Kent-Andre Mardal

Automated Solution of Differential Equations by the Finite Element Method: The FEniCS Book

This book is a tutorial written by researchers and developers behind the FEniCS Project and explores an advanced, expressive approach to the development of mathematical software. The presentation spans mathematical background, software design and the use of FEniCS in applications. Theoretical aspects are complemented with computer code which is available as free/open source software. The book begins with a special introductory tutorial for beginners. Followingare chapters in Part I addressing fundamental aspects of the approach to automating the creation of finite element solvers. Chapters in Part II address the design and implementation of the FEnicS software. Chapters in Part III present the application of FEniCS to a wide range of applications, including fluid flow, solid mechanics, electromagnetics and geophysics.

Computation of Hemodynamics in the Circle of Willis

Background and Purpose— Wall shear stress (WSS) and pressure are important factors in the development of cerebral aneurysms. We aimed to develop a computational fluid dynamics simulator for flow in the complete circle of Willis to study the impact of variations in vessel radii and bifurcation angles on WSS and pressure on vessel walls. Methods— Blood flow was modeled with Navier-Stokes equations as an incompressible newtonian fluid within rigid vessel walls. A model of the circle of Willis geometry was approximated as a network of tubes around cubic curves. Pulsatile inlet flow rates and constant outlet pressure were used as boundary conditions. Results— The simulations confirmed that differences in vessel radii and asymmetric branch angles influence WSS magnitude and spatial distribution. High WSS occurred at locations where aneurysms are frequent and in anatomic variants known to be associated with an increased risk for aneurysm development. Conclusions— Computational fluid dynamics analysis can be applied to the complete circle of Willis and should be used to study the pathophysiology of this complex vascular structure, including risk factors for aneurysm development. Further development of the method should include simulations with flexible vessel walls.

Preconditioning discretizations of systems of partial differential equations

This survey paper is based on three talks given by the second author at the London Mathematical Society Durham Symposium on Computational Linear Algebra for Partial Differential Equations in the summer of 2008. The main focus will be on an abstract approach to the construction of preconditioners for symmetric linear systems in a Hilbert space setting. Typical examples that are covered by this theory are systems of partial differential equations which correspond to saddle point problems. We will argue that the mapping properties of the coefficient operators suggest that block diagonal preconditioners are natural choices for these systems. To illustrate our approach a number of examples will be considered. In particular, parameter-dependent systems arising in areas like incompressible flow, linear elasticity, and optimal control theory will be studied. The paper contains analysis of several models which have previously been discussed in the literature. However, here each example is discussed with reference to a more unified abstract approach. Copyright

Numerical methods for incompressible viscous flow.

Abstract We present an overview of the most common numerical solution strategies for the incompressible Navier–Stokes equations, including fully implicit formulations, artificial compressibility methods, penalty formulations, and operator splitting methods (pressure/velocity correction, projection methods). A unified framework that explains popular operator splitting methods as special cases of a fully implicit approach is also presented and can be used for constructing new and improved solution strategies. The exposition is mostly neutral to the spatial discretization technique, but we cover the need for staggered grids or mixed finite elements and outline some alternative stabilization techniques that allow using standard grids. Emphasis is put on showing the close relationship between (seemingly) different and competing solution approaches for incompressible viscous flow.

Multigrid block preconditioning for a coupled system of partial differential equations modeling the electrical activity in the heart.

The electrical activity of the heart may be modeled with a system of partial differential equations (PDEs) known as the bidomain model. Computer simulations based on these equations may become a helpful tool to understand the relationship between changes in the electrical field and various heart diseases. Because of the rapid variations in the electrical field, sufficiently accurate simulations require a fine-scale discretization of the equations. For realistic geometries this leads to a large number of grid points and consequently large linear systems to be solved for each time step. In this paper, we present a fully coupled discretization of the bidomain model, leading to a block structured linear system. We take advantage of the block structure to construct an efficient preconditioner for the linear system, by combining multigrid with an operator splitting technique.

Direct numerical simulation of transitional flow in a patient-specific intracranial aneurysm

In experiments turbulence has previously been shown to occur in intracranial aneurysms. The effects of turbulence induced oscillatory wall stresses could be of great importance in understanding aneurysm rupture. To investigate the effects of turbulence on blood flow in an intracranial aneurysm, we performed a high resolution computational fluid dynamics (CFD) simulation in a patient specific middle cerebral artery (MCA) aneurysm using a realistic, pulsatile inflow velocity. The flow showed transition to turbulence just after peak systole, before relaminarization occurred during diastole. The turbulent structures greatly affected both the frequency of change of wall shear stress (WSS) direction and WSS magnitude, which reached a maximum value of 41.5Pa. The recorded frequencies were predominantly in the range of 1-500Hz. The current study confirms, through properly resolved CFD simulations that turbulence can occur in intracranial aneurysms.

Unified finite element discretizations of coupled Darcy–Stokes flow

In this paper we discuss some new finite element methods for flows which are governed by the linear stationary Stokes system on one part of the domain and by a second order elliptic equation derived form Darcy’s law in the rest of the domain, and where the solutions in the two domain are coupled by proper interface conditions. All the methods proposed here utilizes the same finite element spaces on the entire domain. In particular, we show how the coupled problem can be solved by using standard Stokes elements like the MINI element or the Taylor–Hood element in the entire domain. Furthermore, for all the methods the handling of the interface conditions are straightforward.The purpose of this paper is to provide analytical and numerical solutions of the formation and evolution of the localized plastic zone in a uniaxially loaded bar with variable cross-sectional area. An energy-based variational approach is employed and the governing equations with appropriate physical boundary conditions, jump conditions, and regularity conditions at evolving elasto-plastic interface are derived for a fourth-order explicit gradient plasticity model with linear isotropic softening. Four examples that differ by regularity of the yield stress and stress distributions are presented. Results for the load level, size of the plastic zone, distribution of plastic strain and its spatial derivatives, plastic elongation, and energy balance are constructed and compared to another, previously discussed non-variational gradient formulation.

Uniform preconditioners for the time dependent Stokes problem

Implicit time stepping procedures for the time dependent Stokes problem lead to stationary singular perturbation problems at each time step. These singular perturbation problems are systems of saddle point type, which formally approach a mixed formulation of the Poisson equation as the time step tends to zero. Preconditioners for discrete analogous of these systems are discussed. The preconditioners uses standard positive definite elliptic preconditioners as building blocks and lead to condition numbers which are bounded uniformly with respect to the time step and the spatial discretization. The construction of the discrete preconditioners is related to the mapping properties of the corresponding continuous system.

A study of wall shear stress in 12 aneurysms with respect to different viscosity models and flow conditions.

Recent computational fluid dynamics (CFD) studies relate abnormal blood flow to rupture of cerebral aneurysms. However, it is still debated how to model blood flow with sufficient accuracy. Common assumptions made include Newtonian behaviour of blood, traction free outlet boundary conditions and inlet boundary conditions based on available literature. These assumptions are often required since the available patient specific data is usually restricted to the geometry of the aneurysm and the surrounding vasculature. However, the consequences of these assumptions have so far been inadequately addressed. This study investigates the effects of 4 different viscosity models, 2 different inflow conditions and 2 different outflow conditions in 12 middle cerebral artery aneurysms. The differences are quantified in terms of 3 different wall shear stress (WSS) metrics, involving maximal WSS, average WSS, and proportion of aneurysm sac area with low WSS. The results were compared with common geometrical metrics such as volume, aspect ratio, size ratio and parent vessel diameter and classifications in terms of sex and aneurysm type. The results demonstrate strong correlations between the different viscosity models and boundary conditions. The correlation between the different WSS metrics range from weak to medium. No strong correlations were found between the different WSS metrics and the geometrical metrics or classifications.

High-resolution CFD detects high-frequency velocity fluctuations in bifurcation, but not sidewall, aneurysms

High-frequency flow fluctuations in intracranial aneurysms have previously been reported in vitro and in vivo. On the other hand, the vast majority of image-based computational fluid dynamics (CFD) studies of cerebral aneurysms report periodic, laminar flow. We have previously demonstrated that transitional flow, consistent with in vivo reports, can occur in a middle cerebral artery (MCA) bifurcation aneurysm when ultra-high-resolution direct numerical simulation methods are applied. The object of the present study was to investigate if such high-frequency flow fluctuations might be more widespread in adequately-resolved CFD models. A sample of N=12 anatomically realistic MCA aneurysms (five unruptured, seven ruptured), was digitally segmented from CT angiograms. Four were classified as sidewall aneurysms, the other eight as bifurcation aneurysms. Transient CFD simulations were carried out assuming a steady inflow velocity of 0.5m/s, corresponding to typical peak systolic conditions at the MCA. To allow for detection of clinically-reported high-frequency flow fluctuations and resulting flow structures, temporal and spatial resolutions of the CFD simulations were in the order of 0.1 ms and 0.1 mm, respectively. A transient flow response to the stationary inflow conditions was found in five of the 12 aneurysms, with energetic fluctuations up to 100 Hz, and in one case up to 900 Hz. Incidentally, all five were ruptured bifurcation aneurysms, whereas all four sidewall aneurysms, including one ruptured case, quickly reached a stable, steady state solution. Energetic, rapid fluctuations may be overlooked in CFD models of bifurcation aneurysms unless adequate temporal and spatial resolutions are used. Such fluctuations may be relevant to the mechanobiology of aneurysm rupture, and to a recently reported dichotomy between predictors of rupture likelihood for bifurcation vs. sidewall aneurysms.