Nonlocal bacterial electron transfer to hematite surfaces

Mechanisms by which dissimilatory iron-reducing bacteria utilize iron and manganese oxide minerals as terminal electron acceptors for respiration are poorly understood. In the absence of exogenous electron shuttle compounds, extracellular electron transfer is generally thought to occur through the interfacial contact area between mineral surfaces and attached cells. Possible alternative reduction pathways have been proposed based on the discovery of a link between an excreted quinone and dissimilatory reduction. In this study, we utilize a novel experimental approach to demonstrate that Shewanella putrefaciens reduces the surface of crystalline iron oxides at spatial locations that are distinct from points of attachment.     

Computer simulation of the structure and stability of forsterite surfaces

The aim of this paper is to demonstrate that atomistic simulations can be used to evaluate the structure of mineral surfaces and to provide reliable data for forsterite surfaces up to a plane index of 2 using the code METADISE. The methods used to calculate the surface structure and energy which have more commonly been used to study ceramics are briefly explained as is a comparison with experimental data, most notable the crystal morphology. The predicted morphologies show that all the methods (Donnay-Harker, Attachment energies and equilibrium) show most of the surfaces that are expressed in observed crystals. The equilibrium morphology calculated from the relaxed surface energies is the only method which expresses the {201} surfaces and the {101} surfaces, which appear only upon relaxation. The more stable surfaces are shown to be those which have the highest surface density and more closely resemble close packed structures with highly coordinated surface ions and silicon as far from the surface as possible. The most stable surfaces the {100} which has alternating layers of MgO and SiO₂ terminating with an MgO layer. The structure is similar to the MgO {100} surfaces and has a similar energy (1.28?Jm^?2 compared to 1.20). The second most stable are the {201} which have a stepped surface topology, but is also compact with a relaxed surface energy of 1.56?Jm^?2. The results indicate that atomistic simulation is well suited to the prediction of surface structure and morphology although care must be taken in choosing potentials which model the structure and elastic properties accurately.     

Insights for size-dependent reactivity of hematite nanomineral surfaces through Cu sorption

Macroscopic sorption edges for Cu²⁺ were measured on hematite nanoparticles with average diameters of 7 nm, 25 nm, and 88 nm in 0.1 M NaNO₃. The pH edges for the 7 nm hematite were shifted approximately 0.6 pH units lower than that for the 25 nm and 88 nm samples, demonstrating an affinity sequence of 7 nm > 25 nm = 88 nm. Although, zeta potential data suggest increased proton accumulation at the 7 nm hematite surfaces, changes in surface structure are most likely responsible for the preference of Cu²⁺ for the smallest particles. As Cu²⁺ preferentially binds to sites which accommodate the Jahn-Teller distortion of its coordination to oxygen, this indicates the relative importance of distorted binding environments on the 7 nm hematite relative to the 25 nm and 88 nm particles. This work highlights the uniqueness of surface reactivity for crystalline iron oxide particles with decreasing nanoparticle diameter.     

Structure and oxidation state of hematite surfaces reacted with aqueous Fe(II) at acidic and neutral pH

Structural changes and surface oxidation state were examined following the reaction of hematite (0 0 1), (0 1 2), and (1 1 0) with aqueous Fe(II). X-ray reflectivity measurements indicated that Fe(II) induces changes in the structure of all three surfaces under both acidic (pH 3) and neutral (pH 7) conditions. The structural changes were generally independent of pH although the extent of surface transformation varied slightly between acidic and neutral conditions; no systematic trends with pH were observed. Induced changes on the (1 1 0) and (0 1 2) surfaces include the addition or removal of partial surface layers consistent with either growth or dissolution. In contrast, a <1 nm thick, discontinuous film formed on the (0 0 1) surface that appears to be epitaxial yet is not a perfect extension of the underlying hematite lattice, being either structurally defective, compositionally distinct, or nanoscale in size and highly relaxed. Resonant anomalous X-ray reflectivity measurements determined that the surface concentration of Fe(II) present after reaction at pH 7 was below the detection limit of approximately 0.5-1 μmol/m² on all surfaces. These observations are consistent with Fe(II) oxidative adsorption, whereby adsorbed Fe(II) is oxidized by structural Fe(III) in the hematite lattice, with the extent of this reaction controlled by surface structure at the atomic scale. The observed surface transformations at pH 3 show that Fe(II) oxidatively adsorbs on hematite surfaces at pH values where little net adsorption occurs, based on historical macroscopic Fe(II) adsorption behavior on fine-grained hematite powders. This suggests that Fe(II) plays a catalytic role, in which an electron from an adsorbed Fe(II) migrates to and reduces a lattice Fe(III) cation elsewhere, which subsequently desorbs in a scenario with zero net reduction and zero net adsorption. Given the general pH-independence and substantial mass transfer involved, this electron and atom exchange process appears to be a significant subsystem within macroscopic pH-dependent Fe(II) adsorption.     

Atomistic simulation of oxide surfaces

This paper is concerned with the atomistic simulation of the surfaces of MgO, CaO, SrO, Li₂O, c-ZrO₂, SrTiO₃, -Al₂O₃ and -Fe₂O₃. Details are reported of the structure and energy of pure, non-defective surfaces and the constant electrostatic potential in the bulk that results from surface relaxation and electronic polarisation. Cation impurity segregation is discussed in some detail with an emphasis on calculated heats of segregation, equilibrium surface coverages, the lattice structure of segregated surfaces and the energy of impure surfaces.Paper from Conference on Quantum Theory and Experiment, July 1986     

Computer simulation of reef growth

Light is one of the major controls on reef growth and carbonate production. The growth of present reef builders depends largely upon the amount of light available for photosynthesis. As light decreases with water depth, so does reef growth. The computer model presented extends this principle by combining two functions, one for photosynthesis and the other for the extinction of light in water. The model is used to simulate the growth of Alacran Reef, Mexico, two reefs of the Great Barrier Reef and the reefs of the windward platform of St Croix, US Virgin Islands. The model also gives an accurate simulation of the growth of fore-reef walls in Belize, in agreement with the accretion hypothesis developed for this feature.     

Computer simulation of crystal structures

It is impossible to calculate from first principles the details of crystal structures. However, it is possible to rely on information which is certain, namely on interatomic distances, and calculate the details of a crystal structure based on these. Individual distances between atoms can be predicted accurately if one considers the coordination numbers of anions and cations, the extended electrostatic valence rule, and the effects of shared edges between different coordination polyhedra. The predicted interatomic distances are used as observations in a distance least squares refinement in which the positional parameters and the cell edges are adjusted until the calculated interatomic distances correspond as closely as possible to the predicted distances. The topology of the simulated structure has to be known or assumed. Appropriate weighting can facilitate proper modelling. Applications include: a) solution of pseudosymmetric structures; b) preliminary refinement of trial structures; c) geometric refinement without X-ray intensities; d) comparison of hypothetical structures with observed polymorphs of the same compositions; e) simulation of temperature dependence of structures; f) simulation of pressure dependence; g) calculation of structures isomorphous to known structures; h) calculation of thermal ellipsoids; i) calculation of local environments deviating from the overall symmetry of a structure; j) testing of hypotheses about the behavior of structures at varying conditions.     

Computer simulation of second order faults

SummaryComputer Simulation of Second Order Faults Faults of the second order can be simulated in the computer with an accuracy hitherto unknown, by using Malina's (1969, 1970) program version of the Finite Element Method. The computations show that stress rearrangements occur with shear movements along the principal fault and with propagation of the fault. These stress rearrangements contribute to the development of new secondary faults. The computed second order faults can be classified according to Chinnery (1966) as shear plane typesA, B, E, andF. Moreover, the computation shows two dominant shear planes which cannot be classified according to Chinnery.

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ZusammenfassungSimulation von Störungen zweiter Ordnung im Computer Störungen zweiter Ordnung lassen sich mit einer bisher noch nicht gekannten Genauigkeit mit Hilfe einer von Malina (1969, 1970) entwickelten Programmversion der Finite-Element-Methode im Computer simulieren. Die Rechnungen zeigen, daß mit einer Scherbewegung entlang der Hauptstörung und dem Weiterreißen der Störung Spannungsumlagerungen einhergehen, die mitbewirken, daß neue sekundäre Störungen entstehen. Die ermittelten Störungen zweiter Ordnung lassen sich nach der Klassifikation von Chinnery (1966) als die ScherflächentypenA, B, E undF einordnen. Darüberhinaus liefert die Rechnung zwei sehr häufig auftretende Scherflächen, die sich nach Chinnery nicht klassifizieren lassen.

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RésuméSimulation de failles de deuxième ordre par l'ordinateur Les failles de deuxième ordre peuvent être simulées avec une précision encore jamais atteinte grâce à l'utilisation d'une version d'une programme développé par Malina (1969, 1970) à partir de la méthode des éléments finis. Le calcul montre que, conjointement au cisaillement le long de la faille principale et à la propagation de cette faille, de nouvelles redistributions des contraintes apparaissent. Ces nouvelles redistributions contribuent essentiellement au développement de nouvelles surfaces de failles secondaires. Les failles de deuxième ordre peuvent être classées d'après Chinnery (1966) suivant les catégories de surfaces de cisaillementA, B, E, etF. De plus, le calcul indique fréquemment deux autres types de surfaces de cisaillement n'entrant pas dans la classification de Chinnery.

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With 11 Figures     

Computer simulation of mineral solid solutions

We discuss how two techniques, based on (1) lattice dynamics (lattice statics) simulations and (2) Monte Carlo methods may be used to calculate the thermodynamic properties of solid solutions and highly disordered systems. The lattice dynamics calculations involve a full free-energy structural optimisation of each of a number of configurations, followed by thermodynamic averaging. The Monte Carlo simulations include the explicit interchange of cations and use the semi-grand canonical ensemble for chemical potential differences. Both methods are readily applied to high pressures and elevated temperatures without the need for any new parameterisation. We discuss the application of the Monte Carlo technique to the study of surfaces. A range of examples, including binary oxides, spinels, carbonates and surface segregation, is used to illustrate the methods.     

Computer simulation of fracturing of layered rock

Fracturing of rocks is simulated using an electronic computer, on the assumption that when a stress acts on a model, the fracturing condition is determined according to Mohr's theory and that of Griffith. A rock body is regarded as an aggregate of a grid cell whose strength is expressed by a random number of Gaussian distribution functions and the layered fabric of the rock body is given by inserting layered parts with different strength and with various inclinations. The results displaying the fractures on the grid system suggest that some of the geologic structures such as the echelon or the zigzag pattern of fracture are ascribed to fracturing in a layered or heterogeneous body, and variation of strength and the presence of layered fabric in a rock have a significant influence on fracture patterns developed in the rock.     

计算机模拟引擎及其在铀成矿过程模拟中的应用研究

本文介绍了计算机模拟引擎的设计与开发 ,铀成矿过程模拟的实施步骤 ,并对其在伊犁盆地南缘的应用作了探讨。     

断层几何形态反演的计算机模拟

构造反演是指利用构造变形形态反推使之变形的断层的几何参数。在拉张构造区域,从理论上解决构造反演问题是相当成功的。而对于挤压推覆构造区域,由于其逆断层因上盘上升过程,使得其推算的断层只能获取下盘断点以下的构造形态,所以在实际运用中,特别是对于复杂构造叠加区域,其反演过程更多的是依靠人工干预的方法来进行。鉴于此,利用较成熟的拉张构造区域的理论方法,自行提出了单剪变形的挤压构造反演方法来完善,并通过计算机模拟来实现,以此为正演平衡剖面计算,提供一个初始的断层几何模型,并为验证地震剖面解释的合理性提供辅助作用。     

Computer simulation of sedimentation in meandering streams

A dynamic mathematical model for simulation of sedimentation in meandering streams is briefly described. This is composed of component mathematical models which are formulated to predict the following aspects of the system for a given physical situation and a single time increment. (1) The characteristics of the plan form of the meander; (2) the movement of the meander in plan, and definition of cross-sections across the meander in which erosion and deposition are considered in detail; (3) the hydraulic properties of the channel in the bend and the erosional and depositional activity within the channel as defined in specific cross-sections; (4) the nature and occurrence of cut-off; (5) a relative measure of the discharge during a seasonal high water period, which is used in (3) and (4); (6) aggradation. The model, in the form of a FORTRAN IV computer program, has been used to simulate various aspects of sedimentation in meandering streams by performing a set of experiments with the program under different input conditions. The geometry of simulated point bar sediments, as controlled by channel migration over floodplains with variable sediment type, agrees broadly with the natural situation, however extensive sheets of point bar sediment cannot be simulated because large scale meander-belt movements are not accounted for. In the simulated sediments, successive surfaces of the point bar before falling stage deposition (lateral and vertical) may be picked out, and these delineate the epsilon cross-stratification of Allen (1963b). The epsilon unit thickness is that measured from bankfull stage down to the lowest channel position existing prior to deposition. The model records the characteristic fining upwards of grain sizes in the point bar, and the systematic distribution of sedimentary structures. Channel migration combined with seasonal scouring and filling across the channel section produces a characteristic relief in the basal scoured surfaces and facies boundaries (as defined by variation in grain size and sedimentary structure). A related lensing and inter-fingering of the facies may also be present. The model also records large-scale lateral changes in grain size and sedimentary structure associated with changes in the shape of developing meanders. When channel migration is combined with a constant aggradation rate the model predicts a general slope (relative to the land surface) of facies boundaries and scoured basal surfaces upward in the direction of channel movement. If aggradation sufficiently increases the thickness of fine-grained overbank material, there is a channel stabilization effect. It is shown that a complete sequence of point bar sediments capped by overbank sediments would rarely be preserved in the moving-phase situation. Such preservation only becomes likely when an aggrading section lies out of range of an eroding channel for a considerably longer time span than it takes a meander to move one half-wavelength downvalley. Deep channel scours have a higher preservation potential than contemporary shallower ones. Where appropriate field data exist the model can be used in the more accurate recognition of ancient fluviatile sediments. Inferences may be made about the erosion-deposition processes operating in the ancient channel system, and the geometry and hydraulics of the system can be alluded to. A representative application of the model to the quantitative interpretation of an ancient point bar deposit is illustrated. There is reasonable agreement between the natural and the simulated deposits, and a broad quantitative picture of the palaeoenvironment of sedimentation is obtained.     

Computer simulation of the MgSiO3 polymorphs

Six polymorphs of MgSiO₃ have been studied using molecular dynamic (MD) simulation techniques, based on the empirical potential (MAMOK), which is composed of terms to describe pairwise additive Coulomb, van der Waals attraction, and repulsive interactions. Crystal structures, bulk moduli, volume thermal expansivities, and enthalpies were simulated for the known MgSiO₃ polymorphs; orthoenstatite, clinoenstatite, protoenstatite, garnet, ilmenite, and perovskite. The simulated values compare very well with the available experimental data, and the results are quite satisfactory in view of the diversity of the crystal structures of the six polymorphs, the wide range of simulated properties, and the simplicity of the MAMOK potential. MD simulation was further successfully used to study the possibile existence of a post-protoenstatite phase at high temperature, and a C2/c phase at high pressure, both phases being suggested or inferred previously from experimental works.     

Computer modeling and simulation of coalbed methane resources

Coal seam gas reservoirs are complex both geologically and in the mechanism of gas production. Understanding these naturally fractured reservoirs for two-phase (gas–water) flow conditions is often limited by a lack of data. This paper illustrates that reservoir simulation is a powerful tool which can be used to determine key data requirements, and how variability in reservoir properties and operating practices affect performance at the field level. The paper presents examples of how reservoir simulation can be used to assess the efficiency of well completions (fracturing or cavitation), identify candidate wells for remedial treatment, examine methane drainage in advance of mining, and assess the impact of errors in measured data on long-term gas production forecasts.     

Computer simulation studies of Crystallization under confinement conditions

Crystallization under confinement conditions is a very important process in geochemistry and geophysics. Computer simulations of fluids in nanometer scale pore spaces can provide a unique microscopic insight into the structure, dynamics and forces arising from the crystallization process. We discuss in this paper molecular dynamics computer simulations of crystallization in pores of nanometer dimensions. The crystallization pressure due to the freezing of a model of Argon in a nanopore is computed using molecular dynamics simulations. We also investigate the influence of pore geometry in determining the dynamics of confined fluids, as well as mass separation in binary mixtures. It turns out that the pore geometry reveals itself as an important variable, leading to 1) new mechanisms for fast diffusion in confined spaces, and 2) accumulation of solute in specific regions inside the pore.     

A simple model for the effect of hydration on the distribution of ferrous iron at reduced hematite (0 1 2) surfaces

Using a simple ionic model with polarizable oxygen ions and dissociating water molecules, we have calculated the energetics governing the distribution of Fe(II)/Fe(III) ions at the reduced (2 × 1) surface of α-Fe₂O₃ (hematite) (0 1 2) under dry and hydrated conditions. The results show that systems with Fe(II) ions located in the near-surface region have lower potential energy for both dry and hydrated surfaces. The distribution is governed by coupling of the ferrous iron centers to positive charge associated with missing oxygen atoms on the dry reduced (2 × 1) (0 2 1) surface. As the surface is hydroxylated, the missing oxygen rows are filled and protons from dissociated water molecules become the positive charge centers, which couple more weakly to the ferrous iron centers. At the same time, the first-layer iron centers change from fourfold or fivefold coordination to sixfold coordination lowering the potential energy of ferric iron in the first layer and favoring migration of ferrous iron from the immediate surface sites. This effect can also be understood as reflecting stronger solvation of Fe(III) by the adsorbed water molecules and by hydrolysis reactions favoring Fe(III) ions at the immediate surface. The balance between these two driving forces, which changes as a function of hydration, provides a compelling explanation for the anomalous coverage dependence of water desorption in ultra-high vacuum experiments.     

Computer simulation and modelling of mechanical properties of particulates

The mechanical properties of particulate systems are studied from a micromechanics point of view. Two approaches, namely, computer simulation and micro-structural continuum modelling are used. The computer simulation method is used to study the uniformity of the strain field and effect of particle rotations. These results are then used to evaluate the applicability of the micro-structural continuum model. Potential applications of the micro-structural continuum model in the study of mechanical properties of soils are discussed.