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Multiscale Parallel Simulation of Malignant Pleural Mesothelioma via Adaptive Domain Partitioning – An Efficiency Analysis Study

Authors: Anton Dolganov; Valeria Krzhizhanovskaya; Stefano Trebeschi; Vivek M. Sheraton;

Multiscale Parallel Simulation of Malignant Pleural Mesothelioma via Adaptive Domain Partitioning – An Efficiency Analysis Study

Abstract

A novel parallel efficiency analysis on a framework for simulating the growth of Malignant Pleural Mesothelioma (MPM) tumours is presented. Proliferation of MPM tumours in the pleural space is simulated using a Cellular Potts Model (CPM) coupled with partial differential equations (PDEs). Using segmented lung data from CT scans, an environment is set up with artificial tumour data in the pleural space, representing the simulation domain, onto which a dynamic bounding box is applied to restrict computations to the region of interest, dramatically reducing memory and CPU overhead. This adaptive partitioning of the domain enables efficient use of computational resources by reducing the three-dimensional (3D) domain over which the PDEs are to be solved. The PDEs, representing oxygen, nutrients, and cytokines, are solved using the finite-volume method with a first-order implicit Euler scheme. Parallelization is realized using the public Python library mpi4py in combination with LinearGMRESSolver and PETSc for efficient convergence. Performance analyses have shown that parallelization achieves a reduced solving time compared to serial computation. Also, optimizations enable efficient use of available memory and improved load balancing amongst the cores.

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Keywords

Computational Engineering, Finance, and Science (cs.CE), FOS: Computer and information sciences, Multiscale Modelling, Computer Science - Distributed, Parallel, and Cluster Computing, FOS: Biological sciences, Malignant Pleural Mesothelioma, Parallel Simulation, Distributed, Parallel, and Cluster Computing (cs.DC), Computer Science - Computational Engineering, Finance, and Science, Quantitative Biology - Quantitative Methods, Quantitative Methods (q-bio.QM), Computational Oncology

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
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