<i>IB2d</i>: a Python and MATLAB implementation of the immersed boundary method

Battista, Nicholas A.; Strickland, Christopher; Miller, Laura A.

doi:10.1088/1748-3190/aa5e08

Cited by 52 publications

(130 citation statements)

References 108 publications

(197 reference statements)

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“…The IB method has been successfully applied to a variety of problems in biological fluid dynamics with an intermediate Re f regime, i.e. 0.01 < Re f < 1000, including heart development [21], [22], insect flight [23], swimming [24], [25], and dating and relationships [26]. A fully parallelized implementation of the IB method with adaptive mesh refinement, IBAMR [27], was used for the simulations described here.…”

Section: B Numerical Methodsmentioning

confidence: 99%

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Pulsing corals: A story of scale and mixing

Samson

Battista²,

Khatri³

et al. 2017

BIOMATH

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Abstract-Effective methods of fluid transport vary across scale. A commonly used dimensionless number for quantifying the effective scale of fluid transport is the frequency based Reynolds number, Re f , which gives the ratio of inertial to viscous forces in a fluid flow. What may work well for one Re f regime may not produce significant flows for another. These differences in scale have implications for many organisms, ranging from the mechanics of how organisms move through their fluid environment to how hearts pump at various stages in development. Some organisms, such as soft pulsing corals, actively contract their tentacles to generate mixing currents that enhance photosynthesis. Their unique morphology and the intermediate Re f regime at which they function, where both viscous and inertial forces are significant, make them a unique model organism for understanding fluid mixing. In this paper, 3D fluid-structure interaction simulations of a pulsing soft coral are used to quantify fluid transport and describe fluid mixing across a wide range of Re f . The results show that net transport is negligible for Re f < O(10

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Section: B Numerical Methodsmentioning

confidence: 99%

“…Note that Y(s, t) is a function of both the Lagrangian parameter, s, and time, t. Details on other forcing terms can be found in [26], [35]. The delta functions in these Eqs.…”

Section: A Governing Equations Of Ibmentioning

confidence: 99%

Pulsing corals: A story of scale and mixing

Samson

Battista²,

Khatri³

et al. 2017

BIOMATH

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“…It was first developed by Charles Peskin in 1972 to study blood flow around cardiac valves and in turn, the deformations of valve leaflets due to underlying blood flow [21]. Moreover, it also allows functionality to prescribe motion of immersed structures [1]. It has been successfully applied to study the FSI between an elastic structure immersed within an incompressible fluid for a variety of biological and engineering applications within the intermediate Reynolds number (Re) regime, e.g.…”

Section: Introductionmentioning

confidence: 99%

“…There are many ways to model the fiber elasticity properties of the immersed structure [22,1] giving rise to a wide range of formidable applications. Some immersed boundary examples that illustrate this variety include cardiovascular dynamics [23,24], aquatic locomotion [25,26], insect flight [27,11], parachute dynamics [28], muscle-fluid-structure interactions [29,22,30], plant biomechanics [31,32], soap filaments [33,34], and cellular and other microscale interactions [35,36,37,38].…”

Section: Introductionmentioning

confidence: 99%

“…Some immersed boundary examples that illustrate this variety include cardiovascular dynamics [23,24], aquatic locomotion [25,26], insect flight [27,11], parachute dynamics [28], muscle-fluid-structure interactions [29,22,30], plant biomechanics [31,32], soap filaments [33,34], and cellular and other microscale interactions [35,36,37,38]. Furthermore, the IB framework invites one to add other constitutive models such as electrophysiology, cellular signaling, or chemical reaction equations into the FSI framework [39,37,29,40,41,42,43,44,1,45].…”

Section: Introductionmentioning

confidence: 99%

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IB2d Reloaded: A more powerful Python and MATLAB implementation of the immersed boundary method

Battista

Strickland

Barrett

et al. 2017

Math Methods in App Sciences

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The immersed boundary method (IB) is an elegant way to fully couple the motion of a fluid and deformations of an immersed elastic structure. In that vein, the IB2d software allows for expedited explorations of fluid-structure interaction for beginners and veterans to the field of computational fluid dynamics (CFD). While most open source CFD codes are written in low level programming environments, IB2d was specifically written in highlevel programming environments to make its accessibility extend beyond scientists with vast programming experience. Although introduced previously in [1], many improvements and additions have been made to the software to allow for even more robust models of material properties for the elastic structures, including a data analysis package for both the fluid and immersed structure data, an improved time-stepping scheme for higher accuracy solutions, and functionality for modeling slight fluid density variations as given by the Boussinesq approximation.

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Simulation of microtubule–cytoplasm interaction revealed the importance of fluid dynamics in determining the organization of microtubules

Murshed

Wei

et al. 2023

Plant Direct

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Although microtubules in plant cells have been extensively studied, the mechanisms that regulate the spatial organization of microtubules are poorly understood. We hypothesize that the interaction between microtubules and cytoplasmic flow plays an important role in the assembly and orientation of microtubules. To test this hypothesis, we developed a new computational modeling framework for microtubules based on theory and methods from the fluid-structure interaction. We employed the immersed boundary method to track the movement of microtubules in cytoplasmic flow. We also incorporated details of the encounter dynamics when two microtubules collide with each other. We verified our computational model through several numerical tests before applying it to the simulation of the microtubulecytoplasm interaction in a growing plant cell. Our computational investigation demonstrated that microtubules are primarily oriented in the direction orthogonal to the axis of cell elongation. We validated the simulation results through a comparison with the measurement from laboratory experiments. We found that our computational model, with further calibration, was capable of generating microtubule orientation patterns that were qualitatively and quantitatively consistent with the experimental results. The computational model proposed in this study can be naturally extended to many other cellular systems that involve the interaction between microstructures and the intracellular fluid.

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IB2d: a Python and MATLAB implementation of the immersed boundary method

Cited by 52 publications

References 108 publications

Pulsing corals: A story of scale and mixing

Pulsing corals: A story of scale and mixing

IB2d Reloaded: A more powerful Python and MATLAB implementation of the immersed boundary method

Simulation of microtubule–cytoplasm interaction revealed the importance of fluid dynamics in determining the organization of microtubules

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