Detached eddy simulation of turbulent flow around square and circular cylinders on Cartesian cut cells

© 2016 Elsevier Ltd. All rights reserved. Square and circular cylinders in three-dimensional turbulent flows are studied numerically using the LES and DES turbulence models. One aim of the present study is to implement the LES and DES turbulence models in a cell-centered finite volume method (FVM) developed for solving the Navier-Stokes equations on Cartesian cut cells. The Cartesian cut cell approach is known to be robust for problems in geometrically complex domains with fixed or moving boundaries. For the purpose of validating the present numerical model, the current flow past fixed square and circular cylinders at moderate Reynolds numbers is tested first. Comparison of the computed results with experimental data reveals that the DES models are superior to the conventional LES and RANS models. The second aim of the present study is to assess the performance of different RANS based DES turbulence models. By means of the comparison of results obtained with the 0-equation mixing-length, 1-equation S-A and 2-equation k-ω based DES models for the flow over the same circular cylinder, some recommendations are proposed. According to the present study, in terms of accuracy the 1-equation S-A based DES model is very promising. Beside this, if the computational cost is the main concern, the 0-equation mixing-length based DES model might be an ideal option, achieving a good balance between accuracy and efficiency

Numerical simulation of water impact of solid bodies with vertical and oblique entries

The flow problem of hydrodynamic impact during water entry of solid objects of various shapes and configurations is simulated by a two-fluid free surface code based on the solution of the Navier-Stokes equations (NSE) on a fixed Cartesian grid. In the numerical model the free surface is captured by the level set function, and the partial cell method combined with a local relative velocity approach is applied to the simulation of moving bodies. The code is firstly validated using experimental data and other numerical results in terms of the impact forces and surface pressure distributions for the vertical entry of a semi-circular cylinder and a symmetric wedge. Then configurations of oblique water entry of a wedge are simulated and the predicted free surface profiles during impact are compared with experimental results showing a good agreement. Finally, a series of tests involving vertical and oblique water entry of wedges with different heel angles are simulated and the results compared with published numerical results. It is found that the surface pressure distributions and forces predicted by the present model generally agree very well with other numerical results based on the potential flow theory. However, as the current model is based on the solution of the NSE, it is more robust and can therefore predict, for example, the formation and separation of the thin flow jets (spray) from surface of the wedge and associated ventilation phenomena for the cases of oblique water entry when the horizontal velocity is dominant. It is also noted that the potential flow theory can result in over-estimated negative pressures at the tip of the wedge due to its inherent restriction to nonseparated flows. © 2013 Elsevier Ltd. All rights reserved

Modelling wave interaction with deformable structures based on a multi-region approach within OpenFOAM

© 2017 by the International Society of Offshore and Polar Engineers (ISOPE). This paper presents the development of a multi-region computational fluid-structure dynamics (CFSD) method which is integrated in our virtual wave structure interaction solver wsiFoam, based on the open-source OpenFOAM library, in order to account for the hydro-elastic effects produced by violent wave impacts against deformable bodies. This strategy relies entirely on the finite volume method (FVM) and does not require any third-party solvers, which renders it suitable for efficient parallel computing. We validate this novel approach against previous experimental and numerical results corresponding to a dam break of water impacting on a highly deformable plate as well as a flexible wedge entering water at a constant speed. In general, our preliminary results agree qualitatively well with previous data whilst the performance of parallel implementation evidences the potential of this method to be used in future high performing computing (HPC) applications

A GPU based compressible multiphase hydrocode for modelling violent hydrodynamic impact problems

This paper presents a GPU based compressible multiphase hydrocode for modelling violent hydrodynamic impacts under harsh conditions such as slamming and underwater explosion. An effort is made to extend a one-dimensional five-equation reduced model (Kapila et al., 2001) to compute three-dimensional hydrodynamic impact problems on modern graphics hardware. In order to deal with free-surface problems such as water waves, gravitational terms, which are initially absent from the original model, are now considered and included in the governing equations. A third-order finite volume based MUSCL scheme is applied to discretise the integral form of the governing equations. The numerical flux across a mesh cell face is estimated by means of the HLLC approximate Riemann solver. The serial CPU program is firstly parallelised on multi-core CPUs with the OpenMP programming model and then further accelerated on many-core graphics processing units (GPUs) using the CUDA C programming language. To balance memory usage, computing efficiency and accuracy on multi- and many-core processors, a mixture of single and double precision floating-point operations is implemented. The most important data like conservative flow variables are handled with double-precision dynamic arrays, whilst all the other variables/arrays like fluxes, residual and source terms are treated in single precision. Several benchmark test cases including water-air shock tubes, one-dimensional liquid cavitation tube, dam break, 2D cylindrical underwater explosion near a planar rigid wall, 3D spherical explosion in a rigid cylindrical container and water entry of a 3D rigid flat plate have been calculated using the present approach. The obtained results agree well with experiments, exact solutions and other independent numerical computations. This demonstrates the capability of the present approach to deal with not only violent free-surface impact problems but also hull cavitation associated with underwater explosions. Performance analysis reveals that the running time cost of numerical simulations is dramatically reduced by use of GPUs with much less consumption of electrical energy than on the CPU

Pure and aerated water entry of a flat plate

This paper presents an experimental and numerical investigation of the entry of a rigid square flat plate into pure and aerated water. Attention is focused on the measurement and calculation of the slamming loads on the plate. The experimental study was carried out in the ocean basin at Plymouth University’s COAST laboratory. The present numerical approach extends a two-dimensional hydro-code to compute three-dimensional hydrodynamic impact problems. The impact loads on the structure computed by the numerical model compare well with laboratory measurements. It is revealed that the impact loading consists of distinctive features including (1) shock loading with a high pressure peak, (2) fluid expansion loading associated with very low sub-atmospheric pressure close to the saturated vapour pressure, and (3) less severe secondary reloading with super-atmospheric pressure. It is also disclosed that aeration introduced into water can effectively reduce local pressures and total forces on the flat plate. The peak impact loading on the plate can be reduced by half or even more with 1.6% aeration in water. At the same time, the lifespan of shock loading is prolonged by aeration, and the variation of impulse is less sensitive to the change of aeration than the peak loading

Primary cilia elongation in response to interleukin-1 mediates the inflammatory response

Primary cilia are singular, cytoskeletal organelles present in the majority of mammalian cell types where they function as coordinating centres for mechanotransduction, Wnt and hedgehog signalling. The length of the primary cilium is proposed to modulate cilia function, governed in part by the activity of intraflagellar transport (IFT). In articular cartilage, primary cilia length is increased and hedgehog signaling activated in osteoarthritis (OA). Here, we examine primary cilia length with exposure to the quintessential inflammatory cytokine interleukin-1 (IL-1), which is up-regulated in OA. We then test the hypothesis that the cilium is involved in mediating the downstream inflammatory response. Primary chondrocytes treated with IL-1 exhibited a 50 % increase in cilia length after 3 h exposure. IL-1-induced cilia elongation was also observed in human fibroblasts. In chondrocytes, this elongation occurred via a protein kinase A (PKA)-dependent mechanism. G-protein coupled adenylate cyclase also regulated the length of chondrocyte primary cilia but not downstream of IL-1. Chondrocytes treated with IL-1 exhibit a characteristic increase in the release of the inflammatory chemokines, nitric oxide and prostaglandin E2. However, in cells with a mutation in IFT88 whereby the cilia structure is lost, this response to IL-1 was significantly attenuated and, in the case of nitric oxide, completely abolished. Inhibition of IL-1-induced cilia elongation by PKA inhibition also attenuated the chemokine response. These results suggest that cilia assembly regulates the response to inflammatory cytokines. Therefore, the cilia proteome may provide a novel therapeutic target for the treatment of inflammatory pathologies, including OA

Knowledge and risk behaviors related to HIV/AIDS, and their association with information resource among men who have sex with men in Heilongjiang province, China

<p>Abstract</p> <p>Backgroud</p> <p>In Heilongjiang province, the HIV prevalence in men who have sex with men (MSM) is generally lower than other part of China. However, the official perception for their risk of HIV/AIDS infection has been increasing in the province over the years. Moreover, little information on HIV/AIDS was provided to the communities so that we have disadvantage of controlling HIV/AIDS epidemic in the region. The purpose of this study is to investigate the prevalence of HIV among MSM in Heilongjiang province, to assess their knowledge levels and risk behaviors related to HIV/AIDS, and to explore their associations with information resources.</p> <p>Methods</p> <p>A cross-sectional study using a standardized questionnaire and blood test was administered in 2008 by local interviewers to a sample (1353) of MSM in four cities in Heilongjiang province.</p> <p>Results</p> <p>Among 1353 MSM, 2.3% were identified with HIV infection. About 48.7% of the subjects had multiple male sexual partners and only 37.3% of the subjects had consistent condom use (use every time) in the past 6 months. Most had a fair level of knowledge on HIV/AIDS, with the highest mean knowledge score among the MSM from Jiamusi, those with income 2000-3000 RMB/month, those searching sexual partners via internet and those performed HIV testing over 1 year ago). However, some myths regarding viral transmission (e.g., via mosquito bites or sharing kitchen utensils) also existed. Resources of information from which knowledge and risk behaviors related to HIV/AIDS was most available were television (58.6%) among MSM, followed by sexual partner (51.6%), publicity material (51.0%) and internet (48.7%). Significantly statistical differences of mean knowledge score were revealed in favor of book (<it>P </it>= 0.0002), medical staff (<it>P </it>= 0.0007), publicity material (<it>P </it>= 0.005) and sexual partner (<it>P </it>= 0.02). Press (<it>P </it>= 0.04) and book (<it>P </it>= 0.0003) were contributory to the most frequent condom use (condom use every time), while medical staff (<it>P </it>= 0.005) and publicity material (<it>P </it>= 0.04) is associated with moderate rate of condom use (condom use often).</p> <p>Conclusions</p> <p>Although the prevalence of HIV infection is low among MSM in Heilongjiang province, the situation that the risk behaviors were frequent in the population is alarming. The study suggests that some strategies like condom use and education intervention are practical approaches and need to be strengthened.</p

A self-organized model for cell-differentiation based on variations of molecular decay rates

Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation characteristic to living systems. At any point in time only small subsets of these networks are active. Any active subset of the GRN leads to the expression of particular sets of molecules (expression modes). The subsets of active networks change over time, leading to the observed complex dynamics of expression patterns. Understanding of this dynamics becomes increasingly important in systems biology and medicine. While the importance of transcription rates and catalytic interactions has been widely recognized in modeling genetic regulatory systems, the understanding of the role of degradation of biochemical agents (mRNA, protein) in regulatory dynamics remains limited. Recent experimental data suggests that there exists a functional relation between mRNA and protein decay rates and expression modes. In this paper we propose a model for the dynamics of successions of sequences of active subnetworks of the GRN. The model is able to reproduce key characteristics of molecular dynamics, including homeostasis, multi-stability, periodic dynamics, alternating activity, differentiability, and self-organized critical dynamics. Moreover the model allows to naturally understand the mechanism behind the relation between decay rates and expression modes. The model explains recent experimental observations that decay-rates (or turnovers) vary between differentiated tissue-classes at a general systemic level and highlights the role of intracellular decay rate control mechanisms in cell differentiation.Comment: 16 pages, 5 figure

A Nonaqueous Approach to the Preparation of Iron Phosphide Nanowires

Previous preparation of iron phosphide nanowires usually employed toxic and unstable iron carbonyl compounds as precursor. In this study, we demonstrate that iron phosphide nanowires can be synthesized via a facile nonaqueous chemical route that utilizes a commonly available iron precursor, iron (III) acetylacetonate. In the synthesis, trioctylphosphine (TOP) and trioctylphosphine oxide (TOPO) have been used as surfactants, and oleylamine has been used as solvent. The crystalline structure and morphology of the as-synthesized products were characterized by powder X-ray diffraction (XRD) and transmission electron microscopy (TEM). The obtained iron phosphide nanowires have a typical width of ~16 nm and a length of several hundred nanometers. Structural and compositional characterization reveals a hexagonal Fe2P crystalline phase. The morphology of as-synthesized products is greatly influenced by the ratio of TOP/TOPO. The presence of TOPO has been found to be essential for the growth of high-quality iron phosphide nanowires. Magnetic measurements reveal ferromagnetic characteristics, and hysteresis behaviors below the blocking temperature have been observed

Identification of four novel associations for B-cell acute lymphoblastic leukaemia risk.

There is increasing evidence for a strong inherited genetic basis of susceptibility to acute lymphoblastic leukaemia (ALL) in children. To identify new risk variants for B-cell ALL (B-ALL) we conducted a meta-analysis with four GWAS (genome-wide association studies), totalling 5321 cases and 16,666 controls of European descent. We herein describe novel risk loci for B-ALL at 9q21.31 (rs76925697, P = 2.11 × 10-8), for high-hyperdiploid ALL at 5q31.1 (rs886285, P = 1.56 × 10-8) and 6p21.31 (rs210143 in BAK1, P = 2.21 × 10-8), and ETV6-RUNX1 ALL at 17q21.32 (rs10853104 in IGF2BP1, P = 1.82 × 10-8). Particularly notable are the pleiotropic effects of the BAK1 variant on multiple haematological malignancies and specific effects of IGF2BP1 on ETV6-RUNX1 ALL evidenced by both germline and somatic genomic analyses. Integration of GWAS signals with transcriptomic/epigenomic profiling and 3D chromatin interaction data for these leukaemia risk loci suggests deregulation of B-cell development and the cell cycle as central mechanisms governing genetic susceptibility to ALL