Passively parallel regularized stokeslets

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Passively parallel regularized stokeslets. / Gallagher, Meurig Thomas; Smith, David.

In: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 378, No. 2179, 20190528, 04.09.2020.

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@article{91abc1713745410baebda2ca48c92541,
title = "Passively parallel regularized stokeslets",
abstract = "Stokes flow, discussed by G.G. Stokes in 1851, describes many microscopic biological flow phenomena, including cilia-driven transport and flagellar motility; the need to quantify and understand these flows has motivated decades of mathematical and computational research. Regularized stokeslet methods, which have been used and refined over the past 20 years, offer significant advantages in simplicity of implementation, with a recent modification based on nearest-neighbour interpolation providing significant improvements in efficiency and accuracy. Moreover this method can be implemented with the majority of the computation taking place through built-in linear algebra, entailing that state-of-the-art hardware and software developments in the latter, in particular multicore and GPU computing, can be exploited through minimal modifications ('passive parallelism') to existing Matlab computer code. Hence, and with widely available GPU hardware, significant improvements in the efficiency of the regularized stokeslet method can be obtained. The approach is demonstrated through computational experiments on three model biological flows: undulatory propulsion of multiple Caenorhabditis elegans, simulation of progression and transport by multiple sperm in a geometrically confined region, and left-right symmetry breaking particle transport in the ventral node of the mouse embryo. In general an order-of-magnitude improvement in efficiency is observed. This development further widens the complexity of biological flow systems that are accessible without the need for extensive code development or specialist facilities. This article is part of the theme issue 'Stokes at 200 (part 2)'.",
keywords = "GPU, cilia, flagella, regularized stokeslets",
author = "Gallagher, {Meurig Thomas} and David Smith",
year = "2020",
month = sep,
day = "4",
doi = "10.1098/rsta.2019.0528",
language = "English",
volume = "378",
journal = "Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences",
issn = "0962-8428",
publisher = "Royal Society of London",
number = "2179",

}

RIS

TY - JOUR

T1 - Passively parallel regularized stokeslets

AU - Gallagher, Meurig Thomas

AU - Smith, David

PY - 2020/9/4

Y1 - 2020/9/4

N2 - Stokes flow, discussed by G.G. Stokes in 1851, describes many microscopic biological flow phenomena, including cilia-driven transport and flagellar motility; the need to quantify and understand these flows has motivated decades of mathematical and computational research. Regularized stokeslet methods, which have been used and refined over the past 20 years, offer significant advantages in simplicity of implementation, with a recent modification based on nearest-neighbour interpolation providing significant improvements in efficiency and accuracy. Moreover this method can be implemented with the majority of the computation taking place through built-in linear algebra, entailing that state-of-the-art hardware and software developments in the latter, in particular multicore and GPU computing, can be exploited through minimal modifications ('passive parallelism') to existing Matlab computer code. Hence, and with widely available GPU hardware, significant improvements in the efficiency of the regularized stokeslet method can be obtained. The approach is demonstrated through computational experiments on three model biological flows: undulatory propulsion of multiple Caenorhabditis elegans, simulation of progression and transport by multiple sperm in a geometrically confined region, and left-right symmetry breaking particle transport in the ventral node of the mouse embryo. In general an order-of-magnitude improvement in efficiency is observed. This development further widens the complexity of biological flow systems that are accessible without the need for extensive code development or specialist facilities. This article is part of the theme issue 'Stokes at 200 (part 2)'.

AB - Stokes flow, discussed by G.G. Stokes in 1851, describes many microscopic biological flow phenomena, including cilia-driven transport and flagellar motility; the need to quantify and understand these flows has motivated decades of mathematical and computational research. Regularized stokeslet methods, which have been used and refined over the past 20 years, offer significant advantages in simplicity of implementation, with a recent modification based on nearest-neighbour interpolation providing significant improvements in efficiency and accuracy. Moreover this method can be implemented with the majority of the computation taking place through built-in linear algebra, entailing that state-of-the-art hardware and software developments in the latter, in particular multicore and GPU computing, can be exploited through minimal modifications ('passive parallelism') to existing Matlab computer code. Hence, and with widely available GPU hardware, significant improvements in the efficiency of the regularized stokeslet method can be obtained. The approach is demonstrated through computational experiments on three model biological flows: undulatory propulsion of multiple Caenorhabditis elegans, simulation of progression and transport by multiple sperm in a geometrically confined region, and left-right symmetry breaking particle transport in the ventral node of the mouse embryo. In general an order-of-magnitude improvement in efficiency is observed. This development further widens the complexity of biological flow systems that are accessible without the need for extensive code development or specialist facilities. This article is part of the theme issue 'Stokes at 200 (part 2)'.

KW - GPU

KW - cilia

KW - flagella

KW - regularized stokeslets

UR - http://www.scopus.com/inward/record.url?scp=85089301966&partnerID=8YFLogxK

U2 - 10.1098/rsta.2019.0528

DO - 10.1098/rsta.2019.0528

M3 - Article

C2 - 32762431

VL - 378

JO - Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences

JF - Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences

SN - 0962-8428

IS - 2179

M1 - 20190528

ER -