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.

Electron flow through cytochrome P450

The cytochromes P450 (P450s) are a remarkable class of heme enzymes that catalyze the metabolism of xenobiotics and the biosynthesis of signaling molecules. Controlled electron flow into the thiolate-ligated heme active site allows P450s to activate molecular oxygen and hydroxylate aliphatic C–H bonds via the formation of high-valent metal-oxo intermediates (compounds I and II). Due to the reactive nature and short lifetimes of these intermediates, many of the fundamental steps in catalysis have not been observed directly. The Gray group and others have developed photochemical methods, known as “flash-quench,” for triggering electron transfer (ET) and generating redox intermediates in proteins in the absence of native ET partners. Photo-triggering affords a high degree of temporal precision for the gating of an ET event; the initial ET and subsequent reactions can be monitored on the nanosecond-to-second timescale using transient absorption (TA) spectroscopies. Chapter 1 catalogues critical aspects of P450 structure and mechanism, including the native pathway for formation of compound I, and outlines the development of photochemical processes that can be used to artificially trigger ET in proteins. Chapters 2 and 3 describe the development of these photochemical methods to establish electronic communication between a photosensitizer and the buried P450 heme. Chapter 2 describes the design and characterization of a Ru-P450-BM3 conjugate containing a ruthenium photosensitizer covalently tethered to the P450 surface, and nanosecond-to-second kinetics of the photo-triggered ET event are presented. By analyzing data at multiple wavelengths, we have identified the formation of multiple ET intermediates, including the catalytically relevant compound II; this intermediate is generated by oxidation of a bound water molecule in the ferric resting state enzyme. The work in Chapter 3 probes the role of a tryptophan residue situated between the photosensitizer and heme in the aforementioned Ru-P450 BM3 conjugate. Replacement of this tryptophan with histidine does not perturb the P450 structure, yet it completely eliminates the ET reactivity described in Chapter 2. The presence of an analogous tryptophan in Ru-P450 CYP119 conjugates also is necessary for observing oxidative ET, but the yield of heme oxidation is lower. Chapter 4 offers a basic description of the theoretical underpinnings required to analyze ET. Single-step ET theory is first presented, followed by extensions to multistep ET: electron “hopping.” The generation of “hopping maps” and use of a hopping map program to analyze the rate advantage of hopping over single-step ET is described, beginning with an established rhenium-tryptophan-azurin hopping system. This ET analysis is then applied to the Ru-tryptophan-P450 systems described in Chapter 2; this strongly supports the presence of hopping in Ru-P450 conjugates. Chapter 5 explores the implementation of flash-quench and other phototriggered methods to examine the native reductive ET and gas binding events that activate molecular oxygen. In particular, TA kinetics that demonstrate heme reduction on the microsecond timescale for four Ru-P450 conjugates are presented. In addition, we implement laser flash-photolysis of P450 ferrous–CO to study the rates of CO rebinding in the thermophilic P450 CYP119 at variable temperature. Chapter 6 describes the development and implementation of air-sensitive potentiometric redox titrations to determine the solution reduction potentials of a series of P450 BM3 mutants, which were designed for non-native cyclopropanation of styrene in vivo. An important conclusion from this work is that substitution of the axial cysteine for serine shifts the wild type reduction potential positive by 130 mV, facilitating reduction by biological redox cofactors in the presence of poorly-bound substrates. While this mutation abolishes oxygenation activity, these mutants are capable of catalyzing the cyclopropanation of styrene, even within the confines of an E. coli cell. Four appendices are also provided, including photochemical heme oxidation in ruthenium-modified nitric oxide synthase (Appendix A), general protocols (Appendix B), Chapter-specific notes (Appendix C) and Matlab scripts used for data analysis (Appendix D).

Structural and Biophysical Characterization of Variants of the Mechanosensitive Channel of Large Conductance (MSCL)

The ability to sense mechanical force is vital to all organisms to interact with and respond to stimuli in their environment. Mechanosensation is critical to many physiological functions such as the senses of hearing and touch in animals, gravitropism in plants and osmoregulation in bacteria. Of these processes, the best understood at the molecular level involve bacterial mechanosensitive channels. Under hypo-osmotic stress, bacteria are able to alleviate turgor pressure through mechanosensitive channels that gate directly in response to tension in the membrane lipid bilayer. A key participant in this response is the mechanosensitive channel of large conductance (MscL), a non-selective channel with a high conductance of ~3 nS that gates at tensions close to the membrane lytic tension.

It has been appreciated since the original discovery by C. Kung that the small subunit size (~130 to 160 residues) and the high conductance necessitate that MscL forms a homo-oligomeric channel. Over the past 20 years of study, the proposed oligomeric state of MscL has ranged from monomer to hexamer. Oligomeric state has been shown to vary between MscL homologues and is influenced by lipid/detergent environment. In this thesis, we report the creation of a chimera library to systematically survey the correlation between MscL sequence and oligomeric state to identify the sequence determinants of oligomeric state. Our results demonstrate that although there is no combination of sequences uniquely associated with a given oligomeric state (or mixture of oligomeric states), there are significant correlations. In the quest to characterize the oligomeric state of MscL, an exciting discovery was made about the dynamic nature of the MscL complex. We found that in detergent solution, under mild heating conditions (37 °C – 60 °C), subunits of MscL can exchange between complexes, and the dynamics of this process are sensitive to the protein sequence.

Extensive efforts were made to produce high diffraction quality crystals of MscL for the determination of a high resolution X-ray crystal structure of a full length channel. The surface entropy reduction strategy was applied to the design of S. aureus MscL variants and while the strategy appears to have improved the crystallizability of S. aureus MscL, unfortunately the diffraction qualities of these crystals were not significantly improved. MscL chimeras were also screened for crystallization in various solubilization detergents, but also failed to yield high quality crystals.

MscL is a fascinating protein and continues to serve as a model system for the study of the structural and functional properties of mechanosensitive channels. Further characterization of the MscL chimera library will offer more insight into the characteristics of the channel. Of particular interest are the functional characterization of the chimeras and the exploration of the physiological relevance of intercomplex subunit exchange.

Efficient excitations of radially and azimuthally polarized Nd 3+:YAG ceramic microchip laser by use of subwavelength multilayer concentric gratings composed of Nb2O5/SiO2

Cylindrical vector beams were produced from laser diode end-pumped Nd:YAG ceramic microchip laser by use of two types of subwavelength multilayer gratings as the axisymmetric-polarization output couplers respectively. The grating mirrors are composed of high- and low-refractive-index (Nb2O5/SiO2) layers alternately while each layer is shaped into triangle and concentric corrugations. For radially polarized laser output, the beam power reached 610mW with a polarization extinction ratio ( PER) of 61: 1 and a slope efficiency of 68.2%; for azimuthally polarized laser output, the beam power reached 626mW with a PER of 58: 1 and a slope efficiency of 47.6%. In both cases, the laser beams had near-diffraction limited quality. Small differences of beam power, PER and slope efficiency between radially and azimuthally polarized laser outputs were not critical, and could be minimized by further optimized adjustment to laser cavity and the reflectances of respective grating mirrors. The results manifested, by use of the photonic crystal gratings mirrors and end-pumped microchip laser configuration, CVBs can be generated efficiently with high modal symmetry and polarization purity. (C) 2008 Optical Society of America.

Influence of different post-treatments on the structure and optical properties of zinc oxide thin films

Zinc oxide (ZnO) films with c-oriented were grown on fused quartz glass substrates at room temperature using dc reactive magnetron sputtering. The as-grown films were annealed at 700 degrees C in air and bombarded by ion beam, respectively. The effects of post-treatments on the structural and optical properties of the ZnO films were investigated by X-ray diffraction (XRD), photoluminescence (PL), optical transmittance and absorption measurements. The XRD spectra indicate that the crystal quality of ZnO films has been improved by both the post-treatments. Compared with the as-grown sample, both annealed and bombarded samples exhibited blueshift in the UV emission peaks, and a strong green emission was found in the annealed ZnO film. In both optical transmittance and absorption spectra, a blueshift of the band-gap edge was observed in the bombarded film, while a redshift was observed in the annealed film. (c) 2004 Elsevier B.V. All rights reserved.

The small-scale pelagic and demersal fisheries off Kribi, Cameroon

A description of the small-scale fisheries of the coastal pelagic and demersal resources off Kribi, Cameroon, is presented. The major fishing grounds are within the estuarine zone, an area of high productivity. Catch estimates of 19.5 t year super(-1) and 6.5 t year super(-1) were obtained for the pelagic motorized and nonmotorized canoes, respectively, while estimates of 11 t year super(-1) were obtained for the demersal motorized canoes. The social benefits from these fisheries are also discussed.

System architecture and deployment scenarios for SESAME: Small cEllS coordinAtion for Multi-tenancy and Edge services

The surge of the Internet traffic with exabytes of data flowing over operators mobile networks has created the need to rethink the paradigms behind the design of the mobile network architecture. The inadequacy of the 4G UMTS Long term Evolution (LTE) and even of its advanced version LTE-A is evident, considering that the traffic will be extremely heterogeneous in the near future and ranging from 4K resolution TV to machine-type communications. To keep up with these changes, academia, industries and EU institutions have now engaged in the quest for new 5G technology. In this paper we present the innovative system design, concepts and visions developed by the 5G PPP H2020 project SESAME (Small cEllS coordinAtion for Multi-tenancy and Edge services). The innovation of SESAME is manifold: i) combine the key 5G small cells with cloud technology, ii) promote and develop the concept of Small Cellsas- a-Service (SCaaS), iii) bring computing and storage power at the mobile network edge through the development of nonx86 ARM technology enabled micro-servers, and iv) address a large number of scenarios and use cases applying mobile edge computing. Topics:

Predatory behaviour of a perch, Nandus nandus (Ham.)

Predatory behaviour of Nandus nandus was studied by offering Cyprinus carpio as prey. The study was conducted with six N. namdus (8.2 ±0.2 cm and 7.60 ±0.3g) represented as P 1, P 2, P 3, P 4, P 5 and P 6. Three size categories of prey (C. carpio) such as small (2.0 ±0.1 cm and 0.23 ±0.01g), large (3.6 ±0.1 cm and 0.57 ±O.O.lg) and mixed group consisting of both small and large prey were used for 14 days of trial. Predatory behavior was classified as targeting, driving, catching, handling, resting and next attempt of catching prey. After introduction of prey into the aquarium predators followed the movement of preys by eye movements and tried to target smaller one first. The predator grasped the head of the prey by its jaws by a drive and engulfed it wholly into the mouth. The average handling time (time taken to manipulate and swallow prey from capture to ceasation of pharyngeal movement) was 42±2 sec and 47±2 sec for small and large prey respectively. N. nandus were ingested more small prey than large prey though the size classes were equally available in case of mixed prey used. Although the prey consumption was higher in number when small prey were ingested but in weight the consumption was higher when ingested large size of prey. The study indicated that N. nandus, ingested more small prey and grasped the headfirst.

Estimation of the detection probability for Yangtze finless porpoises (Neophocaena phocaenoides asiaeorientalis) with a passive acoustic method

Yangtze finless porpoises were surveyed by using simultaneous visual and acoustical methods from 6 November to 13 December 2006. Two research vessels towed stereo acoustic data loggers, which were used to store the intensity and sound source direction of the high frequency sonar signals produced by finless porpoises at detection ranges up to 300 m on each side of the vessel. Simple stereo beam forming allowed the separation of distinct biosonar sound source, which enabled us to count the number of vocalizing porpoises. Acoustically, 204 porpoises were detected from one vessel and 199 from the other vessel in the same section of the Yangtze River. Visually, 163 and 162 porpoises were detected from two vessels within 300 m of the vessel track. The calculated detection probability using acoustic method was approximately twice that for visual detection for each vessel. The difference in detection probabilities between the two methods was caused by the large number of single individuals that were missed by visual observers. However, the sizes of large groups were underestimated by using the acoustic methods. Acoustic and visual observations complemented each other in the accurate detection of porpoises. The use of simple, relatively inexpensive acoustic monitoring systems should enhance population surveys of free-ranging, echolocating odontocetes. (C) 2008 Acoustical Society of America.

Field and experimental studies on the combined impacts of cyanobacterial blooms and small algae on crustacean zooplankton in a large, eutrophic, subtropical, Chinese lake

Field and experimental studies were conducted to evaluate the combined impacts of cyanobacterial blooms and small algae on seasonal and long-term changes in the abundance and community structure of crustacean zooplankton in a large, eutrophic, Chinese lake, Lake Chaohu. Seasonal changes of the crustacean zooplankton from 22 sampling stations were investigated during September 2002 and August 2003, and 23 species belonging to 20 genera were recorded. Daphnia spp. dominated in spring but disappeared in mid-summer, while Bosmina coregoni and Ceriodaphnia cornuta dominated in summer and autumn. Both maximum cladoceran density (310 ind. l(-1)) and biomass (5.2 mg l(-1)) appeared in autumn. Limnoithona sinensis, Sinocalanus dorrii and Schmackeria inopinus were the main species of copepods. Microcystis spp. were the dominant phytoplankton species and formed dense blooms in the warm seasons. In the laboratory, inhibitory effects of small colonial Microcystis on growth and reproduction of Daphnia carinata were more remarkable than those of large ones, and population size of D. carinata was negatively correlated with density of fresh large colonial Microcystis within a density range of 0-100 mg l(-1) (r = -0.82, P < 0.05). Both field and experimental results suggested that seasonal and long-term changes in the community structure of crustacean zooplankton in the lake were shaped by cyanobacterial blooms and biomass of the small algae, respectively, i.e., colonial and filamentous cyanobacteria contributed to the summer replacement of dominant crustacean zooplankton from large Daphnia spp. to small B. coregoni and C. cornuta, while increased small algae might be responsible for the increased abundance of crustacean zooplankton during the past decades.

Molecular characterization and subcellular localization of Carassius auratus interferon regulatory factor-1

Interferon (IFN)-regulatory transcription factor-1 (IRF-1) has been studied in mammals and fish but little is known about the relationship between its gene structure and nuclear 'ion of IRF-1 protein. In this study, a cDNA encoding Carassius auratus IRF-1 (CaIRF-1) was isolated from an interferon-producing cell line, C. ouratus blastulae embryonic (CAB) cells, exposed to UV-inactivated grass carp hemorrhagic virus (GCHV). The CaIRF-1 genomic locus exhibits exon-intron arrangements similar to those of other vertebrate IRF-1 loci, with nine exons and eight introns, although together with pufferfish IRF-1, CaIRF-1 distinguishes itself from other vertebrate IRF-1 genes by a relatively compact genomic size. Similar to the known IRF-1 genes, CaIRF-1 is ubiquitously expressed, and is upregulated in vitro and in vivo in response to virus, Poty I:C, or CAB INF-containing supernatant (ICS). Subcellular localization analysis confirms the nuclear distribution of CaIRF-1 protein, and reveals two nuclear localization signals (NILS), any one of which is sufficient for nuclear translocation of CaIRF-1. One NLS Locates to amino acids 117-146, and appears to be the structural and functional equivalent of the NLS in mammalian IRF-1. The second NLS (amino acids 73-115) is found within the DNA-binding domain (DBD) of CaIRF-1, and contains two regions rich in basic amino acids (''(KDKSINK101)-K-95" and ''(75)KTWKANFR(82)"). In comparison with mammalian IRF-1, in which the corresponding amino acid stretch does not seem to drive nuclear translocation, five conserved basic amino acids (K-75, K-78, R-82, K-95, and K-101) and one non-conserved basic amino acid (K-97) are present in this NLS from CaIRF-1. This observation suggests that K97 Of CaIRF-1 might be essential for the function of its second NLS, wherein the six basic aminoacids might cooperate to drive CaIRF-1 to the nucleus. Therefore, the current study has revealed a new nuclear localization motif in the DBD of a vertebrate IRF-1. (C) 2007 Elsevier Ltd. All rights reserved.

Comparison and combination of several stress relief methods for cubic boron nitride films deposited by ion beam assisted deposition

Cubic boron nitride (c-BN) films were prepared by ion beam assisted deposition (IBAD) technique, and the stresses were primary estimated by measuring the frequency shifts in the infrared-absorption peaks of c-BN samples. To test the possible effects of other factors, dependencies of the c-BN transversal optical mode position on film thickness and c-BN content were investigated. Several methods for reducing the stress of c-BN films including annealing, high temperature deposition, two-stage process, and the addition of a small amount of Si were studied, in which the c-BN films with similar thickness and cubic phase content were used to evaluate the effects of the various stress relief methods. It was shown that all the methods can reduce the stress in c-BN films to various extents. Especially, the incorporation of a small amount of Si (2.3 at.%) can result in a remarkable stress relief from 8.4 to similar to 3.6 GPa whereas the c-BN content is nearly unaffected, although a slight degradation of the c-BN crystallinity is observed. The stress can be further reduced down below I GPa by combination of the addition of Si with the two-stage deposition process. (c) 2008 Elsevier B.V. All rights reserved.

Photoluminescence properties of SiGe/Si single wells with fluctuating structural parameters

Photoluminescence properties of SiGe/Si single wells with fluctuating structural parameters are studied. Four SiGe/Si single wells have been grown on Si(001) at 750 degrees C by disilane and solid Ge molecular beam epitaxy with varied disilane cracking-temperatures. Intense NP and TO-phonon replicas are detected up to 70 K in the photoluminescence spectra and the activation energy of the thermal quenching of the photoluminescence is 28 +/- 4 meV. The high growth temperature and purposeful introduction of fluctuation of structural parameters may be responsible for the improvement of the thermal quenching property.

Structural characterization of SiGe/Si single wells grown by disilane and solid-Ge molecular beam epitaxy with varied disilane cracking temperature

Structural properties of SiGe/Si single wells are studied by double-crystal X-ray diffraction. Four SiGe/Si single wells have been grown on Si (0 0 1) at 750 degrees C by disilane and solid-Ge molecular beam epitaxy with varied disilane cracking temperature. Using dynamic theory, together with kinematic theory and the specific growth procedure adopted, structural parameters in the multilayer structure are determined precisely. The results are compared with those obtained from PL and XTEM as well as AES measurements. It is found that disilane adsorption is dependent on cracking temperature as well as Ge incorporation. Disilane adsorption is increased by cracking disilane while it decreased with Ge incorporation (C) 1998 Elsevier Science B.V. All rights reserved.