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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...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Royal Society
2023
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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. |
format | Online Article Text |
id | pubmed-10230328 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | The Royal Society |
record_format | MEDLINE/PubMed |
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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