capable of spectacular leaps the movement of fish over man-made and natural obstacles can be helped, or even made possible, by the judicious use of fish passes. These are designed to give the fish an easier route over or round an obstacle by allowing it to overcome the water head difference in a series of stages ('pool and traverse' fish pass) or by reducing the water velocity in a sloping channel (Denil fish pass). Salmon and sea trout make their spawning runs at different flow conditions, salmon preferring much higher water flows than sea trout. Hence the design of fish passes requires an understanding of the swimming ability of fish (speed and endurance) and the effect of water temperature on this ability. Also the unique features of each site must be appreciated to enable the pass to be positioned so that its entrance is readily located. As well as salmon and sea trout, rivers often have stocks of coarse fish and eels. Coarse fish migrations are generally local in character and although some obstructions such as weirs may allow downstream passages only, they do not cause a significant problem. Eels, like salmon and sea trout, travel both up and down river during the course of their life histories. However, the climbing power of elvers is legendary and it is not normally necessary to offer them help, while adult silver eels migrate at times of high water flow when downstream movement is comparatively easy: for these reasons neither coarse fish nor eels are considered further. The provision of fish passes is, in many instances, mandatory under the Salmon and Freshwater Fisheries Act 1975. This report is intended for those involved in the planning, siting, construction and operation of fish passes and is written to clarify the hydraulic problems for the biologist and the biological problems for the engineer. It is also intended to explain the criteria by which the design of an individual pass is assessed for Ministerial Approval.

A point for comparison: the Flower Garden Banks National Marine Sanctuary

A reoccurring goal listed during the creation of Marine Protected Areas (MPAs) is to return the region to a former state. However, limited data is available that describes or characterizes this former condition. Data collected from ecosystems with comparatively limited anthropogenic impacts, can provide invaluable information in suggesting what former states may have looked like. One example is the Flower Garden Banks National Marine Sanctuary which is located 180 kilometers off the coast of Texas. These relatively isolated and pristine banks are capped by substantial scleractinian coral communities, forming excellent habitat for over 200 species of fish. While fishing is permitted, it is limited by difficulty of access. In 2006, NOAA’s Biogeography Branch, in collaboration with the Sanctuary, initiated the first quantitative assessment of fish resources throughout the diveable portions of the Sanctuary. The sampling design and methodologies employed were identical to those that the Branch has utilized in other more impacted regions of the US Caribbean. Initial analyses reveal that fish density and species richness at the Sanctuary were almost two times greater than that found within the US Caribbean and biomass was approximately six times higher. This was due in large part to the presence of sizeable piscivores of the genera Mycteroperca and Dermatolepis. The Sanctuary is one of few minimally impacted locations remaining within the Tropical Western Atlantic. As such, these findings should be considered when attempting to establish a former state or evaluate effectiveness of an MPA in meeting its management goals.

Deposition of diamond-like carbon films by photon-enhanced chemical vapour deposition of methane using a windowless hydrogen lamp

Thin films of diamond-like carbon (DLC) have been deposited using a novel photon-enhanced chemical vapour deposition (photo-CVD) method. This low energy method may be a way to produce better interfaces in electronic devices by reducing damage due to ion bombardment. Methane requires high energy photons for photolysis to take place and these are not transmitted in most photo-CVD methods owing to the presence of a window between the lamp and the deposition environment. In our photo-CVD system there is no window and all the high energy photons are transmitted into the reaction gas. Initial work has proved promising and this paper presents recent results. Films have been characterized by measuring electron energy loss spectra, by ellipsometry and by fabricating and testing diode structures. Results indicate that the films are of a largely amorphous nature and are semiconducting. Diode structures have on/off current ratios of up to 106.

A novel bradykinin-like peptide from skin secretions of the frog, Rana nigrovittata

A bradykinin-like peptide has been isolated from the skin secretions of the frog Rana nigrovittata. This peptide was named ranakinin-N. Its primary structure, RAEAVPPGFTPFR, was determined by Edman degradation and mass spectrometry. It is structurally related to bradykinin-like peptides identified from skin secretions of other amphibians. Ranakinin-N is composed of 13 amino acid residues and is related to the bradykinin identified from the skin secretions of Odorrana schmackeri, which is composed of 9 amino acid residues. Ranakinin-N was found to exert concentration-dependent contractile effects on isolated guinea pig ileum. cDNA sequence encoding the precursor of ranakinin-N was isolated from a skin cDNA library of R. nigrovittata. The amino acid sequences deduced from the cDNA sequences match well with the results from Edman degradation. Analysis of different amphibian bradykinin cDNA structures revealed that the deficiency of a 15-nucleotide fragment (agaatgatcagacgc in the cDNA encoding bradykinin from O. schmackeri) in the peptide-coding region resulted in the absence of a dibasic site for trypsin-like proteinases and an unusual -AEVA- insertion in the N-terminal part of ranakinin-N. The -AEAV- insertion resulted in neutral net charge at the N-terminus of ranakinin-N. Ranakinin-N is the first reported bradykinin-like peptide with a neutral net charge at the N-terminus. Copyright (C) 2007 European Peptide Society and John Wiley & Sons, Ltd.

Kelvin-Helmholtz-like instabilities in turbulent flows over complex surfaces

Riblets are small surface protrusions aligned with the flow direction, which confer an anisotropic roughness to the surface [6]. We have recently reported that the transitional-roughness effect in riblets, which limits their performance, is due to a Kelvin–Helmholtz-like instability of the overlying mean flow [7]. According to our DNSs, the instability sets on as the Reynolds number based on the roughness size of the riblets increases, and coherent, elongated spanwise vortices begin to develop immediately above the riblet tips, causing the degradation of the drag-reduction effect. This is a very novel concept, since prior studies had proposed that the degradation was due to the interaction of riblets with the flow as independent units, either to the lodging of quasi-streamwise vortices in the surface grooves [2] or to the shedding of secondary streamwise vorticity at the riblet peaks [9]. We have proposed an approximate inviscid analysis for the instability, in which the presence of riblets is modelled through an average boundary condition for an overlying, spanwise-independent mean flow. This simplification lacks the accuracy of an exact analysis [4], but in turn applies to riblet surfaces in general. Our analysis succeeds in predicting the riblet size for the onset of the instability, while qualitatively reproducing the wavelengths and shapes of the spanwise structures observed in the DNSs. The analysis also connects the observations with the Kelvin–Helmholtz instability of mixing layers. The fundamental riblet length scale for the onset of the instability is a ‘penetration length,’ which reflects how easily the perturbation flow moves through the riblet grooves. This result is in excellent agreement with the available experimental evidence, and has enabled the identification of the key geometric parameters to delay the breakdown. Although the appearance of elongated spanwise vortices was unexpected in the case of riblets, similar phenomena had already been observed over other rough [3], porous [1] and permeable [11] surfaces, as well as over plant [5,14] and urban [12] canopies, both in the transitional and in the fully-rough regimes. However, the theoretical analyses that support the connection of these observations with the Kelvin–Helmholtz instability are somewhat scarce [7, 11, 13]. It has been recently proposed that Kelvin–Helmholtz-like instabilities are a dominant feature common to “obstructed” shear flows [8]. It is interesting that the instability does not require an inflection point to develop, as is often claimed in the literature. The Kelvin-Helmholtz rollers are rather triggered by the apparent wall-normal-transpiration ability of the flow at the plane immediately above the obstructing elements [7,11]. Although both conditions are generally complementary, if wall-normal transpiration is not present the spanwise vortices may not develop, even if an inflection point exists within the roughness [10]. REFERENCES [1] Breugem, W. P., Boersma, B. J. & Uittenbogaard, R. E. 2006 J. Fluid Mech. 562, 35–72. [2] Choi, H., Moin, P. & Kim, J. 1993 J. Fluid Mech. 255, 503–539. [3] Coceal, O., Dobre, A., Thomas, T. G. & Belcher, S. E. 2007 J. Fluid Mech. 589, 375–409. [4] Ehrenstein, U. 2009 Phys. Fluids 8, 3194–3196. [5] Finnigan, J. 2000 Ann. Rev. Fluid Mech. 32, 519–571. [6] Garcia-Mayoral, R. & Jimenez, J. 2011 Phil. Trans. R. Soc. A 369, 1412–1427. [7] Garcia-Mayoral, R. & Jimenez, J. 2011 J. Fluid Mech. doi: 10.1017/jfm.2011.114. [8] Ghisalberti, M. 2009 J. Fluid Mech. 641, 51–61. [9] Goldstein, D. B. & Tuan, T. C. 1998 J. Fluid Mech. 363, 115–151. [10] Hahn, S., Je, J. & Choi, H. 2002 J. Fluid Mech. 450, 259–285. [11] Jimenez, J., Uhlman, M., Pinelli, A. & G., K. 2001 J. Fluid Mech. 442, 89–117. [12] Letzel, M. O., Krane, M. & Raasch, S. 2008 Atmos. Environ. 42, 8770–8784. [13] Py, C., de Langre, E. & Moulia, B. 2006 J. Fluid Mech. 568, 425–449. [14] Raupach, M. R., Finnigan, J. & Brunet, Y. 1996 Boundary-Layer Meteorol. 78, 351–382.

Progress in the understanding of Ni silicide formation for advanced MOS structures

Metallic silicides have been used as contact materials on source/drain and gate in metal-oxide semiconductor (MOS) structure for 40 years. Since the 65 nm technology node, NiSi is the preferred material for contact in microelectronic due to low resistivity, low thermal budget, and low Si consumption. Ni(Pt)Si with 10 at.% Pt is currently employed in recent technologies since Pt allows to stabilize NiSi at high temperature. The presence of Pt and the very low thickness (<10 nm) needed for the device contacts bring new concerns for actual devices. In this work, in situ techniques [X-ray diffraction (XRD), X-ray reflectivity (XRR), sheet resistance, differential scanning calorimetry (DSC)] were combined with atom probe tomography (APT) to study the formation mechanisms as well as the redistribution of dopants and alloy elements (Pt, Pd.) during the silicide formation. Phenomena like nucleation, lateral growth, interfacial reaction, diffusion, precipitation, and transient phase formation are investigated. The effect of alloy elements (Pt, Pd.) and dopants (As, B.) as well as stress and defects induced by the confinement in devices on the silicide formation mechanism and alloying element redistribution is examined. In particular APT has been performed for the three-dimensional (3D) analysis of MOSFET at the atomic scale. The advances in the understanding of the mechanisms of formation and redistribution are discussed. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Toward a human-like biped robot with compliant legs

Conventional models of bipedal walking generally assume rigid body structures, while elastic material properties seem to play an essential role in nature. On the basis of a novel theoretical model of bipedal walking, this paper investigates a model of biped robot which makes use of minimum control and elastic passive joints inspired from the structures of biological systems. The model is evaluated in simulation and a physical robotic platform by analyzing the kinematics and ground reaction force. The experimental results show that, with a proper leg design of passive dynamics and elasticity, an attractor state of human-like walking gait patterns can be achieved through extremely simple control without sensory feedback. The detailed analysis also explains how the dynamic human-like gait can contribute to adaptive biped walking. © 2007 Elsevier B.V. All rights reserved.

Magnetic characterisation of large grain, bulk Y-Ba-Cu-O superconductor-soft ferromagnetic alloy hybrid structures

Large grain, bulk Y-Ba-Cu-O (YBCO) high temperature superconductors (HTS) have significant potential for use in a variety of practical applications that incorporate powerful quasi-permanent magnets. In the present work, we investigate how the trapped field of such magnets can be improved by combining bulk YBCO with a soft FeNi, ferromagnetic alloy. This involves machining the alloy into components of various shapes, such as cylinders and rings, which are attached subsequently to the top surface of a solid, bulk HTS cylinder. The effect of these modifications on the magnetic hysteresis curve and trapped field of the bulk superconductor at 77 K are then studied using pick-up coil and Hall probe measurements. The experimental data are compared to finite element modelling of the magnetic flux distribution using Campbell's algorithm. Initially we establish the validity of the technique involving pick-up coils wrapped around the bulk superconductor to obtain its magnetic hysteresis curve in a non-destructive way and highlight the difference between the measured signal and the true magnetization of the sample. We then consider the properties of hybrid ferromagnet/superconductor (F/S) structures. Hall probe measurements, together with the results of the model, establish that flux lines curve outwards through the ferromagnet, which acts, effectively, like a magnetic short circuit. Magnetic hysteresis curves show that the effects of the superconductor and the ferromagnet simply add when the ferromagnet is saturated fully by the applied field. The trapped field of the hybrid structure is always larger than that of the superconductor alone below this saturation level, and especially when the applied field is removed. The results of the study show further that the beneficial effects on the trapped field are enhanced when the ferromagnet covers the entire surface of the superconductor for different ferromagnetic components of various shapes and fixed volume. © 2014 Elsevier B.V. All rights reserved.

Toward a human-like biped robot with compliant legs

Conventional models of bipedal walking generally assume rigid body structures, while elastic material properties seem to play an essential role in nature. On the basis of a novel theoretical model of bipedal walking, this paper investigates a model of biped robot which makes use of minimum control and elastic passive joints inspired from the structures of biological systems. The model is evaluated in simulation and a physical robotic platform with respect to the kinematics and the ground reaction force. The experimental results show that the behavior of this simple locomotion model shows a considerable similarity to that of human walking. © 2006 The authors.

Rickettsia-like organism infection in a freshwater cultured fish Ophiocephalus argus C. in China

From 2001 to 2002, a new and emergent infectious disease of Ophiocephalus argus occurred in a fishery in Hubei Province, China, with an incidence of 60% similar to 70% and a mortality as high as 100 %. The diseased fish showed an enlarged abdomen, the millet-like nodules in internal organs, and the swollen kidney which was composed of 5 similar to 10 sarcoma-like bodies in cream or gray-white colour or ulcerated into beandregs-like substance. Light microscopic observation revealed the basophilic or acidphilic inclusions in cytoplasm of the cells and the granulomas, a diffusive chronic inflammation in internal organs. Further analysis under an electron microscope indicated that the intracytoplasmic inclusions were rickettsia-like organisms (RLOs) that are either spherical or coccoid, with variable size, ranging from 0.5 similar to 1.5 mum in diameter, and enclosed within membrane-bound cytoplasmic vacuoles. RLO had a central nucleoid region with some fine filamentous structures and an electron-dense granule. Its cytoplasm contained abundant ribosomal bodies. Occasionally, RLO appeared to be divided by binary fission. RLOs were also observed in the homogenized tissue of infected fish. The results suggested that the death of cultured O. argus was caused by RLO infection.

Electron tunneling through a planar single barrier in HgTe quantum wells with inverted band structures

We present a theoretical study on the electron tunneling through a single barrier created in a two-dimensional electron gas (2DEG) and quantum spin Hall (QSH) bar in a HgTe/CdTe quantum well with inverted band structures. For the 2DEG, the transmission shows the Fabry-Perot resonances for the interband tunneling process and is blocked when the incident energy lies in the bulk gap of the barrier region. For the QSH bar, the transmission gap is reduced to the edge gap caused by the finite size effect. Instead, transmission dips appear due to the interference between the edge states and the bound states originated from the bulk states. Such a Fano-like resonance leads to a sharp dip in the transmission which can be observed experimentally.

The formation and electronic structures of 3d transition-metal atoms doped in silicon nanowires

Using first-principles methods, we systematically study the mechanism of defect formation and electronic structures for 3d transition-metal impurities (V, Cr, Mn, Fe, and Co) doped in silicon nanowires. We find that the formation energies of 3d transition-metal impurities with electrons or holes at the defect levels always increase as the diameters of silicon nanowires decrease, which suggests that self-purification, i.e., the difficulty of doping in silicon nanowires, should be an intrinsic effect. The calculated results show that the defect formation energies of Mn and Fe impurities are lower than those of V, Cr, and Co impurities in silicon nanowires. It indicates that Mn and Fe can easily occupy substitutional site in the interior of silicon nanowires. Moreover, they have larger localized moments, which means that they are good candidates for Si-based dilute magnetic semiconductor nanowires. The doping of Mn and Fe atom in silicon nanowires introduces a pair of energy levels with t(2) symmetry. One of which is dominated by 3d electrons of Mn or Fe, and the other by neighboring dangling bonds of Si vacancies. In addition, a set of nonbonding states localized on the transition-metal atom with e symmetry is also introduced. (C) 2008 American Institute of Physics. [DOI: 10.1063/1.3000445]