Extreme scalability challenges in micro‐finite element simulations of human bone

Bekas, Costas; Curioni, A.; Arbenz, Peter; Flaig, Cyril; Lenthe, G. Harry van; Müller, Ralph; Wirth, Andreas

doi:10.1002/cpe.1591

Cited by 17 publications

(9 citation statements)

References 9 publications

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“…16, No. 9, 993-1001, http://dx.doi.org/10.1080/10255842.2011 accounts for bone micro-architecture, and typically requires large computing resources (Bekas et al 2010). Numerous studies have successfully reported accurate estimations of bone mechanical properties with microFE at various skeletal sites, such as the distal radius (MacNeil and Boyd 2008), vertebrae (Wolfram et al 2010), tibia (Rajapakse et al 2010) and proximal femur (Pistoia et al 2001).…”

Section: Please Scroll Down For Articlementioning

confidence: 98%

In vivomonitoring of bone–implant bond strength by microCT and finite element modelling

Stadelmann

Conway

Boyd

2013

Computer Methods in Biomechanics and Biomedical Engineering

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Immediately after implantation, a dynamic process of bone formation and resorption takes place around an orthopaedic implant, influencing its mechanical fixation. The delay until complete fixation depends on local bone architecture and metabolism. Despite its importance, the temporal pattern of implant fixation is still unknown. The optimal duration of post-operative care is therefore difficult to establish for an individual situation, and a method to evaluate non-invasively the evolution of the mechanical stability would be a significant asset in a clinical environment. The aim of this study was to evaluate the potential of micro-finite element modelling based on in vivo micro-computed tomography to monitor longitudinally the contact between bone and implant and the implant strength in vivo. The model was first validated for screw pull-out in synthetic bone surrogate. Correlation coefficients of R(2) = 0.94 and 0.85 (p < 0.01) were measured between experimental and numerical results for stiffness and failure loads, respectively. Then, the mechanical integration of screws in the proximal tibia of 12 rats was monitored at seven time points over a period of 1 month. We observed significant increases (p< 0.05) of bone-screw contact (+28%), stiffness (+93%) and failure load (+71%) over the course of the experiment, and more than 75% of these changes occurred during the first 2 weeks. Limitations, such as image artefacts and radiation, still compromise the immediate clinical application of this method, but it has a promising potential in preclinical animal studies, as it provides very valuable data about the dynamic aspect of implant integration with considerably reduced animal resources.

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Section: Please Scroll Down For Articlementioning

confidence: 98%

In vivomonitoring of bone–implant bond strength by microCT and finite element modelling

Stadelmann

Conway

Boyd

2013

Computer Methods in Biomechanics and Biomedical Engineering

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“…For mFE modeling of nonlinear mechanical behavior (yield, failure, etc.) generally requires parallelized computing on high-performance computing (HPC) clusters [111,112].…”

Section: Biomechanical Analysismentioning

confidence: 99%

High-Resolution Imaging Techniques for Bone Quality Assessment

2011

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“…Furthermore, it has become of increasing interest due to the substantial increment in the number of cores available in emerging architectures (Devine et al, 2006; Zhou et al, 2012). In particular, the use of ParMETIS-based partitioning algorithms for parallel finite-element method simulations has been widely reported in the literature (Piggott et al, 2008; Sahni et al, 2009; Bekas et al, 2010; Shadid et al, 2010; Niederer et al, 2011). In the current section, we also consider an often neglected aspect of the problem: the design of a scalable algorithm that, given a ParMETIS partition, reads the mesh from disk and creates the relevant data structures.…”

Section: Parallelisationmentioning

confidence: 99%

Chaste

Bernabéu

Southern

Wilson

et al. 2013

The International Journal of High Performance Computing Applica

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The simulation of cardiac electrophysiology is a mature field in computational physiology. Recent advances in medical imaging, high-performance computing and numerical methods mean that computational models of electrical propagation in human heart tissue are ripe for use in patient-specific simulation for diagnosis, for prognosis and for selection of treatment methods. However, in order to move in this direction, it is necessary to make efficient use of modern petascale computing resources. This paper focuses on an existing open source simulation framework (Chaste) and documents work done to improve the parallel scaling on a small range of electrophysiology benchmark problems.These benchmarks involve the numerical solution of the monodomain or bidomain equations via the finite-element method. At the beginning of this study the electrophysiology libraries within Chaste were already enabled to run in parallel and were able to solve for electrical propagation using the monodomain or bidomain equations, but parallel efficiency dropped rapidly when run on more than about 64 processors.Throughout the course of the study, improvements were made to problem definition input; geometric mesh partitioning; finite-element assembly of large, sparse linear systems; problem-specific matrix preconditioning; numerical solution of the linear system; and output of the approximate solution. The consequence of these improvements is that, at the end of the study, Chaste is able to solve a monodomain benchmark problem in close to real time. While some of the improvements made to the parallel Chaste code are specific to cardiac electrophysiology, many of the techniques documented in this paper are generic to the parallel finite-element method in other scientific application areas.

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Extreme scalability challenges in micro‐finite element simulations of human bone

Cited by 17 publications

References 9 publications

In vivomonitoring of bone–implant bond strength by microCT and finite element modelling

In vivomonitoring of bone–implant bond strength by microCT and finite element modelling

High-Resolution Imaging Techniques for Bone Quality Assessment

Chaste

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