Disorder-induced phase transition in a one-dimensional model of rice pile

We propose a one-dimensional rice-pile model which connects the 1D BTW sandpile model (Phys. Rev. A 38 (1988) 364) and the Oslo rice-pile model (Phys. Rev. Lett. 77 (1997) 107) in a continuous manner. We found that for a sufficiently large system, there is a sharp transition between the trivial critical behaviour of the 1D BTW model and the self-organized critical (SOC) behaviour. When there is SOC, the model belongs to a known universality class with the avalanche exponent tau = 1.53. (C) 1999 Elsevier Science B.V. All rights reserved.

On the universality of a one-dimensional model of a rice pile

A one-dimensional model of a rice pile is numerically studied for different driving mechanisms and different levels of medium disorder. The universality of the scaling exponents for the transit time distribution and avalanche size distribution is discussed. (C) 1997 Published by Elsevier Science B.V.

Investigation of tanpura string vibrations using a two-dimensional time-domain model incorporating coupling and bridge friction

Tanpura string vibrations have been investigated previously using numerical models based on energy conserving schemes derived from a Hamiltonian description in one-dimensional form. Such time-domain models have the property that, for the lossless case, the numerical Hamiltonian (representing total energy of the system) can be proven to be constant from one time step
to the next, irrespective of any of the system parameters; in practice the Hamiltonian can be shown to be conserved within machine precision. Models of this kind can reproduce a jvari effect, which results from the bridge-string interaction. However the one-dimensional formulation has recently been shown to fail to replicate the jvaris strong dependence on the thread placement. As a first step towards simulations which accurately emulate this sensitivity to the thread placement, a twodimensional model is proposed, incorporating coupling of controllable level between the two string polarisations at the string termination opposite from the barrier. In addition, a friction force acting when the string slides across the bridge in horizontal direction is introduced, thus effecting a further damping mechanism. In this preliminary study, the string is terminated at the position of the thread. As in the one-dimensional model, an implicit scheme has to be used to solve the system, employing Newton's method to calculate the updated positions and momentums of each string segment. The two-dimensional model is proven to be energy conserving when the loss parameters are set to zero, irrespective of the coupling constant. Both frequency-dependent and independent losses are then added to the string, so that the model can be compared to analogous instruments. The influence of coupling and the bridge friction are investigated.

A 3-D well-differentiated model of pediatric bronchial epithelium demonstrates unstimulated morphological differences between asthmatic and nonasthmatic cells

There is a need for reproducible and effective models of pediatric bronchial epithelium to study disease states such as asthma. We aimed to develop, characterize, and differentiate an effective, an efficient, and a reliable three-dimensional model of pediatric bronchial epithelium to test the hypothesis that children with asthma differ in their epithelial morphologic phenotype when compared with nonasthmatic children. Primary cell cultures from both asthmatic and nonasthmatic children were grown and differentiated at the air-liquid interface for 28 d. Tight junction formation, MUC5AC secretion, IL-8, IL-6, prostaglandin E2 production, and the percentage of goblet and ciliated cells in culture were assessed. Well-differentiated, multilayered, columnar epithelium containing both ciliated and goblet cells from asthmatic and nonasthmatic subjects were generated. All cultures demonstrated tight junction formation at the apical surface and exhibited mucus production and secretion. Asthmatic and nonasthmatic cultures secreted similar quantities of IL-8, IL-6, and prostaglandin E2. Cultures developed from asthmatic children contained considerably more goblet cells and fewer ciliated cells compared with those from nonasthmatic children. A well-differentiated model of pediatric epithelium has been developed that will be useful for more in vivo like study of the mechanisms at play during asthma.

Automated mixed dimensional modelling from 2D and 3D CAD models

The motivation for this paper is to present procedures for automatically creating idealised finite element models from the 3D CAD solid geometry of a component. The procedures produce an accurate and efficient analysis model with little effort on the part of the user. The technique is applicable to thin walled components with local complex features and automatically creates analysis models where 3D elements representing the complex regions in the component are embedded in an efficient shell mesh representing the mid-faces of the thin sheet regions. As the resulting models contain elements of more than one dimension, they are referred to as mixed dimensional models. Although these models are computationally more expensive than some of the idealisation techniques currently employed in industry, they do allow the structural behaviour of the model to be analysed more accurately, which is essential if appropriate design decisions are to be made. Also, using these procedures, analysis models can be created automatically whereas the current idealisation techniques are mostly manual, have long preparation times, and are based on engineering judgement. In the paper the idealisation approach is first applied to 2D models that are used to approximate axisymmetric components for analysis. For these models 2D elements representing the complex regions are embedded in a 1D mesh representing the midline of the cross section of the thin sheet regions. Also discussed is the coupling, which is necessary to link the elements of different dimensionality together. Analysis results from a 3D mixed dimensional model created using the techniques in this paper are compared to those from a stiffened shell model and a 3D solid model to demonstrate the improved accuracy of the new approach. At the end of the paper a quantitative analysis of the reduction in computational cost due to shell meshing thin sheet regions demonstrates that the reduction in degrees of freedom is proportional to the square of the aspect ratio of the region, and for long slender solids, the reduction can be proportional to the aspect ratio of the region if appropriate meshing algorithms are used.

On the use of OpenFOAM to model Oscillating wave surge converters

The Computational Fluid Dynamic (CFD) toolbox OpenFOAM is used to assess the applicability of Reynolds-Averaged Navier-Stokes (RANS) solvers to the simulation of Oscillating Wave Surge Converters (OWSC) in significant waves. Simulation of these flap type devices requires the solution of the equations of motion and the representation of the OWSC’s motion in a moving mesh. A new way to simulate the sea floor inside a section of the moving mesh with a moving dissipation zone is presented. To assess the accuracy of the new solver, experiments are conducted in regular and irregular wave traces for a full three dimensional model. Results of acceleration and flow features are presented for numerical and experimental data. It is found that the new numerical model reproduces experimental results within the bounds of experimental accuracy.

Discrete-time modelling of woodwind instrument bores using wave variables

A method for simulation of acoustical bores, useful in the context of sound synthesis by physical modeling of woodwind instruments, is presented. As with previously developed methods, such as digital waveguide modeling (DWM) [Smith, Comput. Music J. 16, pp 74-91 (1992)] and the multi convolution algorithm (MCA) [Martinez et al., J. Acoust. Soc. Am. 84, pp 1620-1627 (1988)], the approach is based on a one-dimensional model of wave propagation in the bore. Both the DWM method and the MCA explicitly compute the transmission and reflection of wave variables that represent actual traveling pressure waves. The method presented in this report, the wave digital modeling (WDM) method, avoids the typical limitations associated with these methods by using a more general definition of the wave variables. An efficient and spatially modular discrete-time model is constructed from the digital representations of elemental bore units such as cylindrical sections, conical sections, and toneholes. Frequency-dependent phenomena, such as boundary losses, are approximated with digital filters. The stability of a simulation of a complete acoustic bore is investigated empirically. Results of the simulation of a full clarinet show that a very good concordance with classic transmission-line theory is obtained.

Identification of Determinants of Glucose-Dependent Insulinotropic Polypeptide Receptor That Interact with N-Terminal Biologically Active Region of the Natural Ligand

Glucose-dependent insulinotropic polypeptide receptor (GIPR), a member of family B of the G-protein coupled receptors, is a potential therapeutic target for which discovery of nonpeptide ligands is highly desirable. Structure-activity relationship studies indicated that the N-terminal part of glucose-dependent insulinotropic polypeptide (GIP) is crucial for biological activity. Here, we aimed at identification of residues in the GIPR involved in functional interaction with N-terminal moiety of GIP. A homology model of the transmembrane core of GIPR was constructed, whereas a three-dimensional model of the complex formed between GIP and the N-terminal extracellular domain of GIPR was taken from the crystal structure. The latter complex was docked to the transmembrane domains of GIPR, allowing in silico identification of putative residues of the agonist binding/activation site. All mutants were expressed at the surface of human embryonic kidney 293 cells as indicated by flow cytometry and confocal microscopy analysis of fluorescent GIP binding. Mutation of residues Arg183, Arg190, Arg300, and Phe357 caused shifts of 76-, 71-, 42-, and 16-fold in the potency to induce cAMP formation, respectively. Further characterization of these mutants, including tests with alanine-substituted GIP analogs, were in agreement with interaction of Glu3 in GIP with Arg183 in GIPR. Furthermore, they strongly supported a binding mode of GIP to GIPR in which the N-terminal moiety of GIP was sited within transmembrane helices (TMH) 2, 3, 5, and 6 with biologically crucial Tyr1 interacting with Gln224 (TMH3), Arg300 (TMH5), and Phe357 (TMH6). These data represent an important step toward understanding activation of GIPR by GIP, which should facilitate the rational design of therapeutic agents.

Modeled structure of the whole regulator G-protein signaling-2

There is an increasing interest towards the mechanism by which regulators of G-protein signaling regulate signals of G-protein-coupled receptors. RGS2 is a regulator of Gq protein signaling (RGS), the N-terminal region of which is known to contain determinants for G protein-coupled receptor recognition, but its structure is still unknown. To understand the molecular basis for this recognition, the three-dimensional model of RGS2, including N-terminal region and RGS box, was modeled. For this, RGS4 box structure and data from circular dichroism study of RGS2 N-terminal region were used. Then, membrane-targeting activity of the RGS2 amphipathic helix contained in the N-terminal region was investigated. Furthermore, in cellulo study provided first evidence that an internal sequence within the N-terminal region of RGS2 is involved in RGS2 regulation of cholecystokinin receptor-2 signal. RGS2 modeled structure can now serve to study molecular recognition of RGS2 by signaling molecules. © 2006 Elsevier Inc. All rights reserved.

Docosahexaenoic Acid Improves the Nitroso-Redox Balance and Reduces VEGF-Mediated Angiogenic Signaling in Microvascular Endothelial Cells

Purpose. Disturbances to the cellular production of nitric oxide (NO) and superoxide (O2-) can have deleterious effects on retinal vascular integrity and angiogenic signaling. Dietary agents that could modulate the production of these signaling molecules from their likely enzymatic sources, endothelial nitric oxide synthase (eNOS) and NADPH oxidase, would therefore have a major beneficial effect on retinal vascular disease. The effect of ?-3 polyunsaturated fatty acids (PUFAs) on angiogenic signaling and NO/superoxide production in retinal microvascular endothelial cells (RMECs) was investigated.

Methods. Primary RMECs were treated with docosahexaenoic acid (DHA) or eicosapentaenoic acid (EPA) for 48 hours. RMEC migration was determined by scratch-wound assay, proliferation by the incorporation of BrdU, and angiogenic sprouting using a three-dimensional model of in vitro angiogenesis. NO production was quantified by Griess assay, and phospho-eNOS accumulation and superoxide were measured using the fluorescent probe dihydroethidine. eNOS localization to caveolin-rich microdomains was determined by Western blot analysis after subfractionation on a linear sucrose gradient.

Results. DHA treatment increased nitrite and decreased superoxide production, which correlated with the displacement of eNOS from caveolar subdomains and colocalization with the negative regulator caveolin-1. In addition, both ?-3 PUFAs demonstrated reduced responsiveness to VEGF-stimulated superoxide and nitrite release and significantly impaired endothelial wound healing, proliferation, and angiogenic sprout formation.

Conclusions. DHA improves NO bioavailability, decreases O2- production, and blunts VEGF-mediated angiogenic signaling. These findings suggest a role for ?-3 PUFAs, particularly DHA, in maintaining vascular integrity while reducing pathologic retinal neovascularization.

Computer simulations of seasonal outbreak and diurnal vertical migration of cyanobacteria

Algal blooms caused by cyanobacteria are characterized by two features with different time scales: one is seasonal outbreak and collapse of a bloom and the other is diurnal vertical migration. Our two-component mathematical model can simulate both phenomena, in which the state variables are nutrients and cyanobacteria. The model is a set of one-dimensional reaction-advection-diffusion equations, and temporal changes of these two variables are regulated by the following five factors: (1) annual variation of light intensity, (2) diurnal variation of light intensity, (3) annual variation of water temperature, (4) thermal stratification within a water column and (5) the buoyancy regulation mechanism. The seasonal change of cyanobacteria biomass is mainly controlled by factors, (1), (3) and (4), among which annual variations of light intensity and water temperature directly affect the maximum growth rate of cyanobacteria. The latter also contributes to formation of the thermocline during the summer season. Thermal stratification causes a reduction in vertical diffusion and largely prevents mixing of both nutrients and cyanobacteria between the epilimnion and the hypolimnion. Meanwhile, the other two factors, (2) and (5), play a significant role in diurnal vertical migration of cyanobacteria. A key mechanism of vertical migration is buoyancy regulation due to gas-vesicle synthesis and ballast formation, by which a quick reversal between floating and sinking becomes possible within a water column. The mechanism of bloom formation controlled by these five factors is integrated into the one-dimensional model consisting of two reaction-advection-diffusion equations.

In Silico Prediction of the Mechanobiological Response of Arterial Tissue: Application to Angioplasty and Stenting

One way to restore physiological blood flow to occluded arteries involves the deformation of plaque using an intravascular balloon and preventing elastic recoil using a stent. Angioplasty and stent implantation cause unphysiological loading of the arterial tissue, which may lead to tissue in-growth and reblockage; termed “restenosis.” In this paper, a computational methodology for predicting the time-course of restenosis is presented. Stress-induced damage, computed using a remaining life approach, stimulates inflammation (production of matrix degrading factors and growth stimuli). This, in turn, induces a change in smooth muscle cell phenotype from contractile (as exists in the quiescent tissue) to synthetic (as exists in the growing tissue). In this paper, smooth muscle cell activity (migration, proliferation, and differentiation) is simulated in a lattice using a stochastic approach to model individual cell activity. The inflammation equations are examined under simplified loading cases. The mechanobiological parameters of the model were estimated by calibrating the model response to the results of a balloon angioplasty study in humans. The simulation method was then used to simulate restenosis in a two dimensional model of a stented artery. Cell activity predictions were similar to those observed during neointimal hyperplasia, culminating in the growth of restenosis. Similar to experiment, the amount of neointima produced increased with the degree of expansion of the stent, and this relationship was found to be highly dependant on the prescribed inflammatory response. It was found that the duration of inflammation affected the amount of restenosis produced, and that this effect was most pronounced with large stent expansions. In conclusion, the paper shows that the arterial tissue response to mechanical stimulation can be predicted using a stochastic cell modeling approach, and that the simulation captures features of restenosis development observed with real stents. The modeling approach is proposed for application in three dimensional models of cardiovascular stenting procedures.

Functional analysis of predicted coiled-coil regions in the Escherichia coli K-12 O-antigen polysaccharide chain length determinant Wzz

Wzz is a membrane protein that determines the chain length distribution of the O-antigen lipopolysaccharide by an unknown mechanism. Wzz proteins consist of two transmembrane helices separated by a large periplasmic loop. The periplasmic loop of Escherichia coli K-12 Wzz (244 amino acids from K65 to A308) was purified and found to be a monomer with an extended conformation, as determined by gel filtration chromatography and analytical ultracentrifugation. Circular dichroism showed that the loop has a 60% helical content. The Wzz periplasmic loop also contains three regions with predicted coiled coils. To probe the function of the predicted coiled coils, we constructed amino acid replacement mutants of the E. coli K-12 Wzz protein, which were designed so that the coiled coils could be separate without compromising the helicity of the individual molecules. Mutations in one of the regions, spanning amino acids 108 to 130 (region I), were associated with a partial defect in O-antigen chain length distribution, while mutants with mutations in the region spanning amino acids 209 to 223 (region III) did not have an apparent functional defect. In contrast, mutations in the region spanning amino acids 153 to 173 (region II) eliminated the Wzz function. This phenotype was associated with protein instability, most likely due to conformational changes caused by the amino acid replacements, which was confirmed by limited trypsin proteolysis. Additional mutagenesis based on a three-dimensional model of region I demonstrated that the amino acids implicated in function are all located at the same face of a predicted alpha-helix, suggesting that a coiled coil actually does not exist in this region. Together, our results suggest that the regions predicted to be coiled coils are important for Wzz function because they maintain the native conformation of the protein, although the existence of coiled coils could not be demonstrated experimentally.

Peer tutoring in reading: The effects of role and organization on two dimensions of self-esteem

Background. Paired reading (PR) is an application of peer tutoring. It has been extensively researched, and its efficacy across a range of outcomes has been established. Benefits include improvements in key reading skills, and also in affective aspects of learning. Several studies have shown gains in self-esteem, although measurement methods have varied, and the model of self-esteem has rarely been clearly articulated.
Aims. To investigate the changes in self-esteem of children participating in a randomized trial of PR over a 15-week treatment period. To investigate the relative contribution of self-worth and self-competence to any gains in self-esteem. To investigate whether the pattern of change differs in children who take on different roles in the PR process.
Participants. The participants comprised a subset of a large-scale randomized trial of peer learning (The Fife Peer Learning Project). Four schools were randomly selected from schools allocated to the same-age PR condition, and four schools from those allocated to the cross-age PR condition. The same-age group consisted of 87 primary 6 children (10–11 years old). The cross-age group consisted of 81 primary 6 children. The controls, from schools randomly selected from a neighbouring authority, consisted of 92 primary 6 children.
Method. A pre–post design employing self-report measures of self-esteem. Rosenberg’s Self-Esteem Scale was used, with scores analysed for worth and competence. The treatment period was 15 weeks, with the participants following a prescribed PR process.
Results. Significant pre–post gains were noted in self-esteem, driven predominantly by improved beliefs about competence, in both same-age and cross-age conditions, but not for controls. Gains were also seen in self-worth in the cross-age condition. Further analyses of the influence of organizational condition (same-age or cross-age) and role played (tutor vs. tutee) showed significant differences between same-age tutors and cross-age tutors in relation to self-worth. Effect sizes were generally small or moderate.
Conclusions. The findings provide further support for the belief that PR can enhance self-esteem. Importantly, the use of a two-dimensional model provides extra information about self-perceptions in PR contexts: first, the central role of self- competence; and second, the gains in self-worth which are associated with tutoring younger children (but not same-age peers). This new information has educational significance for schools considering the potential of peer tutoring and the benefits of different organizational conditions.

Performance analysis of an infinite array linear clustered plug nozzle

The effects of module shape, module design, three dimensional flow field generated by modules, and partition of primary nozzle on the performance of an infinite array linear clustered plug nozzle are discussed. The module shape is a critical element for nozzle performance and the partition of the primary nozzle with round-to square modules causes a vacuum thrust reduction with respect to two-dimensional model. The performance analysis of different module configuration allows weighing separately the role of clustering and the role of module design. In operating conditions characterized by turned off modules the performance loss is larger, but the difference due to the module shape are smaller and mostly due to the module contribution. The performance of the plug nozzle can be improved by module design, which reduces the module exit flow nonuniformity.