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Maddison J.R.,University of Edinburgh | Maddison J.R.,University of Oxford | Farrell P.E.,University of Oxford | Farrell P.E.,Center for Biomedical Computing
Computer Methods in Applied Mechanics and Engineering | Year: 2014

Recent advances in high level finite element systems have allowed for the symbolic representation of discretisations and their efficient automated implementation as model source code. This allows for the extremely compact implementation of complex non-linear models in a handful of lines of high level code. In this work we extend the high level finite element FEniCS system to introduce an abstract representation of the temporal discretisation: this enables the similarly rapid development of transient finite element models. Efficiency is achieved via aggressive optimisations that exploit the temporal structure, such as automated pre-assembly and caching of forms, and the robust re-use of matrix factorisations and preconditioner data. The resulting models are as fast or faster than hand-optimised finite element codes. The high level representation of the system remains extremely compact and easily manipulated. This structure is exploited to derive the associated discrete adjoint model automatically, with the adjoint model inheriting the performance advantages of the forward model. Combined, this provides a system for the rapid development of efficient transient models, together with their discrete adjoints. © 2014 Elsevier B.V. Source

Valen-Sendstad K.,University of Toronto | Valen-Sendstad K.,Center for Biomedical Computing | Steinman D.A.,University of Toronto
American Journal of Neuroradiology | Year: 2014

BACKGROUND AND PURPOSE: Computational fluid dynamics has become a popular tool for studying intracranial aneurysm hemodynamics, demonstrating success for retrospectively discriminating rupture status; however, recent highly refined simulations suggest potential deficiencies in solution strategies normally used in the aneurysm computational fluid dynamics literature. The purpose of the present study was to determine the impact of this gap. MATERIALS AND METHODS: Pulsatile flow in 12 realistic MCA aneurysms was simulated by using both high-resolution and normal-resolution strategies. Velocity fields were compared at selected instants via domain-averaged error. We also compared wall shear stress fields and various reduced hemodynamic indices: cycle-averaged mean and maximum wall shear stress, oscillatory shear index, low shear area, viscous dissipation ratio, and kinetic energy ratio. RESULTS: Instantaneous differences in flow and wall shear stress patterns were appreciable, especially for bifurcation aneurysms. Linear regressions revealed strong correlations (R 2 > 0.9) between high-resolution and normal-resolution solutions for all indices except kinetic energy ratio (R2 = 0.25) and oscillatory shear index (R2 = 0.23); however, for most indices, the slopes were significantly <1, reflecting a pronounced underestimation by the normal-resolution simulations. Some high-resolution simulations were highly unstable, with fluctuating wall shear stresses reflected by the poor oscillatory shear index correlation. CONCLUSIONS: Typical computational fluid dynamics solution strategies may ultimately be adequate for augmenting rupture risk assessment on the basis of certain highly reduced indices; however, they cannot be relied on for predicting the magnitude and character of the complex biomechanical stimuli to which the aneurysm wall may be exposed. This impact of the computational fluid dynamics solution strategy is likely greater than that for other modeling assumptions or uncertainties. Source

Logg A.,Center for Biomedical Computing | Wells G.N.,University of Cambridge
ACM Transactions on Mathematical Software | Year: 2010

We describe here a library aimed at automating the solution of partial differential equations using the finite element method. By employing novel techniques for automated code generation, the library combines a high level of expressiveness with efficient computation. Finite element variational forms may be expressed in near mathematical notation, from which low-level code is automatically generated, compiled, and seamlessly integrated with efficient implementations of computational meshes and high-performance linear algebra. Easy-to-use object-oriented interfaces to the library are provided in the form of a C++ library and a Python module. This article discusses the mathematical abstractions and methods used in the design of the library and its implementation. A number of examples are presented to demonstrate the use of the library in application code. © 2010 ACM. Source

Funke S.W.,Imperial College London | Funke S.W.,Center for Biomedical Computing | Farrell P.E.,University of Oxford | Piggott M.D.,Imperial College London
Renewable Energy | Year: 2014

Oceanic tides have the potential to yield a vast amount of renewable energy. Tidal stream generators are one of the key technologies for extracting and harnessing this potential. In order to extract an economically useful amount of power, hundreds of tidal turbines must typically be deployed in an array. This naturally leads to the question of how these turbines should be configured to extract the maximum possible power: the positioning and the individual tuning of the turbines could significantly influence the extracted power, and hence is of major economic interest. However, manual optimisation is difficult due to legal site constraints, nonlinear interactions of the turbine wakes, and the cubic dependence of the power on the flow speed. The novel contribution of this paper is the formulation of this problem as an optimisation problem constrained by a physical model, which is then solved using an efficient gradient-based optimisation algorithm. In each optimisation iteration, a two-dimensional finite element shallow water model predicts the flow and the performance of the current array configuration. The gradient of the power extracted with respect to the turbine positions and their tuning parameters is then computed in a fraction of the time taken for a flow solution by solving the associated adjoint equations. These equations propagate causality backwards through the computation, from the power extracted back to the turbine positions and the tuning parameters. This yields the gradient at a cost almost independent of the number of turbines, which is crucial for any practical application. The utility of the approach is demonstrated by optimising turbine arrays in four idealised scenarios and a more realistic case with up to 256 turbines in the Inner Sound of the Pentland Firth, Scotland. © 2013 The Authors. Source

Hake J.,Center for Biomedical Computing | Kekenes-Huskey P.M.,Howard Hughes Medical Institute | McCulloch A.D.,University of California at San Diego
Current Opinion in Structural Biology | Year: 2014

Numerous signaling processes in the cell are controlled in microdomains that are defined by cellular structures ranging from nm to μm in size. Recent improvements in microscopy enable the resolution and reconstruction of these micro domains, while new computational methods provide the means to elucidate their functional roles. Collectively these tools allow for a biophysical understanding of the cellular environment and its pathological progression in disease. Here we review recent advancements in microscopy, and subcellular modeling on the basis of reconstructed geometries, with a special focus on signaling microdomains that are important for the excitation contraction coupling in cardiac myocytes. © 2014 Elsevier Ltd. Source

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