Computational analysis of laminated glass panels under blast loads: A comparison of two dimensional and three dimensional modelling approaches

This paper illustrates the use of finite element (FE) technique to investigate the behaviour of laminated glass (LG) panels under blast loads. Two and three dimensional (2D and 3D) modelling approaches available in LS-DYNA FE code to model LG panels are presented. Results from the FE analysis for mid-span deflection and principal stresses compared well with those from large deflection plate theory. The FE models are further validated using the results from a free field blast test on a LG panel. It is evident that both 2D and 3D LG models predict the experimental results with reasonable accuracy. The 3D LG models give slightly more accurate results but require considerably more computational time compared to the 2D LG models.

Automated fit quantification of tibial nail designs during the insertion using computer three-dimensional modelling

Intramedullary nailing is the standard fixation method for displaced diaphyseal fractures of the tibia. An optimal nail design should both facilitate insertion and anatomically fit the bone geometry at its final position in order to reduce the risk of stress fractures and malalignments. Due to the nonexistence of suitable commercial software, we developed a software tool for the automated fit assessment of nail designs. Furthermore, we demonstrated that an optimised nail, which fits better at the final position, is also easier to insert. Three-dimensional models of two nail designs and 20 tibiae were used. The fitting was quantified in terms of surface area, maximum distance, sum of surface areas and sum of maximum distances by which the nail was protruding into the cortex. The software was programmed to insert the nail into the bone model and to quantify the fit at defined increment levels. On average, the misfit during the insertion in terms of the four fitting parameters was smaller for the Expert Tibial Nail Proximal bend (476.3 mm2, 1.5 mm, 2029.8 mm2, 6.5 mm) than the Expert Tibial Nail (736.7 mm2, 2.2 mm, 2491.4 mm2, 8.0 mm). The differences were statistically significant (p ≤ 0.05). The software could be used by nail implant manufacturers for the purpose of implant design validation.

Structural and mechanistic motifs in membrane proteins: the three-dimensional modelling of rhodopsin, band 3, and the nicotinic acetylcholine receptor

Because so little is known about the structure of membrane proteins, an attempt has been made in this work to develop techniques by which to model them in three dimensions. The procedures devised rely heavily upon the availability of several sequences of a given protein. The modelling procedure is composed of two parts. The first identifies transmembrane regions within the protein sequence on the basis of hydrophobicity, β-turn potential, and the presence of certain amino acid types, specifically, proline and basic residues. The second part of the procedure arranges these transmembrane helices within the bilayer based upon the evolutionary conservation of their residues. Conserved residues are oriented toward other helices and variable residues are positioned to face the surrounding lipids. Available structural information concerning the protein's helical arrangement, including the lengths of interhelical loops, is also taken into account. Rhodopsin, band 3, and the nicotinic acetylcholine receptor have all been modelled using this methodology, and mechanisms of action could be proposed based upon the resulting structures.

Specific residues in the rhodopsin and iodopsin sequences were identified, which may regulate the proteins' wavelength selectivities. A hinge-like motion of helices M3, M4, and M5 with respect to the rest of the protein was proposed to result in the activation of transducin, the G-protein associated with rhodopsin. A similar mechanism is also proposed for signal transduction by the muscarinic acetylcholine and β-adrenergic receptors.

The nicotinic acetylcholine receptor was modelled with four trans-membrane helices per subunit and with the five homologous M2 helices forming the cation channel. Putative channel-lining residues were identified and a mechanism of channel-opening based upon the concerted, tangential rotation of the M2 helices was proposed.

Band 3, the anion exchange protein found in the erythrocyte membrane, was modelled with 14 transmembrane helices. In general the pathway of anion transport can be viewed as a channel composed of six helices that contains a single hydrophobic restriction. This hydrophobic region will not allow the passage of charged species, unless they are part of an ion-pair. An arginine residue located near this restriction is proposed to be responsible for anion transport. When ion-paired with a transportable anion it rotates across the barrier and releases the anion on the other side of the membrane. A similar process returns it to its original position. This proposed mechanism, based on the three-dimensional model, can account for the passive, electroneutral, anion exchange observed for band 3. Dianions can be transported through a similar mechanism with the additional participation of a histidine residue. Both residues are located on M10.

In silico identification and three-dimensional modelling of the missense mutation in ADAMTS2 in a sheep flock with dermatosparaxis

Background Dermatosparaxis (Ehlers–Danlos syndrome in humans) is characterized by extreme fragility of the skin. It is due to the lack of mature collagen caused by a failure in the enzymatic processing of procollagen I. We investigated the condition in a commercial sheep flock. Hypothesis/Objectives Mutations in the ADAM metallopeptidase with thrombospondin type 1 motif, 2 (ADAMTS2) locus, are involved in the development of dermatosparaxis in humans, cattle and the dorper sheep breed; consequently, this locus was investigated in the flock. Animals A single affected lamb, its dam, the dam of a second affected lamb and the rams in the flock were studied. Methods DNA was purified from blood, PCR primers were used to detect parts of the ADAMS2 gene and nucleotide sequencing was performed using Sanger's procedure. Skin samples were examined using standard histology procedures. Results A missense mutation was identified in the catalytic domain of ADAMTS2. The mutation is predicted to cause the substitution in the mature ADAMTS2 of a valine molecule by a methionine molecule (V15M) affecting the catalytic domain of the enzyme. Both the ‘sorting intolerant from tolerant’ (SIFT) and the PolyPhen-2 methodologies predicted a damaging effect for the mutation. Three-dimensional modelling suggested that this mutation may alter the stability of the protein folding or distort the structure, causing the protein to malfunction. Conclusions and clinical importance Detection of the mutation responsible for the pathology allowed us to remove the heterozygote ram, thus preventing additional cases in the flock.

Three-Dimensional Modelling of Honeybee Venom Allergenic Proteases: Relation to Allergenicity

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Three-dimensional geological modelling and multivariate statistical analysis of water chemistry data to analyse and visualise aquifer structure and groundwater composition in the Wairau Plain, Marlborough District, New Zealand

Concerns regarding groundwater contamination with nitrate and the long-term sustainability of groundwater resources have prompted the development of a multi-layered three dimensional (3D) geological model to characterise the aquifer geometry of the Wairau Plain, Marlborough District, New Zealand. The 3D geological model which consists of eight litho-stratigraphic units has been subsequently used to synthesise hydrogeological and hydrogeochemical data for different aquifers in an approach that aims to demonstrate how integration of water chemistry data within the physical framework of a 3D geological model can help to better understand and conceptualise groundwater systems in complex geological settings. Multivariate statistical techniques(e.g. Principal Component Analysis and Hierarchical Cluster Analysis) were applied to groundwater chemistry data to identify hydrochemical facies which are characteristic of distinct evolutionary pathways and a common hydrologic history of groundwaters. Principal Component Analysis on hydrochemical data demonstrated that natural water-rock interactions, redox potential and human agricultural impact are the key controls of groundwater quality in the Wairau Plain. Hierarchical Cluster Analysis revealed distinct hydrochemical water quality groups in the Wairau Plain groundwater system. Visualisation of the results of the multivariate statistical analyses and distribution of groundwater nitrate concentrations in the context of aquifer lithology highlighted the link between groundwater chemistry and the lithology of host aquifers. The methodology followed in this study can be applied in a variety of hydrogeological settings to synthesise geological, hydrogeological and hydrochemical data and present them in a format readily understood by a wide range of stakeholders. This enables a more efficient communication of the results of scientific studies to the wider community.

Linking three-dimensional geological modelling and multivariate statistical analysis to define groundwater chemistry baseline and identify inter-aquifer connectivity within the Clarence-Moreton Basin, Southeast Queensland, Australia

The Clarence-Moreton Basin (CMB) covers approximately 26000 km2 and is the only sub-basin of the Great Artesian Basin (GAB) in which there is flow to both the south-west and the east, although flow to the south-west is predominant. In many parts of the basin, including catchments of the Bremer, Logan and upper Condamine Rivers in southeast Queensland, the Walloon Coal Measures are under exploration for Coal Seam Gas (CSG). In order to assess spatial variations in groundwater flow and hydrochemistry at a basin-wide scale, a 3D hydrogeological model of the Queensland section of the CMB has been developed using GoCAD modelling software. Prior to any large-scale CSG extraction, it is essential to understand the existing hydrochemical character of the different aquifers and to establish any potential linkage. To effectively use the large amount of water chemistry data existing for assessment of hydrochemical evolution within the different lithostratigraphic units, multivariate statistical techniques were employed.

Three-dimensional geological modelling of the Galilee and central Eromanga basins, Australia: New insights into aquifer/aquitard geometry and potential influence of faults on inter-connectivity

Study region The Galilee and Eromanga basins are located in central Queensland, Australia. Both basins are components of the Great Artesian Basin which host some of the most significant groundwater resources in Australia. Study focus This study evaluates the influence of regional faults on groundwater flow in an aquifer/aquitard interbedded succession that form one of the largest Artesian Basins in the world. In order to assess the significance of regional faults as potential barriers or conduits to groundwater flow, vertical displacements of the major aquifers and aquitards were studied at each major fault and the general hydraulic relationship of units that are juxtaposed by the faults were considered. A three-dimensional (3D) geological model of the Galilee and Eromanga basins was developed based on integration of well log data, seismic surfaces, surface geology and elevation data. Geological structures were mapped in detail and major faults were characterised. New hydrological insights for the region Major faults that have been described in previous studies have been confirmed within the 3D geological model domain and a preliminary assessment of their hydraulic significance has been conducted. Previously unknown faults such as the Thomson River Fault (herein named) have also been identified in this study.

Three-dimensional structure of heat shock protein 90 from Plasmodium falciparum: molecular modelling approach to rational drug design against malaria

We have recently implicated heat shock protein 90 from Plasmodium falciparum (PfHsp90) as a potential drug target against malaria. Using inhibitors specific to the nucleotide binding domain of Hsp90, we have shown potent growth inhibitory effects on development of malarial parasite in human erythrocytes. To gain better understanding of the vital role played by PfHsp90 in parasite growth, we have modeled its three dimensional structure using recently described full length structure of yeast Hsp90. Sequence similarity found between PfHsp90 and yeast Hsp90 allowed us to model the core structure with high confidence. The superimposition of the predicted structure with that of the template yeast Hsp90 structure reveals an RMSD of 3.31 angstrom. The N-terminal and middle domains showed the least RMSD (1.76 angstrom) while the more divergent C-terminus showed a greater RMSD (2.84 angstrom) with respect to the template. The structure shows overall conservation of domains involved in nucleotide binding, ATPase activity, co-chaperone binding as well as inter-subunit interactions. Important co-chaperones known to modulate Hsp90 function in other eukaryotes are conserved in malarial parasite as well. An acidic stretch of amino acids found in the linker region, which is uniquely extended in PfHsp90 could not be modeled in this structure suggesting a flexible conformation. Our results provide a basis to compare the overall structure and functional pathways dependent on PfHsp90 in malarial parasite. Further analysis of differences found between human and parasite Hsp90 may make it possible to design inhibitors targeted specifically against malaria.

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.

Modelling the Geometry of the Repeat Unit Cell of Three-Dimensional Weave Architectures,

The three-dimensional (3D) weaving process offers the ability to tailor the mechanical properties via design of the weave architecture. One repeat of the 3D woven fabric is represented by the unit cell. The model accepts basic weaver and material manufacturer data as inputs in order to calculate the geometric characteristics of the 3D woven unit cell. The specific weave architecture manufactured and subsequently modelled had an angle interlock type binding configuration. The modelled result was shown to have a close approximation compared to the experimentally measured values and highlighted the importance of the representation of the binder tow path.

Monitoring and modelling the three-dimensional flow of water under drip irrigation

The interpretation of soil water dynamics under drip irrigation systems is relevant for crop production as well as on water use and management. In this study a three-dimensional representation of the flow of water under drip irrigation is presented. The work includes analysis of the water balance at point scale as well as area-average, exploring uncertainties in water balance estimations depending on the number of locations sampled. The water flow was monitored by detailed profile water content measurements before irrigation, after irrigation and 24 h later with a dense array of soil moisture access tubes radially distributed around selected drippers. The objective was to develop a methodology that could be used on selected occasions to obtain 'snap shots' of the detailed three-dimensional patterns of soil moisture. Such patterns are likely to be very complex, as spatial variability will be induced for a number of reasons, such as strong horizontal gradients in soil moisture, variations between individual sources in the amount of water applied and spatial variability is soil hydraulic properties. Results are compared with a widely used numerical model, Hydrus-2D. The observed dynamic of the water content distribution is in good agreement with model simulations, although some discrepancies concerning the horizontal distribution of the irrigation bulb are noted due to soil heterogeneity. (c) 2006 Elsevier B.V. All rights reserved.

Modelling the surface circulation and thermal structure of a tropical reservoir using three-dimensional hydrodynamic lake model and remote-sensing data

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)