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The aim of this work was to analyze the influence of sex hormones and anatomical details (trabeculations and false tendons) on the electrophysiology of healthy human hearts. Additionally, sex- and anatomy-dependent effects of ventricular tachycardia (VT) inducibility are presented. To this end, four anatomically normal, human, biventricular geometries (two male, two female), with identifiable trabeculations, were obtained from high-resolution, ex-vivo MRI and represented by detailed and smoothed geometrical models (with and without the trabeculations). Additionally one model was augmented by a scar. The electrophysiology finite element model (FEM) simulations were carried out, using O'Hara-Rudy human myocyte model with sex phenotypes of Yang and Clancy. A systematic comparison between detailed vs smooth anatomies, male vs female normal hearts was carried out. The heart with a myocardial infarction was subjected to a programmed stimulus protocol to identify the effects of sex and anatomical detail on ventricular tachycardia inducibility. All female hearts presented QT-interval prolongation however the prolongation interval in comparison to the male phenotypes was anatomy-dependent and was not correlated to the size of the heart. Detailed geometries showed QRS fractionation and increased T-wave magnitude in comparison to the corresponding smoothed geometries. A variety of sustained VTs were obtained in the detailed and smoothed male geometries at different pacing locations, which provide evidence of the geometry-dependent differences regarding the prediction of the locations of reentry channels. In the female phenotype, sustained VTs were induced in both detailed and smooth geometries with RV apex pacing, however no consistent reentry channels were identified. Anatomical and physiological cardiac features play an important role defining risk in cardiac disease. These are often excluded from cardiac electrophysiology simulations. The assumption that the cardiac endocardium is smooth may produce inaccurate predictions towards the location of reentry channels in in-silico tachycardia inducibility studies. [ABSTRACT FROM AUTHOR]

We present an elaborate preconditioning scheme for Krylov subspace methods which has been developed to improve the performance and reduce the execution time of parallel node-based finite-element (FE) solvers for 3-D electromagnetic (EM) numerical modelling in exploration geophysics. This new preconditioner is based on algebraic multigrid (AMG) that uses different basic relaxation methods, such as Jacobi, symmetric successive over-relaxation (SSOR) and Gauss–Seidel, as smoothers and the wave front algorithm to create groups, which are used for a coarse-level generation. We have implemented and tested this new preconditioner within our parallel nodal FE solver for 3-D forward problems in EM induction geophysics. We have performed series of experiments for several models with different conductivity structures and characteristics to test the performance of our AMG preconditioning technique when combined with biconjugate gradient stabilized method. The results have shown that, the more challenging the problem is in terms of conductivity contrasts, ratio between the sizes of grid elements and/or frequency, the more benefit is obtained by using this preconditioner. Compared to other preconditioning schemes, such as diagonal, SSOR and truncated approximate inverse, the AMG preconditioner greatly improves the convergence of the iterative solver for all tested models. Also, when it comes to cases in which other preconditioners succeed to converge to a desired precision, AMG is able to considerably reduce the total execution time of the forward-problem code—up to an order of magnitude. Furthermore, the tests have confirmed that our AMG scheme ensures grid-independent rate of convergence, as well as improvement in convergence regardless of how big local mesh refinements are. In addition, AMG is designed to be a black-box preconditioner, which makes it easy to use and combine with different iterative methods. Finally, it has proved to be very practical and efficient in the parallel context. [ABSTRACT FROM PUBLISHER]

We present a nodal finite-element method that can be used to compute in parallel highly accurate solutions for 3-D controlled-source electromagnetic forward-modelling problems in anisotropic media. Secondary coupled-potential formulation of Maxwell's equations allows to avoid the singularities introduced by the sources, while completely unstructured tetrahedral meshes and mesh refinement support an accurate representation of geological and bathymetric complexity and improve the solution accuracy. Different complex iterative solvers and an efficient pre-conditioner based on the sparse approximate inverse are used for solving the resulting large sparse linear system of equations. Results are compared with the ones of other researchers to check the accuracy of the method. We demonstrate the performance of the code in large problems with tens and even hundreds of millions of degrees of freedom. Scalability tests on massively parallel computers show that our code is highly scalable. [ABSTRACT FROM AUTHOR]

SUMMARY In this paper, a highly parallel coupled electromechanical model of the heart is presented and assessed. The parallel-coupled model is thoroughly discussed, with scalability proven up to hundreds of cores. This work focuses on the mechanical part, including the constitutive model (proposing some modifications to pre-existent models), the numerical scheme and the coupling strategy. The model is next assessed through two examples. First, the simulation of a small piece of cardiac tissue is used to introduce the main features of the coupled model and calibrate its parameters against experimental evidence. Then, a more realistic problem is solved using those parameters, with a mesh of the Oxford ventricular rabbit model. The results of both examples demonstrate the capability of the model to run efficiently in hundreds of processors and to reproduce some basic characteristic of cardiac deformation. Copyright © 2012 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

The variational multiscale (VMS) method sets a general framework for stabilization methods. By splitting the exact solution into coarse (grid) and fine (subgrid) scales, one can obtain a system of two equations for these unknowns. The grid scale equation is solved using the Galerkin method and contains an additional term involving the subgrid scale. At this stage, several options are usually considered to deal with the subgrid scale equation: this includes the choice of the space where the subgrid scale would be defined as well as the simplifications leading to compute the subgrid scale analytically or numerically. The present study proposes to develop a two-scale variational method for the advection–diffusion–reaction equation. On the one hand, a family of weak forms are obtained by integrating by parts a fraction of the advection term. On the other hand, the solution of the subgrid scale equation is found using the following. First, a two-scale variational method is applied to the one-dimensional problem. Then, a series of approximations are assumed to solve the subgrid space equation analytically. This allows to devise expressions for the ‘stabilization parameter’ τ, in the context of VMS (two-scale) method. The proposed method is equivalent to the traditional Green's method used in the literature to solve residual-free bubbles, although it offers another point of view, as the strong form of the subgrid scale equation is solved explicitly. In addition, the authors apply the methodology to high-order elements, namely quadratic and cubic elements. The proposed model consists in assuming that the subgrid scale vanishes also on interior nodes of the element and applying the strategy used for linear element in the segment between these interior nodes. The proposed scheme is compared with existing ones through the solution of a one-dimensional numerical example for linear, quadratic and cubic elements. In addition, the mesh convergence is checked for high-order elements through the solution of an exact solution in two dimensions. Copyright © 2008 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

We present a new overlapping Dirichlet/Robin Domain Decomposition method. The method uses Dirichlet and Robin transmission conditions on the interfaces of an overlapping partitioning of the computational domain. We derive interface equations to study the convergence of the method and show its properties through four numerical examples. The mathematical framework is general and can be applied to derive overlapping versions of all the classical nonoverlapping methods. [Copyright &y& Elsevier]

We present a Chimera method for the numerical solution of incompressible flows past objects in relative motion. The Chimera method is implemented as an iteration-by-subdomain method based on Dirichlet/Neumann(Robin) coupling. The DD method we propose is not only geometric but also algorithmic, for the solution on each subdomain is obtained on separate processes and the exchange of information between the subdomains is carried out by a master code. This strategy is very flexible as it requires almost no modification to the original numerical code. Therefore, only the master code has to be adapted to the numerical codes and the strategies used on each subdomain. As a basic flow solver, we a use stabilized finite element method. [Copyright &y& Elsevier]

This paper introduces a preconditioned variational multiscale stabilization (P-VMS) method for compressible flows. In this introductory paper we focus on inviscid flow and steady state problems. The Euler equations are solved on fully unstructured grids and discretized using the finite element method. The P-VMS method can be decomposed into three parts. First, a local preconditioner is applied to the continuous equations to reduce the stiffness while covering a wide range of Mach numbers. Then, the resulting preconditioned system is discretized in space using finite elements and stabilized with a variational multiscale stabilization method adapted for the preconditioned equations. In this paper, the solution is advanced in time using a fully explicit time discretization, although P-VMS is general and can be applied to fully implicit solvers. The proposed method is assessed by comparing convergence and accuracy of the solutions between the non-preconditioned and preconditioned cases, in particular for van Leer–Lee–Roe ’s (1991) and Choi-Merkle ’s (1993) preconditioners, in some selected examples covering a large range of Mach numbers. [ABSTRACT FROM AUTHOR]

• The Integral Length Scale Approximation Subfilter Scale Model is applied to separated flows. • A procedure to determine the model constant is proposed. • A low-dissipation finite-element method is used. • The model accounts for interactions between numerical error and turbulence modelling errors. • Flows over a sphere and an Ahmed body are computed, and good agreement with the data is obtained. A new model for the unresolved stresses in large-eddy simulations was recently proposed by Piomelli et al. [J Fluid Mech 2015; 766:499–527] and Rouhi et al., [Phys Rev Fluids 2016; 1(4):0444011], in which the length scale is not related to the grid size, but determined based on turbulence properties. This model, the Integral Length-Scale Approximation (ILSA), has a single parameter, s τ , which represents the contribution of the unresolved scales to the momentum transport, and is assigned by the user. We test ILSA in complex geometries using a low-dissipation finite-element method, and propose a rational method to determine s τ on the basis of a grid-convergence study. The interaction of the model with the numerical method and grid topology is studied first; then, two cases are considered: the subcritical flow around a sphere, and the flow over the Ahmed body, a simplified car model. In each case calculations are performed using three grids and varying s τ. With a consistent combination of grid size and s τ the statistical results are in very good agreement with DNS data and experimental measurements. The eddy viscosity is insensitive to sudden variation of the mesh size, and the model adjusts to the different dissipation and diffusion characteristics associated with different grid topologies and numerical techniques. [ABSTRACT FROM AUTHOR]

Because of their widely generalized use in many industries, composites are the subject of many research campaigns. More particularly, the development of both accurate and flexible numerical models able to capture their intrinsically multiscale modes of failure is still a challenge. The standard finite element method typically requires intensive remeshing to adequately capture the geometry of the cracks and high accuracy is thus often sacrificed in favor of scalability, and vice versa. In an effort to preserve both properties, we present here an extended finite element method (XFEM) for large scale composite fracture simulations. In this formulation, the standard FEM formulation is partially enriched by use of shifted Heaviside functions with special attention paid to the scalability of the scheme. This enrichment technique offers several benefits since the interpolation property of the standard shape function still holds at the nodes. Those benefits include (i) no extra boundary condition for the enrichment degree of freedom, and (ii) no need for transition/blending regions; both of which contribute to maintaining the scalability of the code. Two different cohesive zone models (CZM) are then adopted to capture the physics of the crack propagation mechanisms. At the intralaminar level, an extrinsic CZM embedded in the XFEM formulation is used. At the interlaminar level, an intrinsic CZM is adopted for predicting the failure. The overall framework is implemented in ALYA, a mechanics code specifically developed for large scale, massively parallel simulations of coupled multi-physics problems. The implementation of both intrinsic and extrinsic CZM models within the code is such that it conserves the extremely efficient scalability of ALYA while providing accurate physical simulations of computationally expensive phenomena. The strong scalability provided by the proposed implementation is demonstrated. The model is ultimately validated against a full experimental campaign of loading tests and X-ray tomography analyzes. [ABSTRACT FROM AUTHOR]

Abstract: A variational multiscale stabilized finite element scheme is presented for the solution of moist atmospheric flows. The fully compressible Euler equations are coupled to a system of three advection equations that model the transport of water quantities in the atmosphere. A Kessler-type parametrization of microphysical processes of warm rain is used. Because analytic solutions to this problem are not available, the model is assessed by comparison with similar simulations presented in the literature. The metrics for evaluation are the intensity and spatial distribution of the storm, its duration, the location of precipitation, and water accumulation at different grid resolutions. The current model is able to capture the principal features of two-dimensional convective storms and orographic clouds at the grid scales typical of mesoscale atmospheric simulations. [Copyright &y& Elsevier]

Abstract: We present a compressible version of the variational multiscale stabilization (VMS) method applied to the finite element (FE) solution of the Euler equations for nonhydrostatic stratified flows. This paper is meant to verify how the algorithm performs when solving problems in the framework of nonhydrostatic atmospheric dynamics. This effort is justified by the previously observed good performance of VMS and by the advantages that a compact Galerkin formulation offers on massively parallel architectures – a paradigm for both computational fluid dynamics (CFD) and numerical weather prediction (NWP) practitioners. We also propose a simple technique to construct a well-balanced approximation of the dominant hydrostatics that, if not properly discretized, may cause unacceptable vertical oscillations. This is a relevant problem in NWP, especially in the proximity of steep topography. To evaluate the performance of the method for stratified environments, six standard 2D and two 3D test cases are selected. Of these, two admit a semi-analytic solution, while the remaining six are non-steady and non-linear thermal problems with dominant buoyancy effects that challenge the algorithm in terms of stability. [Copyright &y& Elsevier]