A Hybrid Immersed Boundary/Coarse-Graining Method for Modeling Inextensible Semi-Flexible Filaments in Thermally Fluctuating Fluids

Papadopoulos, Magdalini Ntetsika and Panayiotis

doi:10.32604/cmes.2021.017404

Cited by 2 publications

(1 citation statement)

References 39 publications

(55 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Moreau et al [12] highlighted the high efficiency of the formalism in two dimensions (2D), and showed excellent agreement with classical formulations, even for relatively large CG segments. Following this, the CG method has gained momentum, and was adopted and generalized in several ways: (i) non-local hydrodynamics have been accounted for passive and active filaments in 2D, including wall interactions [27][28][29], (ii) 3D filament deformations were accounted for in [30,31], though limited to a local hydrodynamic resistive force theory (RFT), as in [12], (iii) it has been applied to study sperm flagellum propulsion in 2D [32], (iv) expanded into a hybrid immersed boundary method [33], as well as a stochastic method [34], and (v) used for analytical and numerical study of the well-posedness of Newtonian and viscoelastic elastohydrodynamic propulsion [35,36].…”

Section: Introductionmentioning

confidence: 99%

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

Fuchter

Bloomfield-Gadêlha

2023

J. R. Soc. Interface.

View full text Add to dashboard Cite

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.

show abstract

Section: Introductionmentioning

confidence: 99%

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

Fuchter

Bloomfield-Gadêlha

2023

J. R. Soc. Interface.

View full text Add to dashboard Cite

show abstract

The 3D coarse-graining formulation of interacting elastohydrodynamic filaments and multi-body microhydrodynamics

Fuchter

Bloomfield-Gadêlha

2023

Preprint

View full text Add to dashboard Cite

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 generalised 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 three-dimensional 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 micro-structures 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.

show abstract

A Hybrid Immersed Boundary/Coarse-Graining Method for Modeling Inextensible Semi-Flexible Filaments in Thermally Fluctuating Fluids

Cited by 2 publications

References 39 publications

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

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

The 3D coarse-graining formulation of interacting elastohydrodynamic filaments and multi-body microhydrodynamics

Contact Info

Product

Resources

About