Publications
401 results found
Mohri Z, Rowland EM, Clarke LA, et al., 2014, Elevated Uptake of Plasma Macromolecules by Regions of Arterial Wall Predisposed to Plaque Instability in a Mouse Model, PLoS One, Vol: 9, ISSN: 1932-6203
Atherosclerosis may be triggered by an elevated net transport of lipid-carryingmacromolecules from plasma into the arterial wall. We hypothesised that whetherlesions are of the thin-cap fibroatheroma (TCFA) type or are less fatty and morefibrous depends on the degree of elevation of transport, with greater uptake leadingto the former. We further hypothesised that the degree of elevation can depend onhaemodynamic wall shear stress characteristics and nitric oxide synthesis. Placinga tapered cuff around the carotid artery of apolipoprotein E -/- mice modifiespatterns of shear stress and eNOS expression, and triggers lesion development atthe upstream and downstream cuff margins; upstream but not downstream lesionsresemble the TCFA. We measured wall uptake of a macromolecular tracer in thecarotid artery of C57bl/6 mice after cuff placement. Uptake was elevated in theregions that develop lesions in hyperlipidaemic mice and was significantly moreelevated where plaques of the TCFA type develop. Computational simulations andeffects of reversing the cuff orientation indicated a role for solid as well as fluidmechanical stresses. Inhibiting NO synthesis abolished the difference in uptakebetween the upstream and downstream sites. The data support the hypothesis thatexcessively elevated wall uptake of plasma macromolecules initiates thedevelopment of the TCFA, suggest that such uptake can result from solid and fluidmechanical stresses, and are consistent with a role for NO synthesis. Modificationof wall transport properties might form the basis of novel methods for reducingplaque rupture.
Xu H, Hall P, sherwin S, 2014, Effect of curvature modulation on Gortler vortices in boundary layers, 67th Annual Meeting of the APS Division of Fluid Dynamics
Burovskiy PA, Girdlestone S, Davies C, et al., 2014, Dataflow acceleration of Krylov subspace sparse banded problems, 24th International Conference on Field Programmable Logic and Applications (FPL), 2014, Publisher: IEEE
Most of the efforts in the FPGA community related to sparse linear algebra focus on increasing the degree of internal parallelism in matrix-vector multiply kernels. We propose a parametrisable dataflow architecture presenting an alternative and complementary approach to support acceleration of banded sparse linear algebra problems which benefit from building a Krylov subspace. We use banded structure of a matrix A to overlap the computations Ax, A2x,..., Akx by building a pipeline of matrix-vector multiplication processing elements (PEs) each performing Aix. Due to on-chip data locality, FLOPS rate sustainable by such pipeline scales linearly with k. Our approach enables trade-off between the number k of overlapped matrix power actions and the level of parallelism in a PE. We illustrate our approach for Google PageRank computation by power iteration for large banded single precision sparse matrices. Our design scales up to 32 sequential PEs with floating point accumulation and 80 PEs with fixed point accumulation on Stratix V D8 FPGA. With 80 single-pipe fixed point PEs clocked at 160Mhz, our design sustains 12.7 GFLOPS.
Ferrer E, Moxey D, Willden RHJ, et al., 2014, Stability of Projection Methods for Incompressible Flows Using High Order Pressure-Velocity Pairs of Same Degree: Continuous and Discontinuous Galerkin Formulations, COMMUNICATIONS IN COMPUTATIONAL PHYSICS, Vol: 16, Pages: 817-840, ISSN: 1815-2406
De Grazia D, Mengaldo G, Moxey D, et al., 2014, Connections between the discontinuous Galerkin method and high-order flux reconstruction schemes, INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, Vol: 75, Pages: 860-877, ISSN: 0271-2091
Roney CH, Cantwell C, Qureshi NA, et al., 2014, An Automated Algorithm for Determining Conduction Velocity, Wavefront Direction and Focal Source Location using a Multipolar Catheter, IEEE Engineering in Medicine and Biology Conference
Determining locations of focal arrhythmia sources and quantifying myocardial conduction velocity (CV) are two major challenges in clinical catheter ablation cases. CV, wavefront direction and focal source location can be estimated from multipolar catheter data, but currently available methods are time-consuming, limited to specific electrode configurations, and can be inaccurate. We developed automated algorithms to rapidly identify CV from multipolar catheter data with any arrangement of electrodes, whilst providing estimates of wavefront direction and focal source position, which can guide the catheter towards a focal arrhythmic source. We validated our methods using simulations on realistic human left atrial geometry. We subsequently applied them to clinically-acquired intracardiac electrogram data, where CV and wavefront direction were accurately determined in all cases, whilst focal source locations were correctly identified in 2/3 cases. Our novel automated algorithms can potentially be used to guide ablation of focal arrhythmias in real-time in cardiac catheter laboratories.
King J, Yakovlev S, Fu Z, et al., 2014, Exploiting Batch Processing on Streaming Architectures to Solve 2D Elliptic Finite Element Problems: A Hybridized Discontinuous Galerkin (HDG) Case Study, JOURNAL OF SCIENTIFIC COMPUTING, Vol: 60, Pages: 457-482, ISSN: 0885-7474
Bolis A, Cantwell CD, Kirby RM, et al., 2014, From h to p efficiently: optimal implementation strategies for explicit time-dependent problems using the spectral/hp element method, International Journal for Numerical Methods in Fluids, Vol: 75, Pages: 591-607, ISSN: 1097-0363
We investigate the relative performance of a second-order Adams–Bashforth scheme and second-order andfourth-order Runge–Kutta schemes when time stepping a 2D linear advection problem discretised using aspectral/hp element technique for a range of different mesh sizes and polynomial orders. Numerical experimentsexplore the effects of short (two wavelengths) and long (32 wavelengths) time integration for sets ofuniform and non-uniform meshes. The choice of time-integration scheme and discretisation together fixes aCFL limit that imposes a restriction on the maximum time step, which can be taken to ensure numerical stability.The number of steps, together with the order of the scheme, affects not only the runtime but also theaccuracy of the solution. Through numerical experiments, we systematically highlight the relative effects ofspatial resolution and choice of time integration on performance and provide general guidelines on how bestto achieve the minimal execution time in order to obtain a prescribed solution accuracy. The significant roleplayed by higher polynomial orders in reducing CPU time while preserving accuracy becomes more evident,especially for uniform meshes, compared with what has been typically considered when studying this typeof problem.
Xu H, Sherwin S, Hall P, 2014, Transmission coefficient of Tollmien-Schlichting waves undergoing small indentation/hump distortion, The 29th Congress of the International Council of the Aeronautical Sciences
Warboys CM, de Luca A, Amini N, et al., 2014, Disturbed flow promotes endothelial senescence via a p53-dependent Ppathway, Arteriosclerosis, Thrombosis and Vascular Biology, Vol: 34, Pages: 985-995, ISSN: 1079-5642
Objective—Although atherosclerosis is associated with systemic risk factors such as age, high cholesterol, and obesity, plaque formation occurs predominately at branches and bends that are exposed to disturbed patterns of blood flow. The molecular mechanisms that link disturbed flow–generated mechanical forces with arterial injury are uncertain. To illuminate them, we investigated the effects of flow on endothelial cell (EC) senescence.Approach and Results—LDLR−/− (low-density lipoprotein receptor−/−) mice were exposed to a high-fat diet for 2 to 12 weeks (or to a normal chow diet as a control) before the assessment of cellular senescence in aortic ECs. En face staining revealed that senescence-associated β-galactosidase activity and p53 expression were elevated in ECs at sites of disturbed flow in response to a high-fat diet. By contrast, ECs exposed to undisturbed flow did not express senescence-associated β-galactosidase or p53. Studies of aortae from healthy pigs (aged 6 months) also revealed enhanced senescence-associated β-galactosidase staining at sites of disturbed flow. These data suggest that senescent ECs accumulate at disturbed flow sites during atherogenesis. We used in vitro flow systems to examine whether a causal relationship exists between flow and EC senescence. Exposure of cultured ECs to flow (using either an orbital shaker or a syringe-pump flow bioreactor) revealed that disturbed flow promoted EC senescence compared with static conditions, whereas undisturbed flow reduced senescence. Gene silencing studies demonstrated that disturbed flow induced EC senescence via a p53-p21 signaling pathway. Disturbed flow–induced senescent ECs exhibited reduced migration compared with nonsenescent ECs in a scratch wound closure assay, and thus may be defective for arterial repair. However, pharmacological activation of sirtuin 1 (using resveratrol or SRT1720) protected ECs from disturbed flow&ndas
Jordi BE, Cotter CJ, Sherwin SJ, 2014, Encapsulated formulation of the selective frequency damping method, Physics of Fluids, Vol: 26, ISSN: 1089-7666
We present an alternative “encapsulated” formulation of the selective frequencydamping method for finding unstable equilibria of dynamical systems, which isparticularly useful when analysing the stability of fluid flows. The formulation makesuse of splitting methods, which means that it can be wrapped around an existingtime-stepping code as a “black box.” The method is first applied to a scalar problemin order to analyse its stability and highlight the roles of the control coefficient χand the filter width in the convergence (or not) towards the steady-state. Then thesteady-state of the incompressible flow past a two-dimensional cylinder at Re = 100,obtained with a code which implements the spectral/hp element method, is presented.
Bailey EL, Peiffer V, Mohamied Y, et al., 2014, SPATIAL CORRELATION BETWEEN PATTERNS OF WALL PERMEABILITY AND PATTERNS OF MULTIDIRECTIONAL DISTURBED BLOOD FLOW IN RABBIT AORTA, Autumn Meeting of the British-Atherosclerosis-Society (BAS), Publisher: ELSEVIER IRELAND LTD, Pages: E2-E2, ISSN: 0021-9150
Cantwell CD, Yakovlev S, Kirby RM, et al., 2014, High-order spectral/hp element discretisation for reaction-diffusion problems on surfaces: application to cardiac electrophysiology, Journal of Computational Physics, Vol: 257, Pages: 813-829, ISSN: 0021-9991
We present a numerical discretisation of an embedded two-dimensional manifold using high-order continuous Galerkin spectral/hp elements, which provide exponential convergence of the solution with increasing polynomial order, while retaining geometric flexibility in the representation of the domain. Our work is motivated by applications in cardiac electrophysiology where sharp gradients in the solution benefit from the high-order discretisation, while the compu- tational cost of anatomically-realistic models can be reduced through the surface representation. We describe and validate our discretisation and provide a demonstration of its application to modeling electrochemical propagation across a human left atrium.
Loh SA, Blackburn HM, Sherwin SJ, 2014, Transient growth in an airfoil separation bubble
In this work, transient growth in a laminar separation bubble in a low-to-moderate Reynolds number airfoil flow is investigated. Optimal two and three-dimensional initial perturbations are computed for the flow over a NACA 0012 airfoil at angle-of-attack α = 5° with chord based Re = 5 × 104. At this Reynolds number, the pressure surface boundary layer remains attached over the length of the airfoil while the suction surface boundary layer undergoes separation before becoming two-dimensionally unstable leading to periodic vortex shedding and reattachment. Transient growth analysis shows that this flow supports large energy growth for both two and three-dimensional perturbations. Optimal growth values and flow topologies show that two-dimensional mechanisms are the primary energy growth mechanisms. Upstream of vortex shedding, the primary growth mechanism appears to be the Orr mechanism while a separate mechanism appears to drive further energy growth downstream in the base flow shed vorticity.
, 2014, A guide to the implementation of boundary conditions in compact high-order methods for compressible aerodynamics
The nature of boundary conditions, and how they are implemented, can have a significant impact on the stability and accuracy of a Computational Fluid Dynamics (CFD) solver. The objective of this paper is to assess how different boundary conditions impact the performance of compact discontinuous high-order spectral element methods (such as the discontinuous Galerkin method and the Flux Reconstruction approach), when these schemes are used to solve the Euler and compressible Navier-Stokes equations on unstructured grids. Specifically, the paper will investigate inflow/outflow and wall boundary conditions. In all studies the boundary conditions were enforced by modifying the boundary flux. For Riemann invariant (characteristic), slip and no-slip conditions we have considered a direct and an indirect enforcement of the boundary conditions, the first obtained by calculating the flux using the known solution at the given boundary while the second achieved by using a ghost state and by solving a Riemann problem. All computations were performed using the open-source software Nektar++ (www.nektar.info).
Mengaldo G, De Grazia D, Peiro J, et al., 2014, A guide to the implementation of boundary conditions in compact high-order methods for compressible aerodynamics
The nature of boundary conditions, and how they are implemented, can have a significant impact on the stability and accuracy of a Computational Fluid Dynamics (CFD) solver. The objective of this paper is to assess how different boundary conditions impact the performance of compact discontinuous high-order spectral element methods (such as the discontinuous Galerkin method and the Flux Reconstruction approach), when these schemes are used to solve the Euler and compressible Navier-Stokes equations on unstructured grids. Specifically, the paper will investigate inflow/outflow and wall boundary conditions. In all studies the boundary conditions were enforced by modifying the boundary flux. For Riemann invariant (characteristic), slip and no-slip conditions we have considered a direct and an indirect enforcement of the boundary conditions, the first obtained by calculating the flux using the known solution at the given boundary while the second achieved by using a ghost state and by solving a Riemann problem. All computations were performed using the open-source software Nektar++ (www.nektar.info).
Comerford A, Chooi KY, Nowak M, et al., 2014, A combined numerical and experimental framework for determining permeability properties of the arterial media, Biomechanics and Modeling in Mechanobiology, accepted
Cantwell CD, Sherwin SJ, Moxey D, 2014, 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.
Ali RL, Cantwell CD, Roney CH, et al., 2014, A novel method for quantifying localised correlation of late-gadolinium intensity with conduction velocity, Computing in Cardiology (CinC) 2014, Pages: 193-196
Patient-specific computer models of the human atria have the potential to aid clinical intervention in the treatment of cardiac arrhythmias. However, quantifying and integrating the heterogeneous qualities of the myocardium through imaging is particularly challenging due to the unknown relationship between voxel intensity and tissue conductivities. We establish a method to determine the relationship between local conduction velocity and scar density, extracted through the analysis of late-gadolinium enhanced magnetic resonance imaging data.
Moxey D, Ekelschot D, Keskin U, et al., 2014, A thermo-elastic analogy for high-order curvilinear meshing with control of mesh validity and quality, 23rd International Meshing Roundtable (IMR), Publisher: ELSEVIER SCIENCE BV, Pages: 127-135, ISSN: 1877-7058
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- Citations: 16
Ekelschot D, Biotto C, Peiro J, et al., 2013, P-adaption for compressible flows, Pages: 215-220
We present a p-adaptive method which takes advantage of the ability of a discontinuity sensor used to quantify the difference between the actual solution and a projected reduced order solution in order to vary the polynomial resolution in an element.
Peiffer V, Sherwin SJ, Weinberg PD, 2013, Computation in the rabbit aorta of a new metric - the transverse wall shear stress - to quantify the multidirectional character of disturbed blood flow, JOURNAL OF BIOMECHANICS, Vol: 46, Pages: 2651-2658, ISSN: 0021-9290
Spatial variation of the haemodynamic stresses acting on the arterial wall is commonly assumed to explain the focal development of atherosclerosis. Disturbed flow in particular is thought to play a key role. However, widely-used metrics developed to quantify its extent are unable to distinguish between uniaxial and multidirectional flows. We analysed pulsatile flow fields obtained in idealised and anatomically-realistic arterial geometries using computational fluid dynamics techniques, and in particular investigated the multidirectionality of the flow fields, capturing this aspect of near-wall blood flow with a new metric – the transverse wall shear stress (transWSS) – calculated as the time-average of wall shear stress components perpendicular to the mean flow direction. In the idealised branching geometry, multidirectional flow was observed downstream of the branch ostium, a region of flow stagnation, and to the sides of the ostium. The distribution of the transWSS was different from the pattern of traditional haemodynamic metrics and more dependent on the velocity waveform imposed at the branch outlet. In rabbit aortas, transWSS patterns were again different from patterns of traditional metrics. The near-branch pattern varied between intercostal ostia, as is the case for lesion distribution; for some branches there were striking resemblances to the age-dependent patterns of disease seen in rabbit and human aortas. The new metric may lead to improved understanding of atherogenesis.
Peiffer V, Sherwin SJ, Weinberg PD, 2013, Does low and oscillatory wall shear stress correlate spatially with early atherosclerosis? A systematic review, CARDIOVASCULAR RESEARCH, Vol: 99, Pages: 242-250, ISSN: 0008-6363
Blackburn HM, Hall P, Sherwin SJ, 2013, Lower branch equilibria in Couette flow: the emergence of canonical states for arbitrary shear flows, JOURNAL OF FLUID MECHANICS, Vol: 726, ISSN: 0022-1120
De Luca A, Warboys C, Amini N, et al., 2013, TRANSCRIPTOME PROFILING IN PORCINE ARTERIES TO IDENTIFY NOVEL SHEAR-RESPONSIVE REGULATORS OF ENDOTHELIAL CELL FATE, Annual Conference of the British-Cardiovascular-Society (BCS), Publisher: BMJ PUBLISHING GROUP, ISSN: 1355-6037
Assi GRS, Bearman PW, Carmo BS, et al., 2013, The role of wake stiffness on the wake-induced vibration of the downstream cylinder of a tandem pair, JOURNAL OF FLUID MECHANICS, Vol: 718, Pages: 210-245, ISSN: 0022-1120
When a pair of tandem cylinders is immersed in a flow the downstream cylinder can be excited into wake-induced vibrations (WIV) due to the interaction with vortices coming from the upstream cylinder. Assi, Bearman & Meneghini (J. Fluid Mech., vol. 661, 2010, pp. 365–401) concluded that the WIV excitation mechanism has its origin in the unsteady vortex–structure interaction encountered by the cylinder as it oscillates across the wake. In the present paper we investigate how the cylinder responds to that excitation, characterising the amplitude and frequency of response and its dependency on other parameters of the system. We introduce the concept of wake stiffness, a fluid dynamic effect that can be associated, to a first approximation, with a linear spring with stiffness proportional to Re and to the steady lift force occurring for staggered cylinders. By a series of experiments with a cylinder mounted on a base without springs we verify that such wake stiffness is not only strong enough to sustain oscillatory motion, but can also dominate over the structural stiffness of the system. We conclude that while unsteady vortex–structure interactions provide the energy input to sustain the vibrations, it is the wake stiffness phenomenon that defines the character of the WIV response.
Fogell NA, Sherwin S, Cotter CJ, et al., 2013, Fluid-structure iInteraction simulation of theinflated shape of ram-air parachutes, 22nd AIAA Aerodynamic Decelerator Systems Technology Conference, Daytona Beach, Florida [Best Student Paper Award]
Mao X, Blackburn HM, Sherwin SJ, 2013, Calculation of global optimal initial and boundary perturbations for the linearised incompressible Navier-Stokes equations, JOURNAL OF COMPUTATIONAL PHYSICS, Vol: 235, Pages: 258-273, ISSN: 0021-9991
Peiffer V, Bharath AA, Sherwin SJ, et al., 2013, A Novel Method for Quantifying Spatial Correlations Between Patterns of Atherosclerosis and Hemodynamic Factors, JOURNAL OF BIOMECHANICAL ENGINEERING-TRANSACTIONS OF THE ASME, Vol: 135, ISSN: 0148-0731
Steinman DA, Hoi Y, Fahy P, et al., 2013, Variability of Computational Fluid Dynamics Solutions for Pressure and Flow in a Giant Aneurysm: The ASME 2012 Summer Bioengineering Conference CFD Challenge, JOURNAL OF BIOMECHANICAL ENGINEERING-TRANSACTIONS OF THE ASME, Vol: 135, ISSN: 0148-0731
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