Finite element modelling of rock alteration and metamorphic process in hydrothermal systems

We use the finite element method to simulate the rock alteration and metamorphic process in hydrothermal systems. In particular, we consider the fluid-rock interaction problems in pore-fluid saturated porous rocks. Since the fluid rock interaction takes place at the contact interface between the pore-fluid and solid minerals, it is governed by the chemical reaction which usually takes place very slowly at this contact interface, from the geochemical point of view. Due to the relative slowness of the rate of the chemical reaction to the velocity of the pore-fluid flow in the hydrothermal system to be considered, there exists a retardation zone, in which the conventional static theory in geochemistry does not hold true. Since this issue is often overlooked by some purely numerical modellers, it is emphasized in this paper. The related results from a typical rock alteration and metamorphic problem in a hydrothermal system have shown not only the detailed rock alteration and metamorphic process, but also the size of the retardation zone in the hydrothermal system. Copyright (C) 2001 John Wiley & Sons, Ltd.

The BCD transient recorder revisited: firmware for the ISA-to-USB bridging card and software for the graphical user interface

This report describes recent updates to the custom-built data-acquisition hardware operated by the Center for Hypersonics. In 2006, an ISA-to-USB bridging card was developed as part of Luke Hillyard's final-year thesis. This card allows the hardware to be connected to any recent personal computers via a (USB or RS232) serial port and it provides a number of simple text-based commands for control of the hardware. A graphical user interface program was also updated to help the experimenter manage the data acquisition functions. Sampled data is stored in text files that have been compressed with the gzip for mat. To simplify the later archiving or transport of the data, all files specific to a shot are stored in a single directory. This includes a text file for the run description, the signal configuration file and the individual sampled-data files, one for each signal that was recorded.

Using the level set method to model endogenous lava dome growth

Modeling volcanic phenomena is complicated by free-surfaces often supporting large rheological gradients. Analytical solutions and analogue models provide explanations for fundamental characteristics of lava flows. But more sophisticated models are needed, incorporating improved physics and rheology to capture realistic events. To advance our understanding of the flow dynamics of highly viscous lava in Peléean lava dome formation, axi-symmetrical Finite Element Method (FEM) models of generic endogenous dome growth have been developed. We use a novel technique, the level-set method, which tracks a moving interface, leaving the mesh unaltered. The model equations are formulated in an Eulerian framework. In this paper we test the quality of this technique in our numerical scheme by considering existing analytical and experimental models of lava dome growth which assume a constant Newtonian viscosity. We then compare our model against analytical solutions for real lava domes extruded on Soufrière, St. Vincent, W.I. in 1979 and Mount St. Helens, USA in October 1980 using an effective viscosity. The level-set method is found to be computationally light and robust enough to model the free-surface of a growing lava dome. Also, by modeling the extruded lava with a constant pressure head this naturally results in a drop in extrusion rate with increasing dome height, which can explain lava dome growth observables more appropriately than when using a fixed extrusion rate. From the modeling point of view, the level-set method will ultimately provide an opportunity to capture more of the physics while benefiting from the numerical robustness of regular grids.

Finite element analysis of steady-state natural convection problems in fluid-saturated porous media heated from below

In this paper, a progressive asymptotic approach procedure is presented for solving the steady-state Horton-Rogers-Lapwood problem in a fluid-saturated porous medium. The Horton-Rogers-Lapwood problem possesses a bifurcation and, therefore, makes the direct use of conventional finite element methods difficult. Even if the Rayleigh number is high enough to drive the occurrence of natural convection in a fluid-saturated porous medium, the conventional methods will often produce a trivial non-convective solution. This difficulty can be overcome using the progressive asymptotic approach procedure associated with the finite element method. The method considers a series of modified Horton-Rogers-Lapwood problems in which gravity is assumed to tilt a small angle away from vertical. The main idea behind the progressive asymptotic approach procedure is that through solving a sequence of such modified problems with decreasing tilt, an accurate non-zero velocity solution to the Horton-Rogers-Lapwood problem can be obtained. This solution provides a very good initial prediction for the solution to the original Horton-Rogers-Lapwood problem so that the non-zero velocity solution can be successfully obtained when the tilted angle is set to zero. Comparison of numerical solutions with analytical ones to a benchmark problem of any rectangular geometry has demonstrated the usefulness of the present progressive asymptotic approach procedure. Finally, the procedure has been used to investigate the effect of basin shapes on natural convection of pore-fluid in a porous medium. (C) 1997 by John Wiley & Sons, Ltd.

When oceans meet: a teleost shows secondary intergradation at an Indian-Pacific interface

The Indo-West Pacific is characterized by extraordinary marine species diversity. The evolutionary mechanisms responsible for generating this diversity remain puzzling, but are often linked to Pleistocene sea level fluctuations. The impact of these sea level changes on the population genetic architecture of the estuarine fish Lates calcarifer are investigated via a natural experiment in a region of the Indo-West Pacific known to have undergone considerable change during the Pleistocene. L. calcarifer, a coastline-restricted catadromous teleost, provides an excellent model for studying the effects of sea level change as its habitat requirements potentially make it sensitive to the region's physical history. Evidence was found for a large phylogenetic break (4% mtDNA control region; 0.47% ATPase 6 and 8) either side of the Torres Strait, which separates the Western Pacific and Indian Oceans, although some mixing of the clades was evident. This suggests clinal secondary introgression of the clades via contemporary gene flow. Further, populations on Australia's east coast appear to have passed through a bottleneck. This was linked to the historical drying of the Great Barrier Reef coastal lagoon, which resulted in a significant loss of habitat and forced retreat into isolated refugia. These results suggest that historical eustatic changes have left a significant imprint on the molecular diversity within marine species as well as among them in the Indo-West Pacific.

Determination of pore size distributions by regularization and finite element collocation

The problem of extracting pore size distributions from characterization data is solved here with particular reference to adsorption. The technique developed is based on a finite element collocation discretization of the adsorption integral, with fitting of the isotherm data by least squares using regularization. A rapid and simple technique for ensuring non-negativity of the solutions is also developed which modifies the original solution having some negativity. The technique yields stable and converged solutions, and is implemented in a package RIDFEC. The package is demonstrated to be robust, yielding results which are less sensitive to experimental error than conventional methods, with fitting errors matching the known data error. It is shown that the choice of relative or absolute error norm in the least-squares analysis is best based on the kind of error in the data. (C) 1998 Elsevier Science Ltd. All rights reserved.

Finite element modelling of temperature gradient driven rock alteration and mineralization in porous rock masses

We present finite element simulations of temperature gradient driven rock alteration and mineralization in fluid saturated porous rock masses. In particular, we explore the significance of production/annihilation terms in the mass balance equations and the dependence of the spatial patterns of rock alteration upon the ratio of the roll over time of large scale convection cells to the relaxation time of the chemical reactions. Special concepts such as the gradient reaction criterion or rock alteration index (RAI) are discussed in light of the present, more general theory. In order to validate the finite element simulation, we derive an analytical solution for the rock alteration index of a benchmark problem on a two-dimensional rectangular domain. Since the geometry and boundary conditions of the benchmark problem can be easily and exactly modelled, the analytical solution is also useful for validating other numerical methods, such as the finite difference method and the boundary element method, when they are used to dear with this kind of problem. Finally, the potential of the theory is illustrated by means of finite element studies related to coupled flow problems in materially homogeneous and inhomogeneous porous rock masses. (C) 1998 Elsevier Science S.A. All rights reserved.

A relative gradient theory for layered materials

It is possible to remedy certain difficulties with the description of short wave length phenomena and interfacial slip in standard models of a laminated material by considering the bending stiffness of the layers. If the couple or moment stresses are assumed to be proportional to the relative deformation gradient, then the bending effect disappears for vanishing interface slip, and the model correctly reduces to an isotropic standard continuum. In earlier Cosserat-type models this was not the case. Laminated materials of the kind considered here occur naturally as layered rock, or at a different scale, in synthetic layered materials and composites. Similarities to the situation in regular dislocation structures with couple stresses, also make these ideas relevant to single slip in crystalline materials. Application of the theory to a one-dimensional model for layered beams demonstrates agreement with exact results at the extremes of zero and infinite interface stiffness. Moreover, comparison with finite element calculations confirm the accuracy of the prediction for intermediate interfacial stiffness.

Observation of a cubic phase in mesoporous silicate films grown at the air/water interface

X-Ray diffraction is reported from mesoporous silicate films grown at the air/water interface. The films were studied both as powdered films, and oriented on silicon or mica sheets. At early stages of growth we observe Bragg diffraction from a highly ordered cubic phase, with both long and short d-spacing peaks. We have assigned this as a discontinuous micellar Pm3n phase in which the silica is partly ordered. Later films retain only the known hexagonal p6m peaks and have lost any order both at short d-spacings and the longer d-spacing Bragg peaks characteristic of the cubic structure. The silica framework is considerably expanded from that in bulk amorphous silica, average Si Si distances are some 30% greater. Incorporation of glycerol or polyethylene glycol preserves the earlier cubic structure. To be consistent with earlier, in situ, X-ray and neutron reflectivity data we infer that both structures are produced after a phase transition from a less-ordered him structure late in the induction phase. The structural relations between the film Pm3n and p6m phase(s) and the known bulk SBA-1 and MCM-41 phases are briefly discussed.

Modelling the large deformations in stratified media - the Cosserat continuum approach

Methods employing continuum approximation in describing the deformation of layered materials possess a clear advantage over explicit models, However, the conventional implicit models based on the theory of anisotropic continua suffers from certain difficulties associated with interface slip and internal instabilities. These difficulties can be remedied by considering the bending stiffness of the layers. This implies the introduction of moment (couple) stresses and internal rotations, which leads to a Cosserat-type theory. In the present model, the behaviour of the layered material is assumed to be linearly elastic; the interfaces are assumed to be elastic perfectly plastic. Conditions of slip or no slip at the interfaces are detected by a Coulomb criterion with tension cut off at zero normal stress. The theory is valid for large deformation analysis. The model is incorporated into the finite element program AFENA and validated against analytical solutions of elementary buckling problems in layered medium. A problem associated with buckling of the roof and the floor of a rectangular excavation in jointed rock mass under high horizontal in situ stresses is considered as the main application of the theory. Copyright (C) 1999 John Wiley & Sons, Ltd.

Binding of YY1 and Oct1 to a novel element that downregulates expression of IL-5 in human T cells

Background: IL-5 controls development of eosinophilia and has been shown to be involved in the pathogenesis of allergic diseases. In both atopic and nonatopic asthma, elevated IL-5 has been detected in peripheral blood and the airways. IL-5 is produced mainly by activated T cells, and its expression is regulated at the transcriptional level. Objective: This study focuses on the functional analysis of the human IL-5 (hIL-5) promoter and characterization of eis-regulatory elements and transcription factors involved in the suppression of IL-5 transcription in T cells. Methods: Methods used in this study include DNase I footprint assays, electrophoretic mobility shift assays, and functional analysis by mammalian cell transfection involving deletion analysis and site-directed mutagenesis. Results: We identified 5 protein binding regions (BRs) located within the proximal hIL-5 promoter. Functional analysis indicates that the BRs are involved in control of hIL-5 promoter activity. Two of these regions, BR3 and BR4 located at positions -102 to -73, have not previously been described as regulators of IL-5 expression in T cells. We show that the BR3 sequence contains a novel negative regulatory element located at positions -90 to -79 of the hIL-5 promoter, which binds Oct1, octamer-like, and YY1 nuclear factors. Substitution mutations, which abolished binding of these proteins to the BR3 sequence, significantly increased hIL-5 promoter activity in activated T cells. Conclusion: We suggest that Oct1, YY1, and octamer-like factors binding to the -90/-79 sequence within the proximal IL-5 promoter are involved in suppression of IL-5 transcription in T cells.

Finite element analysis of flow patterns near geological lenses in hydrodynamic and hydrothermal systems

We use theoretical and numerical methods to investigate the general pore-fluid flow patterns near geological lenses in hydrodynamic and hydrothermal systems respectively. Analytical solutions have been rigorously derived for the pore-fluid velocity, stream function and excess pore-fluid pressure near a circular lens in a hydrodynamic system. These analytical solutions provide not only a better understanding of the physics behind the problem, but also a valuable benchmark solution for validating any numerical method. Since a geological lens is surrounded by a medium of large extent in nature and the finite element method is efficient at modelling only media of finite size, the determination of the size of the computational domain of a finite element model, which is often overlooked by numerical analysts, is very important in order to ensure both the efficiency of the method and the accuracy of the numerical solution obtained. To highlight this issue, we use the derived analytical solutions to deduce a rigorous mathematical formula for designing the computational domain size of a finite element model. The proposed mathematical formula has indicated that, no matter how fine the mesh or how high the order of elements, the desired accuracy of a finite element solution for pore-fluid flow near a geological lens cannot be achieved unless the size of the finite element model is determined appropriately. Once the finite element computational model has been appropriately designed and validated in a hydrodynamic system, it is used to examine general pore-fluid flow patterns near geological lenses in hydrothermal systems. Some interesting conclusions on the behaviour of geological lenses in hydrodynamic and hydrothermal systems have been reached through the analytical and numerical analyses carried out in this paper.

Finite element modelling of reactive mass transport problems in fluid-saturated porous media

We use the finite element method to solve reactive mass transport problems in fluid-saturated porous media. In particular, we discuss the mathematical expression of the chemical reaction terms involved in the mass transport equations for an isothermal, non-equilibrium chemical reaction. It has turned out that the Arrhenius law in chemistry is a good mathematical expression for such non-equilibrium chemical reactions especially from the computational point of view. Using the finite element method and the Arrhenius law, we investigate the distributions of PH (i.e. the concentration of H+) and the relevant reactive species in a groundwater system. Although the main focus of this study is on the contaminant transport problems in groundwater systems, the related numerical techniques and principles are equally applicable to the orebody formation problems in the geosciences. Copyright (C) 1999 John Wiley & Sons, Ltd.

Finite element modelling of dissipative structures for nonequilibrium chemical reactions in fluid-saturated porous media

We use the finite element method to model and predict the dissipative structures of chemical species for a nonequilibrium chemical reaction system in a fluid-saturated porous medium. In particular, we explore the conditions under which dissipative structures of the species may exist in the Brusselator type of nonequilibrium chemical reaction. Since this is the first time the finite element method and related strategies have been used to study the chemical instability problems in a fluid-saturated porous medium, it is essential to validate the method and strategies before they are put into application. For this purpose, we have rigorously derived the analytical solutions for dissipative structures of chemical species in a benchmark problem, which geometrically is a square. Comparison of the numerical solutions with the analytical ones demonstrates that the proposed numerical method and strategy are robust enough to solve chemical instability problems in a fluid-saturated porous medium. Finally, the related numerical results from two application examples indicate that both the regime and the magnitude of pore-fluid flow have significant effects on the nature of the dissipative structures that developed for a nonequilibrium chemical reaction system in a fluid-saturated porous medium. The motivation for this study is that self-organization under conditions of pore-fluid flow in a porous medium is a potential mechanism of the orebody formation and mineralization in the upper crust of the Earth. (C) 2000 Elsevier Science S.A. All rights reserved.