User guide for shock and blast simulation with the OctVCE code (version 3.5+), Department of Mechanical Engineering Report 2007/13

OctVCE is a cartesian cell CFD code produced especially for numerical simulations of shock and blast wave interactions with complex geometries. Virtual Cell Embedding (VCE) was chosen as its cartesian cell kernel as it is simple to code and sufficient for practical engineering design problems. This also makes the code much more ‘user-friendly’ than structured grid approaches as the gridding process is done automatically. The CFD methodology relies on a finite-volume formulation of the unsteady Euler equations and is solved using a standard explicit Godonov (MUSCL) scheme. Both octree-based adaptive mesh refinement and shared-memory parallel processing capability have also been incorporated. For further details on the theory behind the code, see the companion report 2007/12.

Adopting turtle excluder devices in Australia and the United States: What are the differences in technology transfer, promotion, and acceptance?

Turtle excluder devices (TEDs) are being trialed on a voluntary basis in many Australian prawn (shrimp) trawl fisheries to reduce sea turtle captures. Analysis of TED introductions into shrimp trawl fisheries of the United States provided major insights into why conflicts occurred between shrimpers, conservationists, and government agencies. A conflict over the introduction and subsequent regulation of TEDs occurred because the problem and the solution were perceived differently by the various stakeholders. Attempts to negotiate and mediate the conflict broke down, resulting in litigation against the U.S. government by conservationists and shrimpers. Litigation was not an efficient resolution to the sea turtle-TED-trawl conflict but it appears that litigation was the only remaining path of resolution once the issue became polarized. We review two major Australian trawl fisheries to identify any significant differences in circumstances that may affect TED acceptance. Australian trawl fisheries are structured differently and good communication occurs between industry and researchers. TEDs are being introduced as mature technology. Furthermore, bycatch issues are of increasing concern to all stakeholders. These factors, combined with insights derived from previous conflicts concerning TEDs in the United Stares, increase the possibilities that TEDs will be introduced to Australian fishers with better acceptance.

A phase-segregated model for plant cell culture: The effect of cell volume fraction

Plant cells are characterized by low water content, so the fraction of cell volume (volume fraction) in a vessel is large compared with other cell systems, even if the cell concentrations are the same. Therefore, concentration of plant cells should preferably be expressed by the liquid volume basis rather than by the total vessel volume basis. In this paper, a new model is proposed to analyze behavior of a plant cell culture by dividing the cell suspension into the biotic- and abiotic-phases, Using this model, we analyzed the cell-growth and the alkaloid production by Catharanthus roseus, Large errors in the simulated results were observed if the phase-segregation was not considered.

Solution structure of amyloid beta-peptide(1-40) in a water-micelle environment. Is the membrane-spanning domain where we think it is?

The three-dimensional solution structure of the 40 residue amyloid beta-peptide, A beta(1-40), has been determined using NMR spectroscopy at pH 5.1, in aqueous sodium dodecyl sulfate (SDS) micelles, In this environment, which simulates to some extent a water-membrane medium, the peptide is unstructured between residues 1 and 14 which are mainly polar and likely solvated by water. However, the rest of the protein adopts an alpha-helical conformation between residues 15 and 36 with a kink or hinge at 25-27. This largely hydrophobic region is likely solvated by SDS. Based on the derived structures, evidence is provided in support of a possible new location for the transmembrane domain of A beta within the amyloid precursor protein (APP). Studies between pH 4.2 and 7.9 reveal a pH-dependent helix-coil conformational switch. At the lower pH values, where the carboxylate residues are protonated, the helix is uncharged, intact, and lipid-soluble. As the pH increases above 6.0, part of the helical region (15-24) becomes less structured, particularly near residues E22 and D23 where deprotonation appears to facilitate unwinding of the helix. This pH-dependent unfolding to a random coil conformation precedes any tendency of this peptide to aggregate to a beta-sheet as the pH increases. The structural biology described herein for A beta(1-40) suggests that (i) the C-terminal two-thirds of the peptide is an alpha-helix in membrane-like environments, (ii) deprotonation of two acidic amino acids in the helix promotes a helix-coil conformational transition that precedes aggregation, (iii) a mobile hinge exists in the helical region of A beta(1-40) and this may be relevant to its membrane-inserting properties and conformational rearrangements, and (iv) the location of the transmembrane domain of amyloid precursor proteins may be different from that accepted in the Literature. These results may provide new insight to the structural properties of amyloid beta-peptides of relevance to Alzheimer's disease.

Behavior and interactions of children in cooperative groups in lower and middle elementary grades

The study investigated the behaviors and interactions of children in structured and unstructured groups as they worked together on a 6-week social studies activity each term for 3 school terms. Two hundred and twelve children in Grade 1 and 184 children in Grade 3 participated in the study. Stratified random assignment occurred so that each gender-balanced group consisted of 1 high-, 2 medium-, and 1 low-ability student. The results show that the children in the structured groups were consistently more cooperative and they provided more elaborated and nonelaborated help than did their peers in the unstructured groups. The children in the structured groups in Grade 3 obtained higher reading and learning outcome scores than their peers in the unstructured groups.

The role of parental anxiety in the treatment of childhood anxiety

Sixty-seven children aged 7 to 14 who met diagnostic criteria for an anxiety disorder were assigned to conditions according to parental anxiety level. Within these conditions, children were randomly assigned to I of 2 treatments: child-focused cognitive-behavioral therapy (CBT) or child-focused CBT plus parental anxiety management (CBT + PAM). At posttreatment, results indicated that within the child-anxiety-only condition, 82% of the children in the CBT condition no longer met criteria for an anxiety disorder compared with 80% in the CBT + PAM condition. Within the child + parental anxiety condition, 39% in the CBT condition no longer met criteria compared with 77% in the CBT + PAM condition. At follow-up, these differences were maintained, with some weakening over time. Results were not consistent across outcome measures. The interpretation and potential clinical implications of these findings are discussed.

A mathematical model for estimating the extent of solute- and water-flux heterogeneity in multiple sample percolation experiments

Multiple sampling is widely used in vadose zone percolation experiments to investigate the extent in which soil structure heterogeneities influence the spatial and temporal distributions of water and solutes. In this note, a simple, robust, mathematical model, based on the beta-statistical distribution, is proposed as a method of quantifying the magnitude of heterogeneity in such experiments. The model relies on fitting two parameters, alpha and zeta to the cumulative elution curves generated in multiple-sample percolation experiments. The model does not require knowledge of the soil structure. A homogeneous or uniform distribution of a solute and/or soil-water is indicated by alpha = zeta = 1, Using these parameters, a heterogeneity index (HI) is defined as root 3 times the ratio of the standard deviation and mean. Uniform or homogeneous flow of water or solutes is indicated by HI = 1 and heterogeneity is indicated by HI > 1. A large value for this index may indicate preferential flow. The heterogeneity index relies only on knowledge of the elution curves generated from multiple sample percolation experiments and is, therefore, easily calculated. The index may also be used to describe and compare the differences in solute and soil-water percolation from different experiments. The use of this index is discussed for several different leaching experiments. (C) 1999 Elsevier Science B.V. All rights reserved.

Autoinhibition by an internal nuclear localization signal revealed by the crystal structure of mammalian importin alpha

Importin alpha is the nuclear import receptor that recognizes classical monopartite and bipartite nuclear localization signals (NLSs). The structure of mouse importin alpha has been determined at 2.5 Angstrom resolution. The structure shows a large C-terminal domain containing armadillo repeats, and a less structured N-terminal importin beta-binding domain containing an internal NLS bound to the NLS-binding site. The structure explains the regulatory switch between the cytoplasmic, high-affinity form, and the nuclear, low-affinity form for NLS binding of the nuclear import receptor predicted by the current models of nuclear import. Importin beta conceivably converts the low- to high-affinity form by binding to a site overlapping the autoinhibitory sequence. The structure also has implications for understanding NLS recognition, and the structures of armadillo and HEAT repeats.

Anxious children and their parents: What do they expect?

Assigned 73 children, ages 7 to 14, to 1 of 3 groups (anxious, clinical control, and nonclinical control) according to their diagnostic status. Within the anxious group, children were assigned to 1 of 2 further groups on the basis of self-reported parental anxiety-either the child anxiety only group or the child + parent anxiety group. All children completed an experimental task (giving a brief talk in front of a video camera), which was the focus for a series of structured family discussions between the child and his or her parents. The aims of the study were to measure and compare across groups (a) the evaluations of children and their parents regarding the child's predicted anxiety and skill level and (b) the effect of the family discussion on children's expectations. Results indicated that, prior to the family discussion, anxious children's expectations of their future performance did not differ from those of control children. Similarly, there were no differences in children's expectations between the child anxiety group and the child + parent anxiety group. Second, compared to mothers in the child anxiety group, mothers in the child + parent anxiety group expected that their children would be more anxious and more likely to choose an avoidant problem solution (but not less skilled). Finally, the family discussion was found to produce no changes in anxious children's expectations of their future performance. The implications of these findings are discussed.

Accuracy of predicting a child's response to potential threat: A comparison of children and their mothers

Considerable research has indicated that children and their parents often demonstrate marked discrepancies in their reporting of anxiety-related phenomena. In such cases, the question arises as to whether children are capable of accurately reporting on their anxiety. In the present study, 50 children (aged 5 to 14 years) were asked to approach a large, German Shepherd dog. Prior to the task, both the mother and child independently predicted the closest point likely to be reached by the child and the degree of anxiety likely to be experienced. These predictions were then compared with the actual phenomena displayed by the child during the task. On the behavioural measure (closest step reached), both the child and mother demonstrated equivalent predictive accuracy. On the subjective measure (fear ratings) children were considerably more accurate than their mothers. The data were not influenced by gender, age, or clinical status. The results indicate the ability of children to accurately predict their anxious responses, and support the value of incorporating children's self-reports in the assessment of emotional disorders.

Differentiation of soil properties related to the spatial association of wheat roots and soil macropores

Under certain soil conditions, e.g. hardsetting clay B-horizons of South-Eastern Australia, wheat plants do not perform as well as would be expected given measurements of bulk soil attributes. In such soils, measurement indicates that a large proportion (80%) of roots are preferentially located in the soil within 1 mm of macropores. This paper addresses the question of whether there are biological and soil chemical effects concomitant with this observed spatial relationship. The properties of soil manually dissected from the 1-3 mm wide region surrounding macropores, the macropore sheath, were compared to those that are measured in a conventional manner on the bulk soil. Field specimens of two different soil materials were dissected to examine biological differentiation. To ascertain whether the macropore sheath soil differs from rhizosphere soil, wheat was grown in structured and repacked cores under laboratory conditions. The macropore sheath soil contained more microbial biomass per unit mass than both the bulk soil and the rhizosphere. The bacterial population in the macropore sheath was able to utilise a wider range of carbon substrates and to a greater extent than the bacterial population in the corresponding bulk soil. These differences between the macropore sheath and bulk soil were almost non-existent in the repacked cores. Evidence for larger numbers of propagules of the broad host range fungus Pythium in the macropore sheath soil were also obtained.

Quantifying the influence of intra-aggregate concentration gradients on solute transport

The physical nonequilibrium of solute concentration resulting from preferential now of soil water has often led to models where the soil is partitioned into two regions: preferential flow paths, where solute transport occurs mainly by advection, and the remaining region, where significant solute transport occurs through diffusive exchange with the flow paths. These two-region models commonly ignore concentration gradients within the regions. Our objective was to develop a simple model to assess the influence of concentration gradients on solute transport and to compare model results with experiments conducted on structured materials. The model calculates the distribution of solutes in a single spherical aggregate surrounded by preferential now paths and subjected to alternating boundary conditions representing either an exchange of solutes between the two regions (a wet period) or no exchange but redistribution of solutes within the aggregate (a dry period). The key parameter in the model is the aggregate radius, which defines the diffusive time scales. We conducted intermittent leaching experiments on a column of packed porous spheres and on a large (300 mm long by 216 mm diameter) undisturbed field soil core to test the validity of the model and its application to field soils. Alternating wet and dry periods enhanced leaching by up to 20% for this soil, which was consistent with the model's prediction, given a fitted equivalent aggregate radius of 1.8 cm, If similar results are obtained for other soils, use of alternating wet and dry periods could improve management of solutes, for example in salinity control and in soil remediation.

Effect of smoke-free policies on the behaviour of social smokers

Objective-To test the hypothesis that proposed amendments to the Occupational Safety and Health Act making all enclosed workplaces in Western Australia smoke free would result in a decrease in cigarette consumption by patrons at nightclubs, pubs, and restaurants without adversely affecting attendance. Design-Cross sectional structured interview survey. Participants and setting-Patrons of several inner city pubs and nightclubs in Perth were interviewed while queuing for admission to these venues. Outcome measures-Current social habits, smoking habits, and how these might be affected by the proposed regulations. Persons who did not smoke daily were classified as social smokers. Results-Half (50%) of the 374 patrons interviewed were male, 51% currently did not smoke at all, 34.3% smoked every day, and the remaining 15.7% smoked, brat not every day. A clear majority (62.5%) of all 374 respondents anticipated no change to the frequency of their patronage of hospitality venues if smoke-free policies became mandatory One in five (19.3%) indicated that they would,ao out more often, and 18.2% said they would go out less often. Half (52%) of daily smokers anticipated no change to their cigarette consumption, while 44.5% of daily smokers anticipated a reduction in consumption. A majority of social smokers (54%) predicted a reduction in their cigarette consumption, with 42% of these anticipating quitting. Conclusions-One in nine (11.5%) of smokers say that adoption of smoke-Pi ee policies would prompt them to quit smoking entirely without a significant decrease in attendance at pubs and nightclubs. There can be few other initiatives as simple, cheap, and popular that would achieve so much for public health.

Conformational selection of inhibitors and substrates by proteolytic enzymes: Implications for drug design and polypeptide processing

Inhibitors of proteolytic enzymes (proteases) are emerging as prospective treatments for diseases such as AIDS and viral infections, cancers, inflammatory disorders, and Alzheimer's disease. Generic approaches to the design of protease inhibitors are limited by the unpredictability of interactions between, and structural changes to, inhibitor and protease during binding. A computer analysis of superimposed crystal structures for 266 small molecule inhibitors bound to 48 proteases (16 aspartic, 17 serine, 8 cysteine, and 7 metallo) provides the first conclusive proof that inhibitors, including substrate analogues, commonly bind in an extended beta-strand conformation at the active sites of all these proteases. Representative superimposed structures are shown for (a) multiple inhibitors bound to a protease of each class, (b) single inhibitors each bound to multiple proteases, and (c) conformationally constrained inhibitors bound to proteases. Thus inhibitor/substrate conformation, rather than sequence/composition alone, influences protease recognition, and this has profound implications for inhibitor design. This conclusion is supported by NMR, CD, and binding studies for HIV-1 protease inhibitors/ substrates which, when preorganized in an extended conformation, have significantly higher protease affinity. Recognition is dependent upon conformational equilibria since helical and turn peptide conformations are not processed by proteases. Conformational selection explains the resistance of folded/structured regions of proteins to proteolytic degradation, the susceptibility of denatured proteins to processing, and the higher affinity of conformationally constrained 'extended' inhibitors/substrates for proteases. Other approaches to extended inhibitor conformations should similarly lead to high-affinity binding to a protease.

Simultaneous steady state and dynamic design of process systems using structural indicators

The simultaneous design of the steady-state and dynamic performance of a process has the ability to satisfy much more demanding dynamic performance criteria than the design of dynamics only by the connection of a control system. A method for designing process dynamics based on the use of a linearised systems' eigenvalues has been developed. The eigenvalues are associated with system states using the unit perturbation spectral resolution (UPSR), characterising the dynamics of each state. The design method uses a homotopy approach to determine a final design which satisfies both steady-state and dynamic performance criteria. A highly interacting single stage forced circulation evaporator system, including control loops, was designed by this method with the goal of reducing the time taken for the liquid composition to reach steady-state. Initially the system was successfully redesigned to speed up the eigenvalue associated with the liquid composition state, but this did not result in an improved startup performance. Further analysis showed that the integral action of the composition controller was the source of the limiting eigenvalue. Design changes made to speed up this eigenvalue did result in an improved startup performance. The proposed approach provides a structured way to address the design-control interface, giving significant insight into the dynamic behaviour of the system such that a systematic design or redesign of an existing system can be undertaken with confidence.