Molecular simulations of metal adsorption to bacterial surfaces     

Kelly J. Johnson  Jeremy B. Fein 《Geochimica et cosmochimica acta》2006,70(20):5075-5088

The atomic-scale interactions that occur between cations and the metal-binding cell wall components common to many gram-positive bacteria were investigated using molecular simulations techniques. We examined the adsorption of Cd and Pb onto peptidoglycan and teichoic acid components of the bacterial cell wall using classical energy force field methods. Within the framework of molecular mechanics and the Cerius² modeling software, we used energy minimization, conformational analysis, and molecular dynamics to examine the different components of the cell wall and to determine relative binding energies and structural configurations of the cell wall components, both with and without the metals present. Electronic structure calculations of representative metal-organic complexes validate the more practical classical methods required in simulating the large number of atoms associated with the cell wall components. The classical force field simulations were conducted in both gas phase and solvated periodic cells. Force field-based simulation techniques can adequately describe the interactions of Cd with the cell wall, defining both metal ion coordinations and binding distances. However, the classical force field approach is inconsistent in describing the observed Pb-cell wall interactions due to possible limitations in the force field parameters, the propensity for Pb to form hydroxides at circumneutral pH, or the dominance of other adsorption mechanisms.  相似文献   

Introduction to special issue: Dynamics of seismicity patterns and earthquake triggering     

Sebastian Hainzl  Gert Zller  Ian Main 《Tectonophysics》2006,424(3-4):135

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Monazite behaviour and age significance in poly-metamorphic high-grade terrains: A case study from the western Musgrave Block, central Australia     

Nigel M. Kelly  Geoffrey L. Clarke  Simon L. Harley 《Lithos》2006,88(1-4):100-134

Integrated, in situ textural, chemical and electron microprobe age analysis of monazite grains in a migmatitic metapelitic gneiss from the western Musgrave Block, central Australia has identified evidence for multiple events of growth and recrystallisation during poly-metamorphism in the Mesoproterozoic. Garnet + sillimanite-bearing metapelite underwent partial melting and segregation to palaeosome and leucosome during metamorphism between 1330 and 1296 Ma, with monazite grains in leucosome recording crystallisation at 1300 Ma. Monazite breakdown during melting is inferred to have occurred in the palaeosome. During a subsequent granulite facies event at 1200 Ma, deformation and metamorphism of leucosome and palaeosome resulted in partial disturbance of ages and potential minor growth on 1300 Ma monazite in leucosome. Growth of new, high-Y (+HREE) monazite in palaeosome domains occurred during garnet breakdown in the presence of sillimanite to cordierite and spinel, as a result of post-peak isothermal decompression. Diffusive enrichment of resorbed garnet rims in Y + HREE suggests garnet breakdown occurred slower than volume diffusion of REE. Monazite in both palaeosome and leucosome were subsequently partially to penetratively recrystallised during a retrogression event that is suggested to have occurred at 1150–1130 Ma. The intensity of recrystallisation and disturbance of ages appears linked to proximity to retrogressed garnet porphyroblasts and their occurrence in the relatively reactive or ‘fertile’ local environments provided by the palaeosome/mesosome volumes, which caused localised changes in retrogressive fluids towards compositions more aggressive to monazite. Like reaction textures, it is apparent that domainal equilibrium and reaction may control or at least strongly influence monazite REE and U–Th–Pb chemistry and hence ages.  相似文献   

Shape and distribution analysis of Merensky Reef potholing, Northam Platinum Mine, western Bushveld Complex: implications for pothole formation and growth     

Damian S. Smith  Ian J. Basson 《Mineralium Deposita》2006,41(3):281-295

Syn-magmatic removal of the cumulate pile during the formation of the Bushveld Complex resulted in “potholes”. Erosion progressed downward in the cumulate pile, resulting in a series of steep, transgressive contacts between locally conformable potholed reefs in the regional pothole sub-facies of the Swartklip Facies in the western limb of the Bushveld Complex. The deepest of these potholes, “third-order” or “FWP2” potholing, occurs where the base of the Merensky Cyclic Unit transgresses the Upper Pseudo-Reef Chromitite marker horizon. The base of a FWP2 pothole on Northam Platinum Mine consists of an unconformable stringer Merensky Chromitite overlain by a medium-grained, poikilitic orthopyroxenite and underlain by either a pegmatitic harzburgite or the medium-grained Lower Pseudo-Reef Anorthosite. Detailed shape and distribution analysis of FWP2 potholes reveals underlying patterns in their shape and distribution which, in turn, suggest a structural control. The ratio between pothole short vs long axes is 0.624 (N=1,385), although the ratio increases from 0.48 to 0.61 in the long axis range 10 to 60 m, then decreases from 0.61 to 0.57 from 61 to 100 m, increasing again from 0.57 to 0.61 from 101 to 400 m, suggesting that there is not a simple relationship between pothole shape and size. Shape (circularity, eccentricity, and dendricity) analysis of a subset of 638 potholes indicates that potholes with long axes <100 m have an elliptical, average normalized shape, elongate on a 120–150° orientation. Potholes with long axis lengths >100 m have an average normalized shape that is bilobate and elongate on a 120° orientation. The average aspect ratio (short axis length divided by long axis length) of potholes is highest for potholes with long axis lengths >100 m and lowest for potholes with long axis lengths between 35 and 60 m. The most common long axis orientation for potholes with long axis lengths <100 m is 150° but 120° for long axis lengths >100 m. Fractal analysis indicates that the distribution of pothole centers is controlled neither by a single nor several interacting fractal dimensions. Autocorrelation (Fry) analysis of the distribution of pothole centers shows recurring pothole distribution trends at 038, 070, and 110° for potholes over the full range of long axis lengths, while the trends of 008 and 152° occur in potholes with long axes lengths between 60 and 100 m. Chi-squared (X ²) analysis of the locations of pothole centers suggests that the distribution of small potholes is highly non-uniform but becomes exponentially more uniform with increasing pothole size. The model which best fits the observed shape and distribution analysis is a combination of protracted independent growth and “nearest neighbor” merging along specific orientations. For instance, the clustered distribution of original pothole centers resulted in merged potholes with long axes lengths of up to 60 m, exhibiting short vs long axes ratios of 0.61, preferred orientations of 150°, and alignment along 010 and 150° trends. Further independent growth allowed for merging of similar-sized (and smaller) neighboring potholes, generating potholes with long axes of up to 100 m in length, a preferred long axis orientation of 150°, and alignment along 010, 040, 075, and 150°. Subsequent preferential merging occurred along a 120° trend, thereby preserving a bilobate form. This implies that while pothole initiation and enlargement may be driven by a “top-down” (i.e., possibly thermomechanical) process, an underlying linear or structural catalyst/control is revealed in changes in pothole shape during enlargement and, furthermore, in the preferred trends along which potholes merged over a considerable period, possibly concomitant with adjustment of major structures in the footwall to the Bushveld Complex and pulses into the magma chamber.  相似文献   

Mixing and differentiation in the Oruanui rhyolitic magma, Taupo, New Zealand: evidence from volatiles and trace elements in melt inclusions     

Yang Liu  Alfred T. Anderson  Colin J. N. Wilson  Andrew M. Davis  Ian M. Steele 《Contributions to Mineralogy and Petrology》2006,151(1):71-87

Large pyroclastic rhyolites are snapshots of evolving magma bodies, and preserved in their eruptive pyroclasts is a record of evolution up to the time of eruption. Here we focus on the conditions and processes in the Oruanui magma that erupted at 26.5 ka from Taupo Volcano, New Zealand. The 530 km³ (void-free) of material erupted in the Oruanui event is comparable in size to the Bishop Tuff in California, but differs in that rhyolitic pumice and glass compositions, although variable, did not change systematically with eruption order. We measured the concentrations of H₂O, CO₂ and major and trace elements in zoned phenocrysts and melt inclusions from individual pumice clasts covering the range from early to late erupted units. We also used cathodoluminescence imaging to infer growth histories of quartz phenocrysts. For quartz-hosted inclusions, we studied both fully enclosed melt inclusions and reentrants (connecting to host melt through a small opening). The textures and compositions of inclusions and phenocrysts reflect complex pre-eruptive processes of incomplete assimilation/partial melting, crystallization differentiation, magma mixing and gas saturation. ‘Restitic’ quartz occurs in seven of eight pumice clasts studied. Variations in dissolved H₂O and CO₂ in quartz-hosted melt inclusions reflect gas saturation in the Oruanui magma and crystallization depths of ∼3.5–7 km. Based on variations of dissolved H₂O and CO₂ in reentrants, the amount of exsolved gas at the beginning of eruption increased with depth, corresponding to decreasing density with depth. Pre-eruptive mixing of magma with varying gas content implies variations in magma bulk density that would have driven convective mixing. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.  相似文献   

Near Wall Flow over Urban-like Roughness   总被引：3，自引：35，他引：3  

Hong Cheng  Ian P. Castro 《Boundary-Layer Meteorology》2002,104(2):229-259

In this study, comprehensive measurements over a number of urban-type surfaces with the same area density of 25% have been performed in a wind tunnel. The experiments were conducted at a free stream velocity of 10 m s^-1 and the main instrumentation was 120 ° x-wire anemometry, but measurement accuracy was checked using laser Doppler anemometry.The results haveconfirmed the strong three-dimensionalityof the turbulent flow inthe roughness sublayer and the depths of the inertial sublayer (log-law region) and roughness sublayer for each surface have been determined. Spatial averaging has been used to remove the variability of the flow in the roughness sublayer due to individual obstacles and it is shown that the spatially averaged mean velocity in the inertial sublayer and roughness sublayer can,together, be described by a single log-law with a mean zero-plane displacement and roughness length for the surface, provided that the proper surface stress is known. The spatially averaged shear stresses in the inertial sublayer and roughness sublayer are compared with the surface stress deduced from form drag measurements on the roughness elements themselves.The dispersive stress arising from the spatial inhomogeneity in the mean flow profiles was deduced from the data and is shown to be negligible compared with the usual Reynolds stresses in the roughness sublayer. Comparisons have been made between a homogeneous (regular element array) surface and one consisting of random height elements of the same total volume. Although the upper limits of the inertial sublayer for both surfaces were almost identical at equivalent fetch, the roughness sublayer was much thicker for the random surface than for the uniform surface, the friction velocity and the roughness length were significantly larger and the `roughness efficiency' was greater. It is argued that the inertial sublayer may not exist at all in some of the more extreme rough urban areas. These results will provide fundamental information for modelling urban air quality and forecasting urban wind climates.  相似文献   

Near-Wall Flow Development After A Step Change In Surface Roughness     

H. Cheng  Ian P. Castro 《Boundary-Layer Meteorology》2002,105(3):411-432

An experimental study of the initial flow field downstream of a step change in surface roughness is presented. The roughness length of the downstream surface was approximately tenfold that of the upstream roughness and, unlike all previous studies, attention was concentrated on the roughness sublayer region beneath the inertial (log-law) region. The experiments were conducted at a boundary layer Reynolds number of about 6 × 10⁴ (based on layer thickness andfree-stream velocity) and around a longitudinal location where the (downstream) roughness length, z_o2, was about 1% of the boundary-layer thickness atthe roughness change point.The thickness of the roughness sublayer was found for the two roughness. It was observed that the vertical profiles of mean velocity and turbulence characteristics started to show similarity after about 160z₀₂ downstream of the roughness change. The presence of a shear stress overshoot is shown to depend strongly on the precise location (with respect to the roughness elements) at which the measurements are made and the thickness of the equilibrium layer is shown to be very sensitive to the way it is defined. It is demonstrated that the growing equilibrium layer has first to encompass the roughness sublayer before any thickness of inertial sublayer can be developed. It follows that, in somepractical cases, like flows across some urban environments, the latter(log-law) region may never exist at all.  相似文献   

Loess Mantle of the Earth and its Properties: Ed. V.T. Trofimov, Moscow University Press 2001, 464 pp. (in Russian) ISBN 5-211-04336-7 price not known     

Ian Smalley 《Engineering Geology》2002,66(3-4):319-320

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Citation for presentation of 2001 Alfred E. Treibs award to John W. Smith May 22, 2001     

Isaac Ian Kaplan 《Geochimica et cosmochimica acta》2002,66(4):545-546

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Implications of Nb/U, Th/U and Sm/Nd in plume magmas for the relationship between continental and oceanic crust formation and the development of the depleted mantle   总被引：1，自引：0，他引：1  

Ian H. Campbell 《Geochimica et cosmochimica acta》2002,66(9):1651-1661

The Nb/U and Th/U of the primitive mantle are 34 and 4.04 respectively, which compare with 9.7 and 3.96 for the continental crust. Extraction of continental crust from the mantle therefore has a profound influence on its Nb/U but little influence on its Th/U. Conversely, extraction of midocean ridge-type basalts lowers the Th/U of the mantle residue but has little influence on its Nb/U. As a consequence, variations in Th/U and Nb/U with Sm/Nd can be used to evaluate the relative importance of continental and basaltic crust extraction in the formation of the depleted (Sm/Nd enriched) mantle reservoir.This study evaluates Nb/U, Th/U, and Sm/Nd variations in suites of komatiites, picrites, and their associated basalts, of various ages, to determine whether basalt and/or continental crust have been extracted from their source region. Emphasis is placed on komatiites and picrites because they formed at high degrees of partial melting and are expected to have Nb/U, Th/U, and Sm/Nd that are essentially the same as the mantle that melted to produce them. The results show that all of the studied suites, with the exception of the Barberton, have had both continental crust and basaltic crust extracted from their mantle source region. The high Sm/Nd of the Gorgona and Munro komatiites require the elevated ratios seen in these suites to be due primarily to extraction of basaltic crust from their source regions, whereas basaltic and continental crust extraction are of subequal importance in the source regions of the Yilgarn and Belingwe komatiites. The Sm/Nd of modern midocean ridge basalts lies above the crustal extraction curve on a plot of Sm/Nd against Nb/U, which requires the upper mantle to have had both basaltic and continental crust extracted from it.It is suggested that the extraction of the basaltic reservoir from the mantle occurs at midocean ridges and that the basaltic crust, together with its complementary depleted mantle residue, is subducted to the core-mantle boundary. When the two components reach thermal equilibrium with their surroundings, the lighter depleted component separates from the denser basaltic component. Both are eventually returned to the upper mantle, but the lighter depleted component has a shorter residence time in the lower mantle than the denser basaltic component. If the difference in the recycling times for the basaltic and depleted components is ∼1.0 to 1.5 Ga, a basaltic reservoir is created in the lower mantle, equivalent to the amount of basalt that is subducted in 1.0 to 1.5 Ga, and that reservoir is isolated from the upper mantle. It is this reservoir that is responsible for the Sm/Nd ratio of the upper mantle lying above the trend predicted by extraction of continental crust on the plot of Sm/Nd against Nb/U.  相似文献