A Hybrid Continuous-Discrete Model of Tumour-Induced Angiogenesis is Solved Numerically in Parallel and Performance Improvements Analysed
European Journal of Biophysics
Volume 3, Issue 5, October 2015, Pages: 27-37
Received: Aug. 30, 2015; Accepted: Sep. 22, 2015; Published: Oct. 13, 2015
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Author
Paul M. Darbyshire, Department of Computational Biophysics, Algenet Cancer Research, Nottingham, UK
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Abstract
The main aim of this paper is to investigate the potential performance improvements gained from a serial versus parallel implementation of the numerical solution to a system of coupled nonlinear PDEs describing tumour-induced angiogenesis. After applying a suitable finite difference scheme, the resulting hybrid continuous discreet model is solved based on a set of cellular rules defining endothelial cell movement towards a tumour. In addition, the model explicitly incorporates the processes of branching, anastomosis and cell proliferation. Parallel implementations are based on the CUDA programming model with a detailed look at efficient thread deployment and memory management. Results show substantial speedups for the CUDA C language against that of conventional high performance languages, such as C++. Such increased performance highlights the potential for simulating more complex mathematical models of tumour dynamics, such as vascularisation networks, tumour invasion and metastasis, leading to the potential for more rapid experimental results for a range of complex cancer models.
Keywords
Cancer Modelling, Tumour Angiogenic Factors (TAF), Tumour-Induced Angiogenesis, Anastomoses, Parallel Programming, Compute Unified Device Architecture (CUDA), Graphical Processing Unit (GPU), High Performance Computing (HPC)
To cite this article
Paul M. Darbyshire, A Hybrid Continuous-Discrete Model of Tumour-Induced Angiogenesis is Solved Numerically in Parallel and Performance Improvements Analysed, European Journal of Biophysics. Vol. 3, No. 5, 2015, pp. 27-37. doi: 10.11648/j.ejb.20150305.11
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