348 results found
Calder M, Craig C, Culley D, et al., 2018, Computational modelling for decision-making: where, why, what, who and how, Royal Society Open Science, Vol: 5, ISSN: 2054-5703
In order to deal with an increasingly complex world, we need ever more sophisticated computational models that can help us make decisions wisely and understand the potential consequences of choices. But creating a model requires far more than just raw data and technical skills: it requires a close collaboration between model commissioners, developers, users and reviewers. Good modelling requires its users and commissioners to understand more about the whole process, including the different kinds of purpose a model can have and the different technical bases. This paper offers a guide to the process of commissioning, developing and deploying models across a wide range of domains from public policy to science and engineering. It provides two checklists to help potential modellers, commissioners and users ensure they have considered the most significant factors that will determine success. We conclude there is a need to reinforce modelling as a discipline, so that misconstruction is less likely; to increase understanding of modelling in all domains, so that the misuse of models is reduced; and to bring commissioners closer to modelling, so that the results are more useful.
Cohen J, Marcon J, Turner M, et al., 2019, Simplifying high-order mesh generation for computational scientists, 10th International Workshop on Science Gateways, Publisher: CEUR Workshop Proceedings, ISSN: 1613-0073
Computational modelling is now tightly integrated into many fields of research in science and industry. Computational fluid dynamics software, for example, gives engineers the ability to model fluid flow around complex geometries defined in Computer-Aided Design (CAD) packages, without the expense of constructing large wind tunnel experiments. However, such modelling requires translation from an initial CAD geometry to a mesh of many small elements that modelling software uses to represent the approximate solution in the numerical method. Generating sufficiently high-quality meshes for simulation is a time-consuming, iterative and error-prone process that is often complicated by the need to interact with multiple command-line tools to generate and visualise the mesh data. In this paper we describe our approach to overcoming this complexity through the addition of a meshing console to Nekkloud, a science gateway for simplifying access to the functionality of the Nektar++ spectral/hp element framework. The meshing console makes use of the NekMesh tool in Nektar++ to help reduce the complexity of the mesh generation process. It offers a web-based interface for specifying parameters, undertaking meshing and visualising results. The meshing console enables Nekkloud to offer support for a full, end-to-end simulation pipeline from initial CAD geometry to simulation results.
Alpresa P, Sherwin S, Weinberg P, et al., 2018, Orbitally shaken shallow fluid layers. II. An improved wall shear stress model, PHYSICS OF FLUIDS, Vol: 30, ISSN: 1070-6631
A new model for the analytical prediction of wall shear stress distributions at the base of orbitally shaken shallow fluid layers is developed. This model is a generalisation of the classical extended Stokes solution and will be referred to as the potential theory-Stokes model. The model is validated using a large set of numerical simulations covering a wide range of flow regimes representative of those used in laboratory experiments. It is demonstrated that the model is in much better agreement with the simulation data than the classical Stokes solution, improving the prediction in 63% of the studied cases. The central assumption of the model—which is to link the wall shear stress with the surface velocity—is shown to hold remarkably well over all regimes covered.
Alpresa P, Sherwin S, Weinberg P, et al., 2018, Orbitally shaken shallow fluid layers. I. Regime classification, PHYSICS OF FLUIDS, Vol: 30, ISSN: 1070-6631
Orbital shakers are simple devices that provide mixing, aeration, and shear stress at multiple scales and high throughput. For this reason, they are extensively used in a wide range of applications from protein production to bacterial biofilms and endothelial cell experiments. This study focuses on the behaviour of orbitally shaken shallow fluid layers in cylindrical containers. In order to investigate the behaviour over a wide range of different conditions, a significant number of numerical simulations are carried out under different configuration parameters. We demonstrate that potential theory—despite the relatively low Reynolds number of the system—describes the free-surface amplitude well and the velocity field reasonably well, except when the forcing frequency is close to a natural frequency and resonance occurs. By classifying the simulations into non-breaking, breaking, and breaking with part of the bottom uncovered, it is shown that the onset of wave breaking is well described by Δh/(2R) = 0.7Γ, where Δh is the free-surface amplitude, R is the container radius, and Γ is the container aspect ratio; Δh can be well approximated using the potential theory. This result is in agreement with standard wave breaking theories although the significant inertial forcing causes wave breaking at lower amplitudes.
De Grazia D, Moxey D, Sherwin SJ, et al., 2018, Direct numerical simulation of a compressible boundary-layer flow past an isolated three-dimensional hump in a high-speed subsonic regime, Physical Review Fluids, Vol: 3, ISSN: 2469-990X
In this paper we study the boundary-layer separation produced in a high-speed subsonic boundary layer by a small wall roughness. Specifically, we present a direct numerical simulation (DNS) of a two-dimensional boundary-layer flow over a flat plate encountering a three-dimensional Gaussian-shaped hump. This work was motivated by the lack of DNS data of boundary-layer flows past roughness elements in a similar regime which is typical of civil aviation. The Mach and Reynolds numbers are chosen to be relevant for aeronautical applications when considering small imperfections at the leading edge of wings. We analyze different heights of the hump: The smaller heights result in a weakly nonlinear regime, while the larger result in a fully nonlinear regime with an increasing laminar separation bubble arising downstream of the roughness element and the formation of a pair of streamwise counterrotating vortices which appear to support themselves.
Xu H, Cantwell C, Monteserin C, et al., 2018, Spectral/hp element methods: Recent developments, applications, and perspectives, Journal of Hydrodynamics, Vol: 30, Pages: 1-22, ISSN: 1001-6058
The spectral/hp element method combines the geometric flexibility of the classical h-type finite element technique with the desirable numerical properties of spectral methods, employing high-degree piecewise polynomial basis functions on coarse finite element-type meshes. The spatial approximation is based upon orthogonal polynomials, such as Legendre or Chebychev polynomials, modified to accommodate a C0 - continuous expansion. Computationally and theoretically, by increasing the polynomial order p, high-precision solutions and fast convergence can be obtained and, in particular, under certain regularity assumptions an exponential reduction in approximation error between numerical and exact solutions can be achieved. This method has now been applied in many simulation studies of both fundamental and practical engineering flows. This paper briefly describes the formulation of the spectral/hp element method and provides an overview of its application to computational fluid dynamics. In particular, it focuses on the use of the spectral/hp element method in transitional flows and ocean engineering. Finally, some of the major challenges to be overcome in order to use the spectral/hp element method in more complex science and engineering applications are discussed.
Mengaldo G, De Grazia D, Moura RC, et al., 2018, Spatial eigensolution analysis of energy-stable flux reconstruction schemes and influence of the numerical flux on accuracy and robustness, Journal of Computational Physics, Vol: 358, Pages: 1-20, ISSN: 0021-9991
This study focusses on the dispersion and diffusion characteristics of high-order energy-stable flux recon-struction (ESFR) schemes via the spatial eigensolution analysis framework proposed in . The analysis isperformed for five ESFR schemes, where the parameter ‘c’ dictating the properties of the specific schemerecovered is chosen such that it spans the entire class of ESFR methods, also referred to as VCJH schemes,proposed in . In particular, we used five values of ‘c’, two that correspond to its lower and upper boundsand the others that identify three schemes that are linked to common high-order methods, namely theESFR recovering two versions of discontinuous Galerkin methods and one recovering the spectral differencescheme. The performance of each scheme is assessed when using different numerical intercell fluxes (e.g.different levels of upwinding), ranging from “under-” to “over-upwinding”. In contrast to the more commontemporal analysis, the spatial eigensolution analysis framework adopted here allows one to grasp crucialinsights into the diffusion and dispersion properties of FR schemes for problems involving non-periodicboundary conditions, typically found in open-flow problems, including turbulence, unsteady aerodynamicsand aeroacoustics.
Bao Y, Palacios R, Graham M, et al., 2018, A strip modelling of flow past a freely vibrating cable, ERCOFTAC Series, Vol: 24, Pages: 221-227, ISSN: 1382-4309
© 2018, Springer International Publishing AG. Vortex-induced vibration of long flexible structures with cylindrical cross-section are widely encountered in various engineering fields.
Marcon J, Turner M, Moxey D, et al., 2017, A variational approach to high-order r-adaptation, 26th International Meshing Roundtable
A variational framework, initially developed for high-order mesh optimisation, is being extended for r-adaptation. The method is based on the minimisation of a functional of the mesh deformation. To achieve adaptation, elements of the initial mesh are manipulated using metric tensors to obtain target elements. The nonlinear optimisation in turns adapts the final high-order mesh to best fit the description of the target elements by minimising the element distortion. Encouraging preliminary results prove that the method behaves well and can be used in the future for more extensive work which shall include the use of error indicators from CFD simulations.
Serson D, Meneghini JR, Sherwin SJ, 2017, Direct numerical simulations of the flow around wings with spanwise waviness, Journal of Fluid Mechanics, Vol: 826, Pages: 714-731, ISSN: 0022-1120
The use of spanwise waviness in wings has been proposed in the literature as a possible mechanism for obtaining improved aerodynamic characteristics, motivated by the tubercles that cover the leading edge of the pectoral flippers of the humpback whale. We investigate the effect of this type of waviness on the incompressible flow around infinite wings with a NACA0012 profile, using direct numerical simulations employing the spectral/hp method. Simulations were performed for Reynolds numbers of and , considering different angles of attack in both the pre-stall and post-stall regimes. The results show that the waviness can either increase or decrease the lift coefficient, depending on the particular and flow regime. We observe that the flow around the wavy wing exhibits a tendency to remain attached behind the waviness peak, with separation restricted to the troughs, which is consistent with results from the literature. Then, we identify three important physical mechanisms in this flow. The first mechanism is the weakening of the suction peak on the sections corresponding to the waviness peaks. This characteristic had been observed in a previous investigation for a very low Reynolds number of , and we show that this is still important even at . As a second mechanism, the waviness has a significant effect on the stability of the separated shear layers, with transition occurring earlier for the wavy wing. In the pre-stall regime, for , the flow around the baseline wing is completely laminar, and the earlier transition leads to a large increase in the lift coefficient, while for , the earlier transition leads to a shortening of the separation bubble which does not lead to an increased lift coefficient. The last mechanism corresponds to a sub-harmonic behaviour, with the flow being notably different between subsequent wavelengths. This allows the wing to maintain higher lift coefficients in some portions of the span.
Ghim M, Alpresa P, Yang S, et al., 2017, Visualization of three pathways for macromolecule transport across cultured endothelium and their modification by flow., AJP - Heart and Circulatory Physiology, Vol: 313, Pages: H959-H973, ISSN: 1522-1539
Transport of macromolecules across vascular endothelium and its modification by fluid mechanical forces are important for normal tissue function and in the development of atherosclerosis. However, the routes by which macromolecules cross endothelium, the hemodynamic stresses that maintain endothelial physiology or trigger arterial disease, and the dependence of transendothelial transport on hemodynamic stresses are controversial. Here we visualised pathways for macromolecule transport and determined the effect on these pathways of different types of flow. Endothelial monolayers were cultured under static conditions or on an orbital shaker producing different flow profiles in different parts of the wells. Fluorescent tracers that bound to the substrate after crossing the endothelium were used to identify transport pathways. Maps of tracer distribution were compared with numerical simulations of flow to determine effects of different shear stress metrics on permeability. Albumin-sized tracers dominantly crossed the cultured endothelium via junctions between neighbouring cells, high-density-lipoprotein-sized tracers crossed at tricelluar junctions whilst low-density-lipoprotein-sized tracers crossed through cells. Cells aligned close to the angle that minimised shear stresses across their long axis. The rate of paracellular transport under flow correlated with the magnitude of these minimised transverse stresses, whereas transport across cells was uniformly reduced by all types of flow. These results contradict the long-standing two-pore theory of solute transport across microvessel walls and the consensus view that endothelial cells align with the mean shear vector. They suggest that endothelial cells minimise transverse shear, supporting its postulated pro-atherogenic role. Preliminary data show that similar tracer techniques are practicable in vivo.
Mao X, Zaki TA, Sherwin SJ, et al., 2017, Transition induced by linear and nonlinear perturbation growth in flow past a compressor blade, Journal of Fluid Mechanics, Vol: 820, Pages: 604-632, ISSN: 0022-1120
Flow past a NACA 65 blade at chord-based Reynolds number 138 500 is studied using stability analysis, generalized (spatially weighted) transient growth analysis and direct numerical simulations (DNS). The mechanisms of transition on various sections of the blade observed in previous work by Zaki et al. (J. Fluid Mech., vol. 665, 2010, pp. 57-98) are examined, with a focus on the pressure side around the leading edge. In this region, the linearly most energetic perturbation has spanwise wavenumber 40π (five boundary-layer thicknesses) and is tilted against the mean shear to take advantage of the Orr mechanism. In a DNS, the nonlinear development of this optimal perturbation induces Λ structures, which are further stretched to hairpin vortices before breaking down to turbulence. At higher spanwise wavenumber, e.g. 120π, a free-stream optimal perturbation is obtained upstream of the leading edge, in the form of streamwise vortices. During its nonlinear evolution, this optimal perturbation tilts the mean shear and generates spanwise periodic high- and low-speed streaks. Then through a nonlinear lift-up mechanism, the low-speed streaks are lifted above the high-speed ones. This layout of streaks generates a mean shear with two inflectional points and activates secondary instabilities, namely inner and outer instabilities previously reported in the literature.
Xu H, Mughal SM, Gowree E, et al., 2017, Destabilisation and modification of Tollmien-Schlichting disturbances by athree dimensional surface indentation, Journal of Fluid Mechanics, Vol: 819, Pages: 592-620, ISSN: 1469-7645
We consider the influence of a smooth three-dimensional (3-D) indentation on the instability of an incompressible boundary layer by linear and nonlinear analyses. The numerical work was complemented by an experimental study to investigate indentations of approximately 11δ99 and 22δ99 width at depths of 45 %, 52 % and 60 % of δ99 , where δ99 indicates 99% boundary layer thickness. For these indentations a separation bubble confined within the indentation arises. Upstream of the indentation, spanwise-uniform Tollmien–Schlichting (TS) waves are assumed to exist, with the objective to investigate how the 3-D surface indentation modifies the 2-D TS disturbance. Numerical corroboration against experimental data reveals good quantitative agreement. Comparing the structure of the 3-D separation bubble to that created by a purely 2-D indentation, there are a number of topological changes particularly in the case of the widest indentation; more rapid amplification and modification of the upstream TS waves along the symmetry plane of the indentation is observed. For the shortest indentations, beyond a certain depth there are then no distinct topological changes of the separation bubbles and hence on flow instability. The destabilising mechanism is found to be due to the confined separation bubble and is attributed to the inflectional instability of the separated shear layer. Finally for the widest width indentation investigated ( 22δ99 ), results of the linear analysis are compared with direct numerical simulations. A comparison with the traditional criteria of using N -factors to assess instability of properly 3-D disturbances reveals that a general indication of flow destabilisation and development of strongly nonlinear behaviour is indicated as N=6 values are attained. However N -factors, based on linear models, can only be used to provide indications and severity of the destabilisation, since the process of disturbance breakdown to turbu
Burovskiy P, Grigoras P, Sherwin S, et al., 2017, Efficient Assembly for High-Order Unstructured FEM Meshes (FPL 2015), ACM TRANSACTIONS ON RECONFIGURABLE TECHNOLOGY AND SYSTEMS, Vol: 10, ISSN: 1936-7406
Xu H, Lombard J, Sherwin S, 2017, Influence of localised smooth steps on the instability of a boundary layer, Journal of Fluid Mechanics, Vol: 817, Pages: 138-170, ISSN: 1469-7645
We consider a smooth, spanwise-uniform forward facing step de ned by the Gauss error function of height 4-30% and four times the width of the local boundary layer thickness δ_99. The boundary layer flow over a smooth forward-facing stepped plate is studied with particular emphasis on stabilisation and destabilisation of the two-dimensional Tollmien-Schlichting (TS) waves and subsequently on three-dimensional disturbances at transition. The interaction between TS waves at a range of frequencies and a base flow over a single or two forward facing smooth steps is conducted by linear analysis. The results indicate thatfor a TS wave with a frequency F 2 [140; 160] (F=! =U21 106 where ! and U1 denote the perturbation angle frequency and freestream velocity magnitude, respectively), the amplitude of the TS wave is attenuated in the unstable regime of the neutral stability curve corresponding to a at plate boundary layer. Furthermore, it is observed thattwo smooth forward facing steps lead to a more acute reduction of the amplitude of the TS wave. When the height of a step is increased to more than 20% of the local boundary layer thickness for a xed width parameter, the TS wave is amplified and thereby a destabilisation e ect is introduced. Therefore, stabilisation or destabilisation effect of a smooth step is typically dependent on its shape parameters. To validate the results of the linear stability analysis, where a TS wave is damped by the forward facingsmooth steps direct numerical simulation (DNS) is performed. The results of the DNS correlate favorably with the linear analysis and show that for the investigated frequency of the TS wave, the K-type transition process is altered whereas the onset of the H-type transition is delayed. The results of the DNS suggest that for the perturbation with the non-dimensional frequency parameter F = 150 and in the absence of other externalperturbations, two forward facing smooth steps of height 5% and 12% of the boundary lay
Cantwell C, Sherwin S, 2017, Nektar++
Nektar++ is a tensor product based finite element package designed to allow one to construct efficient classical low polynomial order h-type solvers (where h is the size of the finite element) as well as higher p-order piecewise polynomial order solvers.
Chooi KY, Comerford A, Sherwin SJ, et al., 2017, Noradrenaline has opposing effects on the hydraulic conductance of arterial intima and media., Journal of Biomechanics, Vol: 54, Pages: 4-10, ISSN: 1873-2380
The uptake of circulating macromolecules by the arterial intima is thought to be a key step in atherogenesis. Such transport is dominantly advective, so elucidating the mechanisms of water transport is important. The relation between vasoactive agents and water transport in the arterial wall is incompletely understood. Here we applied our recently-developed combination of computational and experimental methods to investigate the effects of noradrenaline (NA) on hydraulic conductance of the wall (Lp), medial extracellular matrix volume fraction (ϕ(ECM)) and medial permeability (K1(1)) in the rat abdominal aorta. Experimentally, we found that physiological NA concentrations were sufficient to induce SMC contraction and produced significant decreases in Lp and increases in ϕ(ECM). Simulation results based on 3D confocal images of the extracellular volume showed a corresponding increase in K1(1), attributed to the opening of the ECM. Conversion of permeabilities to layer-specific resistances revealed that although the total wall resistance increased, medial resistance decreased, suggesting an increase in intimal resistance upon application of NA.
Serson D, Meneghini JR, Sherwin SJ, 2017, Direct numerical simulations of the flow around wings with spanwise waviness at a very low Reynolds number, Computers & Fluids, Vol: 146, Pages: 117-124, ISSN: 0045-7930
Inspired by the pectoral flippers of the humpback whale, the use of spanwise waviness in the leading edge has been considered in the literature as a possible way of improving the aerodynamic performance of wings. In this paper, we present an investigation based on direct numerical simulations of the flow around infinite wavy wings with a NACA0012 profile, at a Reynolds number Re=1000Re=1000. The simulations were carried out using the Spectral/hp Element Method, with a coordinate system transformation employed to treat the waviness of the wing. Several combinations of wavelength and amplitude were considered, showing that for this value of Re the waviness leads to a reduction in the lift-to-drag ratio (L/D), associated with a suppression of the fluctuating lift coefficient. These changes are associated with a regime where the flow remains attached behind the peaks of the leading edge while there are distinct regions of flow separation behind the troughs, and a physical mechanism explaining this behaviour is proposed.
Moura RC, Mengaldo G, Peiró J, et al., 2017, An LES Setting for DG-Based Implicit LES with Insights on Dissipation and Robustness, Pages: 161-173, ISSN: 1439-7358
© 2017, Springer International Publishing AG. We suggest a new interpretation of implicit large eddy simulation (iLES) approaches based on discontinuous Galerkin (DG) methods by analogy with the LES-PLB framework (Pope, Fluid mechanics and the environment: dynamical approaches. Springer, Berlin, 2001), where PLB stands for ‘projection onto local basis functions’. Within this framework, the DG discretization of the unfiltered compressible Navier-Stokes equations can be recognized as a Galerkin solution of a PLB-based (and hence filtered) version of the equations with extra terms originating from DG’s implicit subgrid-scale modelling. It is shown that for under-resolved simulations of isotropic turbulence at very high Reynolds numbers, energy dissipation is primarily determined by the property-jump term of the Riemann flux employed. Additionally, in order to assess how this dissipation is distributed in Fourier space, we compare energy spectra obtained from inviscid simulations of the Taylor-Green vortex with different Riemann solvers and polynomial orders. An explanation is proposed for the spectral ‘energy bump’ observed when the Lax-Friedrichs flux is employed.
Moxey D, Cantwell CD, Mengaldo G, et al., 2017, Towards p-adaptive spectral/hp element methods for modelling industrial flows, ICOSAHOM-2016 - International Conference on Spectral and High-order Methods, Publisher: Springer International Publishing AG, Pages: 63-79, ISSN: 1439-7358
There is an increasing requirement from both academia and industry for high-fidelity flow simulations that are able to accurately capture complicated and transient flow dynamics in complex geometries. Coupled with the growing availability of high-performance, highly parallel computing resources, there is therefore a demand for scalable numerical methods and corresponding software frameworks which can deliver the next-generation of complex and detailed fluid simulations to scientists and engineers in an efficient way. In this article we discuss recent and upcoming advances in the use of the spectral/hp element method for addressing these modelling challenges. To use these methods efficiently for such applications, is critical that computational resolution is placed in the regions of the flow where it is needed most, which is often not known a priori. We propose the use of spatially and temporally varying polynomial order, coupled with appropriate error estimators, as key requirements in permitting these methods to achieve computationally efficient high-fidelity solutions to complex flow problems in the fluid dynamics community.
Serson D, Meneghini JR, Sherwin SJ, 2017, Extension of the Velocity-Correction Scheme to General Coordinate Systems, Pages: 331-342, ISSN: 1439-7358
© 2017, Springer International Publishing AG. The velocity-correction scheme is a time-integration method for the incompressible Navier-Stokes equations, and is a common choice in the context of spectral/hp methods. Although the spectral/hp discretization allows the representation of complex geometries, in some cases the use of a coordinate transformation is desirable, since it may lead to symmetries which allow a more efficient solution of the equations. One example of this occurs when the transformed geometry has a homogeneous direction, in which case a Fourier expansion can be applied in this direction, reducing the computational cost. In this paper, we revisit two recently proposed forms of extending the velocity-correction scheme to general coordinate systems, the first treating the mapping terms explicitly and the second treating them semi-implicitly. We then present some numerical examples illustrating the properties and applicability of these methods, including new tests focusing on the time-accuracy of these schemes.
Moura RC, Peiro J, Sherwin SJ, 2017, On the accuracy and robustness of implicit LES/under-resolved DNS approaches based on spectral element methods
We present a study on the suitability of under-resolved DNS (uDNS)-also called implicit LES (iLES)-approaches based on spectral element methods (SEM), with emphasis on high-order continuous and discontinuous Galerkin (i.e. CG and DG) schemes. Broadly speaking, these are model-free eddy-resolving approaches to turbulence which solve the governing equations in unfiltered form and rely on numerical stabilization techniques for small-scale regularization. Model problems in 1D, 2D and 3D are used in the assessment of solution quality and numerical stability. A rationale for the excellent potential of these methods for transitional and turbulent flows is offered on the basis of linear dispersion-diffusion analysis.
Mohamied Y, Sherwin SJ, Weinberg PD, 2016, Understanding the fluid mechanics behind transverse wall shear stress, Journal of Biomechanics, Vol: 50, Pages: 102-109, ISSN: 1873-2380
The patchy distribution of atherosclerosis within arteries is widely attributed to local variation in haemodynamic wall shear stress (WSS). A recently-introduced metric, the transverse wall shear stress (transWSS), which is the average over the cardiac cycle of WSS components perpendicular to the temporal mean WSS vector, correlates particularly well with the pattern of lesions around aortic branch ostia. Here we use numerical methods to investigate the nature of the arterial flows captured by transWSS and the sensitivity of transWSS to inflow waveform and aortic geometry. TransWSS developed chiefly in the acceleration, peak systolic and deceleration phases of the cardiac cycle; the reverse flow phase was too short, and WSS in diastole was too low, for these periods to have a significant influence. Most of the spatial variation in transWSS arose from variation in the angle by which instantaneous WSS vectors deviated from the mean WSS vector rather than from variation in the magnitude of the vectors. The pattern of transWSS was insensitive to inflow waveform; only unphysiologically high Womersley numbers produced substantial changes. However, transWSS was sensitive to changes in geometry. The curvature of the arch and proximal descending aorta were responsible for the principal features, the non-planar nature of the aorta produced asymmetries in the location and position of streaks of high transWSS, and taper determined the persistence of the streaks down the aorta. These results reflect the importance of the fluctuating strength of Dean vortices in generating transWSS.
Serbanovic-Canic J, de Luca A, Warboys C, et al., 2016, Zebrafish model for functional screening of flow-responsive genes, Arteriosclerosis Thrombosis and Vascular Biology, Vol: 36, ISSN: 1524-4636
OBJECTIVE: Atherosclerosis is initiated at branches and bends of arteries exposed to disturbed blood flow that generates low shear stress. This mechanical environment promotes lesions by inducing endothelial cell (EC) apoptosis and dysfunction via mechanisms that are incompletely understood. Although transcriptome-based studies have identified multiple shear-responsive genes, most of them have an unknown function. To address this, we investigated whether zebrafish embryos can be used for functional screening of mechanosensitive genes that regulate EC apoptosis in mammalian arteries. APPROACH AND RESULTS: First, we demonstrated that flow regulates EC apoptosis in developing zebrafish vasculature. Specifically, suppression of blood flow in zebrafish embryos (by targeting cardiac troponin) enhanced that rate of EC apoptosis (≈10%) compared with controls exposed to flow (≈1%). A panel of candidate regulators of apoptosis were identified by transcriptome profiling of ECs from high and low shear stress regions of the porcine aorta. Genes that displayed the greatest differential expression and possessed 1 to 2 zebrafish orthologues were screened for the regulation of apoptosis in zebrafish vasculature exposed to flow or no-flow conditions using a knockdown approach. A phenotypic change was observed in 4 genes; p53-related protein (PERP) and programmed cell death 2-like protein functioned as positive regulators of apoptosis, whereas angiopoietin-like 4 and cadherin 13 were negative regulators. The regulation of perp, cdh13, angptl4, and pdcd2l by shear stress and the effects of perp and cdh13 on EC apoptosis were confirmed by studies of cultured EC exposed to flow. CONCLUSIONS: We conclude that a zebrafish model of flow manipulation coupled to gene knockdown can be used for functional screening of mechanosensitive genes in vascular ECs, thus providing potential therapeutic targets to prevent or treat endothelial injury at atheroprone sites.
Moura RC, Mengaldo G, Peiro J, et al., 2016, On the eddy-resolving capability of high-order discontinuous Galerkin approaches to implicit LES / under-resolved DNS of Euler turbulence, Journal of Computational Physics, Vol: 330, Pages: 615-623, ISSN: 0021-9991
We present estimates of spectral resolution power for under-resolved turbulent Euler flows obtained with high-orderdiscontinuous Galerkin (DG) methods. The ‘1% rule’ based on linear dispersion–diusion analysis introduced byMoura et al. [J. Comput. Phys.298 (2015) 695–710] is here adapted for 3D energy spectra and validated throughthe inviscid Taylor–Green vortex problem. The 1% rule estimates the wavenumber beyond which numerical diusioninduces an artificial dissipation range on turbulent spectra. As the original rule relies on standard upwinding, dierentRiemann solvers are tested. Very good agreement is found for solvers which treat the dierent physical waves in aconsistent manner. Relatively good agreement is still found for simpler solvers. The latter however displayed spuriousfeatures attributed to the inconsistent treatment of dierent physical waves. It is argued that, in the limit of vanishingviscosity, such features might have a significant impact on robustness and solution quality. The estimates proposed areregarded as useful guidelines for no-model DG-based simulations of free turbulence at very high Reynolds numbers.
Grigoras P, Burovskiy P, Luk W, et al., 2016, Optimising Sparse Matrix Vector multiplication for large scale FEM problems on FPGA, 2016 26th International Conference on Field Programmable Logic and Applications (FPL), ISSN: 1946-1488
Sparse Matrix Vector multiplication (SpMV) is an important kernel in many scientific applications. In this work we propose an architecture and an automated customisation method to detect and optimise the architecture for block diagonal sparse matrices. We evaluate the proposed approach in the context of the spectral/hp Finite Element Method, using the local matrix assembly approach. This problem leads to a large sparse system of linear equations with block diagonal matrix which is typically solved using an iterative method such as the Preconditioned Conjugate Gradient. The efficiency of the proposed architecture combined with the effectiveness of the proposed customisation method reduces BRAM resource utilisation by as much as 10 times, while achieving identical throughput with existing state of the art designs and requiring minimal development effort from the end user. In the context of the Finite Element Method, our approach enables the solution of larger problems than previously possible, enabling the applicability of FPGAs to more interesting HPC problems.
Xu H, Mughal MS, Gowree ER, et al., 2016, Effect of a 3d indentation on boundary layer instability, ICAS 2016, 30th Congress of the International Council of the Aeronautical Sciences, Publisher: ICAS
Xu H, Mughal MS, Gowree ER, et al., 2016, Effect of a 3d surface indentation on boundary layer stability, 24th International Congress of Theoretical and Applied Mechanics ICTAM 2016, Publisher: ICAS
We are concerned about effect of a 3D surfaceindentation on instability and laminar-turbulenttransition in a boundary layer. For naturaltransition in a boundary layer, the transitiononset is dominated by growth of the Tollmien-Schlichting (TS) wave and its subsequentsecondary instability. In the paper, both linearanalysis and nonlinear calculations are carriedout to address the 3D surface indentation effecton amplifying TS waves’ amplitudes andprompting transition onset. By the linearanalysis, we address sudden amplification of theTS modes by a separation bubble in a surfaceindentation region. The nonlinear calculationsare implemented to validate the traditionaltransition criteria predicted by the linear theorywhen a 3D indentation is present. Finally,applicability of the traditional transitioncriteria is assessed.
Moxey D, Cantwell C, Kirby RM, et al., 2016, Optimizing the performance of the spectral/hp element method with collective linear algebra operations, Computer Methods in Applied Mechanics and Engineering, Vol: 310, Pages: 628-645, ISSN: 0045-7825
As computing hardware evolves, increasing core counts mean that memory bandwidth is becomingthe deciding factor in attaining peak performance of numerical methods. High-orderfinite element methods, such as those implemented in the spectral/hp framework Nektar++,are particularly well-suited to this environment. Unlike low-order methods that typicallyutilize sparse storage, matrices representing high-order operators have greater density andricher structure. In this paper, we show how these qualities can be exploited to increaseruntime performance on nodes that comprise a typical high-performance computing system,by amalgamating the action of key operators on multiple elements into a single, memorye!cientblock. We investigate di↵erent strategies for achieving optimal performance acrossa range of polynomial orders and element types. As these strategies all depend on externalfactors such as BLAS implementation and the geometry of interest, we present a techniquefor automatically selecting the most e!cient strategy at runtime.
Serson D, Meneghini JR, Sherwin SJ, 2016, Velocity-correction schemes for the incompressible Navier-Stokes equations in general coordinate systems, Journal of Computational Physics, Vol: 316, Pages: 243-254, ISSN: 1090-2716
This paper presents methods of including coordinate transformations into the solution of the incompressible Navier–Stokes equations using the velocity-correction scheme, which is commonly used in the numerical solution of unsteady incompressible flows. This is important when the transformation leads to symmetries that allow the use of more efficient numerical techniques, like employing a Fourier expansion to discretize a homogeneous direction. Two different approaches are presented: in the first approach all the influence of the mapping is treated explicitly, while in the second the mapping terms related to convection are treated explicitly, with the pressure and viscous terms treated implicitly. Through numerical results, we demonstrate how these methods maintain the accuracy of the underlying high-order method, and further apply the discretisation strategy to problems where mixed Fourier-spectral/hp element discretisations can be applied, thereby extending the usefulness of this discretisation technique.
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