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The three-dimensional coarse-graining formulation of interacting elastohydrodynamic filaments and multi-body microhydrodynamics

Elastic filaments are vital to biological, physical and engineering systems, from cilia driving fluid in the lungs to artificial swimmers and micro-robotics. Simulating slender structures requires intricate balance of elastic, body, active and hydrodynamic moments, all in three dimensions. Here, we...

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Autores principales: Fuchter, Paul, Bloomfield-Gadêlha, Hermes
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Royal Society 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10230328/
https://www.ncbi.nlm.nih.gov/pubmed/37254703
http://dx.doi.org/10.1098/rsif.2023.0021
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author Fuchter, Paul
Bloomfield-Gadêlha, Hermes
author_facet Fuchter, Paul
Bloomfield-Gadêlha, Hermes
author_sort Fuchter, Paul
collection PubMed
description Elastic filaments are vital to biological, physical and engineering systems, from cilia driving fluid in the lungs to artificial swimmers and micro-robotics. Simulating slender structures requires intricate balance of elastic, body, active and hydrodynamic moments, all in three dimensions. Here, we present a generalized three-dimensional (3D) coarse-graining formulation that is efficient, simple-to-implement, readily extendable and usable for a wide array of applications. Our method allows for simulation of collections of 3D elastic filaments, capable of full flexural and torsional deformations, coupled non-locally via hydrodynamic interactions, and including multi-body microhydrodynamics of structures with arbitrary geometry. The method exploits the exponential mapping of quaternions for tracking 3D rotations of each interacting element in the system, allowing for computation times up to 150 times faster than a direct quaternion implementation. Spheres are used as a ‘building block’ of both filaments and solid microstructures for straightforward and intuitive construction of arbitrary three-dimensional geometries present in the environment. We highlight the strengths of the method in a series of non-trivial applications including bi-flagellated swimming, sperm–egg scattering and particle transport by cilia arrays. Applications to lab-on-a-chip devices, multi-filaments, mono-to-multi flagellated microorganisms, Brownian polymers, and micro-robotics are straightforward. A Matlab code is provided for further customization and generalizations.
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spelling pubmed-102303282023-06-01 The three-dimensional coarse-graining formulation of interacting elastohydrodynamic filaments and multi-body microhydrodynamics Fuchter, Paul Bloomfield-Gadêlha, Hermes J R Soc Interface Life Sciences–Mathematics interface Elastic filaments are vital to biological, physical and engineering systems, from cilia driving fluid in the lungs to artificial swimmers and micro-robotics. Simulating slender structures requires intricate balance of elastic, body, active and hydrodynamic moments, all in three dimensions. Here, we present a generalized three-dimensional (3D) coarse-graining formulation that is efficient, simple-to-implement, readily extendable and usable for a wide array of applications. Our method allows for simulation of collections of 3D elastic filaments, capable of full flexural and torsional deformations, coupled non-locally via hydrodynamic interactions, and including multi-body microhydrodynamics of structures with arbitrary geometry. The method exploits the exponential mapping of quaternions for tracking 3D rotations of each interacting element in the system, allowing for computation times up to 150 times faster than a direct quaternion implementation. Spheres are used as a ‘building block’ of both filaments and solid microstructures for straightforward and intuitive construction of arbitrary three-dimensional geometries present in the environment. We highlight the strengths of the method in a series of non-trivial applications including bi-flagellated swimming, sperm–egg scattering and particle transport by cilia arrays. Applications to lab-on-a-chip devices, multi-filaments, mono-to-multi flagellated microorganisms, Brownian polymers, and micro-robotics are straightforward. A Matlab code is provided for further customization and generalizations. The Royal Society 2023-05-31 /pmc/articles/PMC10230328/ /pubmed/37254703 http://dx.doi.org/10.1098/rsif.2023.0021 Text en © 2023 The Authors. https://creativecommons.org/licenses/by/4.0/Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, provided the original author and source are credited.
spellingShingle Life Sciences–Mathematics interface
Fuchter, Paul
Bloomfield-Gadêlha, Hermes
The three-dimensional coarse-graining formulation of interacting elastohydrodynamic filaments and multi-body microhydrodynamics
title The three-dimensional coarse-graining formulation of interacting elastohydrodynamic filaments and multi-body microhydrodynamics
title_full The three-dimensional coarse-graining formulation of interacting elastohydrodynamic filaments and multi-body microhydrodynamics
title_fullStr The three-dimensional coarse-graining formulation of interacting elastohydrodynamic filaments and multi-body microhydrodynamics
title_full_unstemmed The three-dimensional coarse-graining formulation of interacting elastohydrodynamic filaments and multi-body microhydrodynamics
title_short The three-dimensional coarse-graining formulation of interacting elastohydrodynamic filaments and multi-body microhydrodynamics
title_sort three-dimensional coarse-graining formulation of interacting elastohydrodynamic filaments and multi-body microhydrodynamics
topic Life Sciences–Mathematics interface
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10230328/
https://www.ncbi.nlm.nih.gov/pubmed/37254703
http://dx.doi.org/10.1098/rsif.2023.0021
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