Characterisation of sea-water intrusion in the Pioneer Valley, Australia using hydrochemistry and three-dimensional numerical modelling

Sea-water intrusion is actively contaminating fresh groundwater reserves in the coastal aquifers of the Pioneer Valley,north-eastern Australia. A three-dimensional sea-water intrusion model has been developed using the MODHMS code to explore regional-scale processes and to aid assessment of management strategies for the system. A sea-water intrusion potential map, produced through analyses of the hydrochemistry, hydrology and hydrogeology, offsets model limitations by providing an alternative appraisal of susceptibility. Sea-water intrusion in the Pioneer Valley is not in equilibrium, and a potential exists for further landward shifts in the extent of saline groundwater. The model required consideration of tidal over-height (the additional hydraulic head at the coast produced by the action of tides), with over-height values in the range 0.5-0.9 m giving improved water-table predictions. The effect of the initial water-table condition dominated the sensitivity of the model to changes in the coastal hydraulic boundary condition. Several salination processes are probably occurring in the Pioneer Valley, rather than just simple landward sea-water advancement from modern sources of marine salts. The method of vertical discretisation (i.e. model-layer subdivision) was shown to introduce some errors in the prediction of watertable behaviour.

Three-dimensional free surface modelling in an unstructured mesh environment for metal processing applications

In the casting of metals, tundish flow, welding, converters, and other metal processing applications, the behaviour of the fluid surface is important. In aluminium alloys, for example, oxides formed on the surface may be drawn into the body of the melt where they act as faults in the solidified product affecting cast quality. For this reason, accurate description of wave behaviour, air entrapment, and other effects need to be modelled, in the presence of heat transfer and possibly phase change. The authors have developed a single-phase algorithm for modelling this problem. The Scalar Equation Algorithm (SEA) (see Refs. 1 and 2), enables the transport of the property discontinuity representing the free surface through a fixed grid. An extension of this method to unstructured mesh codes is presented here, together with validation. The new method employs a TVD flux limiter in conjunction with a ray-tracing algorithm, to ensure a sharp bound interface. Applications of the method are in the filling and emptying of mould cavities, with heat transfer and phase change.

A three dimensional finite volume approach to the thermo-mechanical modelling of the shape casting of metals

This paper presents a three dimensional, thermos-mechanical modelling approach to the cooling and solidification phases associated with the shape casting of metals ei. Die, sand and investment casting. Novel vortex-based Finite Volume (FV) methods are described and employed with regard to the small strain, non-linear Computational Solid Mechanics (CSM) capabilities required to model shape casting. The CSM capabilities include the non-linear material phenomena of creep and thermo-elasto-visco-plasticity at high temperatures and thermo-elasto-visco-plasticity at low temperatures and also multi body deformable contact with which can occur between the metal casting of the mould. The vortex-based FV methods, which can be readily applied to unstructured meshes, are included within a comprehensive FV modelling framework, PHYSICA. The additional heat transfer, by conduction and convection, filling, porosity and solidification algorithms existing within PHYSICA for the complete modelling of all shape casting process employ cell-centred FV methods. The termo-mechanical coupling is performed in a staggered incremental fashion, which addresses the possible gap formation between the component and the mould, and is ultimately validated against a variety of shape casting benchmarks.

Modelling continuum mechanics phenomena using three dimensional unstructured meshes on massively parallel processors

The difficulties encountered in implementing large scale CM codes on multiprocessor systems are now fairly well understood. Despite the claims of shared memory architecture manufacturers to provide effective parallelizing compilers, these have not proved to be adequate for large or complex programs. Significant programmer effort is usually required to achieve reasonable parallel efficiencies on significant numbers of processors. The paradigm of Single Program Multi Data (SPMD) domain decomposition with message passing, where each processor runs the same code on a subdomain of the problem, communicating through exchange of messages, has for some time been demonstrated to provide the required level of efficiency, scalability, and portability across both shared and distributed memory systems, without the need to re-author the code into a new language or even to support differing message passing implementations. Extension of the methods into three dimensions has been enabled through the engineering of PHYSICA, a framework for supporting 3D, unstructured mesh and continuum mechanics modeling. In PHYSICA, six inspectors are used. Part of the challenge for automation of parallelization is being able to prove the equivalence of inspectors so that they can be merged into as few as possible.

Partition alignment in three dimensional unstructured mesh multi-physics modelling

Unstructured mesh codes for modelling continuum physics phenomena have evolved to provide the facility to model complex interacting systems. Parallelisation of such codes using single Program Multi Data (SPMD) domain decomposition techniques implemented with message passing has been demonstrated to provide high parallel efficiency, scalability to large numbers of processors P and portability across a wide range of parallel platforms. High efficiency, especially for large P requires that load balance is achieved in each parallel loop. For a code in which loops span a variety of mesh entity types, for example, elements, faces and vertices, some compromise is required between load balance for each entity type and the quantity of inter-processor communication required to satisfy data dependence between processors.

Three-dimensional orthotropic viscoelastic finite element model of a human ligament

Ligaments undergo finite strain displaying hyperelastic behaviour as the initially tangled fibrils present straighten out, combined with viscoelastic behaviour (strain rate sensitivity). In the present study the anterior cruciate ligament of the human knee joint is modelled in three dimensions to gain an understanding of the stress distribution over the ligament due to motion imposed on the ends, determined from experimental studies. A three dimensional, finite strain material model of ligaments has recently been proposed by Pioletti in Ref. [2]. It is attractive as it separates out elastic stress from that due to the present strain rate and that due to the past history of deformation. However, it treats the ligament as isotropic and incompressible. While the second assumption is reasonable, the first is clearly untrue. In the present study an alternative model of the elastic behaviour due to Bonet and Burton (Ref. [4]) is generalized. Bonet and Burton consider finite strain with constant modulii for the fibres and for the matrix of a transversely isotropic composite. In the present work, the fibre modulus is first made to increase exponentially from zero with an invariant that provides a measure of the stretch in the fibre direction. At 12% strain in the fibre direction, a new reference state is then adopted, after which the material modulus is made constant, as in Bonet and Burton's model. The strain rate dependence can be added, either using Pioletti's isotropic approximation, or by making the effect depend on the strain rate in the fibre direction only. A solid model of a ligament is constructed, based on experimentally measured sections, and the deformation predicted using explicit integration in time. This approach simplifies the coding of the material model, but has a limitation due to the detrimental effect on stability of integration of the substantial damping implied by the nonlinear dependence of stress on strain rate. At present, an artificially high density is being used to provide stability, while the dynamics are being removed from the solution using artificial viscosity. The result is a quasi-static solution incorporating the effect of strain rate. Alternate approaches to material modelling and integration are discussed, that may result in a better model.

Three-dimensional modeling of tongue during speech using MRI data

The tongue is the most important and dynamic articulator for speech formation, because of its anatomic aspects (particularly, the large volume of this muscular organ comparatively to the surrounding organs of the vocal tract) and also due to the wide range of movements and flexibility that are involved. In speech communication research, a variety of techniques have been used for measuring the three-dimensional vocal tract shapes. More recently, magnetic resonance imaging (MRI) becomes common; mainly, because this technique allows the collection of a set of static and dynamic images that can represent the entire vocal tract along any orientation. Over the years, different anatomical organs of the vocal tract have been modelled; namely, 2D and 3D tongue models, using parametric or statistical modelling procedures. Our aims are to present and describe some 3D reconstructed models from MRI data, for one subject uttering sustained articulations of some typical Portuguese sounds. Thus, we present a 3D database of the tongue obtained by stack combinations with the subject articulating Portuguese vowels. This 3D knowledge of the speech organs could be very important; especially, for clinical purposes (for example, for the assessment of articulatory impairments followed by tongue surgery in speech rehabilitation), and also for a better understanding of acoustic theory in speech formation.

Numerical evaluation of three-dimensional scarf repairs in carbon-epoxy structures

The widespread employment of carbon-epoxy laminates in high responsibility and severely loaded applications introduces an issue regarding their handling after damage. Repair of these structures should be evaluated, instead of their disposal, for cost saving and ecological purposes. Under this perspective, the availability of efficient repair methods is essential to restore the strength of the structure. The development and validation of accurate predictive tools for the repairs behaviour are also extremely important, allowing the reduction of costs and time associated to extensive test programmes. Comparing with strap repairs, scarf repairs have the advantages of a higher efficiency and the absence of aerodynamic disturbance. This work reports on a numerical study of the tensile behaviour of three-dimensional scarf repairs in carbon-epoxy structures, using a ductile adhesive (Araldite® 2015). The finite elements analysis was performed in ABAQUS® and Cohesive Zone Modelling was used for the simulation of damage onset and growth in the adhesive layer. Trapezoidal cohesive laws in each pure mode were used to account for the ductility of the specific adhesive mentioned. A parametric study was performed on the repair width and scarf angle. The use of over-laminating plies covering the repaired region at the outer or both repair surfaces was also tested as an attempt to increase the repairs efficiency. The obtained results allowed the proposal of design principles for repairing composite structures.

Constrains on the structure of Maio Island (Cape Verde) by a three-dimensional gravity model: Imaging partially exhumed magma chambers

We propose a 3-D gravity model for the volcanic structure of the island of Maio (Cape Verde archipelago) with the objective of solving some open questions concerning the geometry and depth of the intrusive Central Igneous Complex. A gravity survey was made covering almost the entire surface of the island. The gravity data was inverted through a non-linear 3-D approach which provided a model constructed in a random growth process. The residual Bouguer gravity field shows a single positive anomaly presenting an elliptic shape with a NWSE trending long axis. This Bouguer gravity anomaly is slightly off-centred with the island but its outline is concordant with the surface exposure of the Central Igneous Complex. The gravimetric modelling shows a high-density volume whose centre of mass is about 4500 m deep. With increasing depth, and despite the restricted gravimetric resolution, the horizontal sections of the model suggest the presence of two distinct bodies, whose relative position accounts for the elongated shape of the high positive Bouguer gravity anomaly. These bodies are interpreted as magma chambers whose coeval volcanic counterparts are no longer preserved. The orientation defined by the two bodies is similar to that of other structures known in the southern group of the Cape Verde islands, thus suggesting a possible structural control constraining the location of the plutonic intrusions.

Three-dimensional models of 14α-sterol demethylase (Cyp51A) from Aspergillus lentulus and Aspergillus fumigatus: an insight into differences in voriconazole interaction.

Aspergillus lentulus, an Aspergillus fumigatus sibling species, is increasingly reported in corticosteroid-treated patients. Its clinical significance is unknown, but the fact that A. lentulus shows reduced antifungal susceptibility, mainly to voriconazole, is of serious concern. Heterologous expression of cyp51A from A. fumigatus and A. lentulus was performed in Saccharomyces cerevisiae to assess differences in the interaction of Cyp51A with the azole drugs. The absence of endogenous ERG11 was efficiently complemented in S. cerevisiae by the expression of either Aspergillus cyp51A allele. There was a marked difference between azole minimum inhibitory concentration (MIC) values of the clones expressing each Aspergillus spp. cyp51A. Saccharomyces cerevisiae clones expressing A. lentulus alleles showed higher MICs to all of the azoles tested, supporting the hypothesis that the intrinsic azole resistance of A. lentulus could be associated with Cyp51A. Homology models of A. fumigatus and A. lentulus Cyp51A protein based on the crystal structure of Cyp51p from Mycobacterium tuberculosis in complex with fluconazole were almost identical owing to their mutual high sequence identity. Molecular dynamics (MD) was applied to both three-dimensional protein models to refine the homology modelling and to explore possible differences in the Cyp51A-voriconazole interaction. After 20ns of MD modelling, some critical differences were observed in the putative closed form adopted by the protein upon voriconazole binding. A closer study of the A. fumigatus and A. lentulus voriconazole putative binding site in Cyp51A suggested that some major differences in the protein's BC loop could differentially affect the lock-up of voriconazole, which in turn could correlate with their different azole susceptibility profiles.

A Farewell to Flat Biology. Three-dimensional Cell Culture Models in Cancer Drug Target Identification and Validation

Cells of epithelial origin, e.g. from breast and prostate cancers, effectively differentiate into complex multicellular structures when cultured in three-dimensions (3D) instead of conventional two-dimensional (2D) adherent surfaces. The spectrum of different organotypic morphologies is highly dependent on the culture environment that can be either non-adherent or scaffold-based. When embedded in physiological extracellular matrices (ECMs), such as laminin-rich basement membrane extracts, normal epithelial cells differentiate into acinar spheroids reminiscent of glandular ductal structures. Transformed cancer cells, in contrast, typically fail to undergo acinar morphogenic patterns, forming poorly differentiated or invasive multicellular structures. The 3D cancer spheroids are widely accepted to better recapitulate various tumorigenic processes and drug responses. So far, however, 3D models have been employed predominantly in the Academia, whereas the pharmaceutical industry has yet to adopt a more widely and routine use. This is mainly due to poor characterisation of cell models, lack of standardised workflows and high throughput cell culture platforms, and the availability of proper readout and quantification tools. In this thesis, a complete workflow has been established entailing well-characterised 3D cell culture models for prostate cancer, a standardised 3D cell culture routine based on high-throughput-ready platform, automated image acquisition with concomitant morphometric image analysis, and data visualisation, in order to enable large-scale high-content screens. Our integrated suite of software and statistical analysis tools were optimised and validated using a comprehensive panel of prostate cancer cell lines and 3D models. The tools quantify multiple key cancer-relevant morphological features, ranging from cancer cell invasion through multicellular differentiation to growth, and detect dynamic changes both in morphology and function, such as cell death and apoptosis, in response to experimental perturbations including RNA interference and small molecule inhibitors. Our panel of cell lines included many non-transformed and most currently available classic prostate cancer cell lines, which were characterised for their morphogenetic properties in 3D laminin-rich ECM. The phenotypes and gene expression profiles were evaluated concerning their relevance for pre-clinical drug discovery, disease modelling and basic research. In addition, a spontaneous model for invasive transformation was discovered, displaying a highdegree of epithelial plasticity. This plasticity is mediated by an abundant bioactive serum lipid, lysophosphatidic acid (LPA), and its receptor LPAR1. The invasive transformation was caused by abrupt cytoskeletal rearrangement through impaired G protein alpha 12/13 and RhoA/ROCK, and mediated by upregulated adenylyl cyclase/cyclic AMP (cAMP)/protein kinase A, and Rac/ PAK pathways. The spontaneous invasion model tangibly exemplifies the biological relevance of organotypic cell culture models. Overall, this thesis work underlines the power of novel morphometric screening tools in drug discovery.

An approach to coded structured light to obtain three dimensional information

The human visual ability to perceive depth looks like a puzzle. We perceive three-dimensional spatial information quickly and efficiently by using the binocular stereopsis of our eyes and, what is mote important the learning of the most common objects which we achieved through living. Nowadays, modelling the behaviour of our brain is a fiction, that is why the huge problem of 3D perception and further, interpretation is split into a sequence of easier problems. A lot of research is involved in robot vision in order to obtain 3D information of the surrounded scene. Most of this research is based on modelling the stereopsis of humans by using two cameras as if they were two eyes. This method is known as stereo vision and has been widely studied in the past and is being studied at present, and a lot of work will be surely done in the future. This fact allows us to affirm that this topic is one of the most interesting ones in computer vision. The stereo vision principle is based on obtaining the three dimensional position of an object point from the position of its projective points in both camera image planes. However, before inferring 3D information, the mathematical models of both cameras have to be known. This step is known as camera calibration and is broadly describes in the thesis. Perhaps the most important problem in stereo vision is the determination of the pair of homologue points in the two images, known as the correspondence problem, and it is also one of the most difficult problems to be solved which is currently investigated by a lot of researchers. The epipolar geometry allows us to reduce the correspondence problem. An approach to the epipolar geometry is describes in the thesis. Nevertheless, it does not solve it at all as a lot of considerations have to be taken into account. As an example we have to consider points without correspondence due to a surface occlusion or simply due to a projection out of the camera scope. The interest of the thesis is focused on structured light which has been considered as one of the most frequently used techniques in order to reduce the problems related lo stereo vision. Structured light is based on the relationship between a projected light pattern its projection and an image sensor. The deformations between the pattern projected into the scene and the one captured by the camera, permits to obtain three dimensional information of the illuminated scene. This technique has been widely used in such applications as: 3D object reconstruction, robot navigation, quality control, and so on. Although the projection of regular patterns solve the problem of points without match, it does not solve the problem of multiple matching, which leads us to use hard computing algorithms in order to search the correct matches. In recent years, another structured light technique has increased in importance. This technique is based on the codification of the light projected on the scene in order to be used as a tool to obtain an unique match. Each token of light is imaged by the camera, we have to read the label (decode the pattern) in order to solve the correspondence problem. The advantages and disadvantages of stereo vision against structured light and a survey on coded structured light are related and discussed. The work carried out in the frame of this thesis has permitted to present a new coded structured light pattern which solves the correspondence problem uniquely and robust. Unique, as each token of light is coded by a different word which removes the problem of multiple matching. Robust, since the pattern has been coded using the position of each token of light with respect to both co-ordinate axis. Algorithms and experimental results are included in the thesis. The reader can see examples 3D measurement of static objects, and the more complicated measurement of moving objects. The technique can be used in both cases as the pattern is coded by a single projection shot. Then it can be used in several applications of robot vision. Our interest is focused on the mathematical study of the camera and pattern projector models. We are also interested in how these models can be obtained by calibration, and how they can be used to obtained three dimensional information from two correspondence points. Furthermore, we have studied structured light and coded structured light, and we have presented a new coded structured light pattern. However, in this thesis we started from the assumption that the correspondence points could be well-segmented from the captured image. Computer vision constitutes a huge problem and a lot of work is being done at all levels of human vision modelling, starting from a)image acquisition; b) further image enhancement, filtering and processing, c) image segmentation which involves thresholding, thinning, contour detection, texture and colour analysis, and so on. The interest of this thesis starts in the next step, usually known as depth perception or 3D measurement.

Three-dimensional simulation of the rolling of a saturated fibro-porous media

This paper describes recent advances made in computational modelling of the sugar cane liquid extraction process. The saturated fibro-porous material is rolled between circumferentially grooved rolls, which enhance frictional grip and provide a low-resistance path for liquid flow during the extraction process. Previously reported two-dimensional (2D) computational models, account for the large deformation of the porous material by solving the fully coupled governing fibre stress and fluid-flow equations using finite element techniques. While the 2D simulations provide much insight into the overarching cause-effect relationships, predictions of mechanical quantities such as roll separating force and particularly torque as a function of roll speed and degree of compression are not satisfactory for industrial use. It is considered that the unsatisfactory response in roll torque prediction may be due to the stress levels that exist between the groove tips and roots which have been largely neglected in the geometrically simplified 2D model. This paper gives results for both two- and three-dimensional finite element models and highlights their strengths and weaknesses in predicting key milling parameters. (c) 2005 Elsevier B.V. All rights reserved.

The influence of cutting tool geometry upon aspects of chip flow and tool wear:a theoretical, three dimensional examination of the cutting geometry and the shape of the twist drill

This work is undertaken in the attempt to understand the processes at work at the cutting edge of the twist drill. Extensive drill life testing performed by the University has reinforced a survey of previously published information. This work demonstrated that there are two specific aspects of drilling which have not previously been explained comprehensively. The first concerns the interrelating of process data between differing drilling situations, There is no method currently available which allows the cutting geometry of drilling to be defined numerically so that such comparisons, where made, are purely subjective. Section one examines this problem by taking as an example a 4.5mm drill suitable for use with aluminium. This drill is examined using a prototype solid modelling program to explore how the required numerical information may be generated. The second aspect is the analysis of drill stiffness. What aspects of drill stiffness provide the very great difference in performance between short flute length, medium flute length and long flute length drills? These differences exist between drills of identical point geometry and the practical superiority of short drills has been known to shop floor drilling operatives since drilling was first introduced. This problem has been dismissed repeatedly as over complicated but section two provides a first approximation and shows that at least for smaller drills of 4. 5mm the effects are highly significant. Once the cutting action of the twist drill is defined geometrically there is a huge body of machinability data that becomes applicable to the drilling process. Work remains to interpret the very high inclination angles of the drill cutting process in terms of cutting forces and tool wear but aspects of drill design may already be looked at in new ways with the prospect of a more analytical approach rather than the present mix of experience and trial and error. Other problems are specific to the twist drill, such as the behaviour of the chips in the flute. It is now possible to predict the initial direction of chip flow leaving the drill cutting edge. For the future the parameters of further chip behaviour may also be explored within this geometric model.

A three dimensional numerical investigation of hillslope flow processes

Physically based distributed models of catchment hydrology are likely to be made available as engineering tools in the near future. Although these models are based on theoretically acceptable equations of continuity, there are still limitations in the present modelling strategy. Of interest to this thesis are the current modelling assumptions made concerning the effects of soil spatial variability, including formations producing distinct zones of preferential flow. The thesis contains a review of current physically based modelling strategies and a field based assessment of soil spatial variability. In order to investigate the effects of soil nonuniformity a fully three dimensional model of variability saturated flow in porous media is developed. The model is based on a Galerkin finite element approximation to Richards equation. Accessibility to a vector processor permits numerical solutions on grids containing several thousand node points. The model is applied to a single hillslope segment under various degrees of soil spatial variability. Such variability is introduced by generating random fields of saturated hydraulic conductivity using the turning bands method. Similar experiments are performed under conditions of preferred soil moisture movement. The results show that the influence of soil variability on subsurface flow may be less significant than suggested in the literature, due to the integrating effects of three dimensional flow. Under conditions of widespread infiltration excess runoff, the results indicate a greater significance of soil nonuniformity. The recognition of zones of preferential flow is also shown to be an important factor in accurate rainfall-runoff modelling. Using the results of various fields of soil variability, experiments are carried out to assess the validity of the commonly used concept of `effective parameters'. The results of these experiments suggest that such a concept may be valid in modelling subsurface flow. However, the effective parameter is observed to be event dependent when the dominating mechanism is infiltration excess runoff.