Martin Sandve Alnæs

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.

Unified form language: A domain-specific language for weak formulations of partial differential equations

We present the Unified Form Language (UFL), which is a domain-specific language for representing weak formulations of partial differential equations with a view to numerical approximation. Features of UFL include support for variational forms and functionals, automatic differentiation of forms and expressions, arbitrary function space hierarchies for multifield problems, general differential operators and flexible tensor algebra. With these features, UFL has been used to effortlessly express finite element methods for complex systems of partial differential equations in near-mathematical notation, resulting in compact, intuitive and readable programs. We present in this work the language and its construction. An implementation of UFL is freely available as an open-source software library. The library generates abstract syntax tree representations of variational problems, which are used by other software libraries to generate concrete low-level implementations. Some application examples are presented and libraries that support UFL are highlighted.

Unified framework for finite element assembly

At the heart of any finite element simulation is the assembly of matrices and vectors from discrete variational forms. We propose a general interface between problem-specific and general-purpose components of finite element programs. This interface is called Unified Form-assembly Code (UFC). A wide range of finite element problems is covered, including mixed finite elements and discontinuous Galerkin methods. We discuss how the UFC interface enables implementations of variational form evaluation to be independent of mesh and linear algebra components. UFC does not depend on any external libraries, and is released into the public domain.

On the efficiency of symbolic computations combined with code generation for finite element methods

Efficient and easy implementation of variational forms for finite element discretization can be accomplished with metaprogramming. Using a high-level language like Python and symbolic mathematics makes an abstract problem definition possible, but the use of a low-level compiled language is vital for run-time efficiency. By generating low-level C++ code based on symbolic expressions for the discrete weak form, it is possible to accomplish a high degree of abstraction in the problem definition while surpassing the run-time efficiency of traditional hand written C++ codes. We provide several examples where we demonstrate orders of magnitude in speedup.

UFL: a finite element form language

The Unified Form Language – UFL [Alnaes and Logg, 2009] – is a domain specific language for the declaration of finite element discretizations of variational forms and functionals. More precisely, the language defines a flexible user interface for defining finite element spaces and expressions for weak forms in a notation close to mathematical notation.

Poro-elastic modeling of Syringomyelia – a systematic study of the effects of pia mater, central canal, median fissure, white and gray matter on pressure wave propagation and fluid movement within the cervical spinal cord

Syringomyelia, fluid-filled cavities within the spinal cord, occurs frequently in association with a Chiari I malformation and produces some of its most severe neurological symptoms. The exact mechanism causing syringomyelia remains unknown. Since syringomyelia occurs frequently in association with obstructed cerebrospinal fluid (CSF) flow, it has been hypothesized that syrinx formation is mechanically driven. In this study we model the spinal cord tissue either as a poro-elastic medium or as a solid linear elastic medium, and simulate the propagation of pressure waves through an anatomically plausible 3D geometry, with boundary conditions based on in vivo CSF pressure measurements. Then various anatomic and tissue properties are modified, resulting in a total of 11 variations of the model that are compared. The results show that an open segment of the central canal and a stiff pia (relative to the cord) both increase the radial pressure gradients and enhance interstitial fluid flow in the central canal. The anterior median fissure, anisotropic permeability of the white matter, and Poisson ratio play minor roles.

UFC: a Finite Element Code Generation Interface

A central component of FEniCS is the UFC interface (Unified Form-assembly Code). UFC is an 8703 interface between problem-specific and general-purpose components of finite element programs. In 8704 particular, the UFC interface defines the structure and signature of the code that is generated by 8705 the form compilers FFC and SFC for DOLFIN. The UFC interface applies to a wide range of finite 8706 element problems (including mixed finite elements and discontinuous Galerkin methods) and may be 8707 used with libraries that differ widely in their design.

Adjoint multi-start-based estimation of cardiac hyperelastic material parameters using shear data

Cardiac muscle tissue during relaxation is commonly modeled as a hyperelastic material with strongly nonlinear and anisotropic stress response. Adapting the behavior of such a model to experimental or patient data gives rise to a parameter estimation problem which involves a significant number of parameters. Gradient-based optimization algorithms provide a way to solve such nonlinear parameter estimation problems with relatively few iterations, but require the gradient of the objective functional with respect to the model parameters. This gradient has traditionally been obtained using finite differences, the calculation of which scales linearly with the number of model parameters, and introduces a differencing error. By using an automatically derived adjoint equation, we are able to calculate this gradient more efficiently, and with minimal implementation effort. We test this adjoint framework on a least squares fitting problem involving data from simple shear tests on cardiac tissue samples. A second challenge which arises in gradient-based optimization is the dependency of the algorithm on a suitable initial guess. We show how a multi-start procedure can alleviate this dependency. Finally, we provide estimates for the material parameters of the Holzapfel and Ogden strain energy law using finite element models together with experimental shear data.

Instant: just-in-time compilation of C/C++ in Python

Instant is a small Python module for just-in-time (JIT) compilation (or inlining) of C/C++ code.Instant accepts plain C/C++ code and is therefore conveniently combined with the code generating tools in DOLFIN, FFC and SFC.

SyFi and SFC: symbolic finite elements and form compilation

This chapter concerns the finite element library SyFi and its form compiler SFC. SyFi is a framework 8315 for defining finite elements symbolically, using the C++ library GiNaC [Bauer et al., 2002] and its 8316 Python interface Swiginac [Skavhaug and Certik, 2009].