Numerical method for modeling photosynthesis of algae on pulsing soft corals

Santiago, Matea; Mitchell, Kevin; Khatri, Shilpa

doi:10.1103/physrevfluids.7.033102

Cited by 3 publications

(10 citation statements)

References 81 publications

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“…For more details of the IB implementation in IB2d, see [35,36]. For a treatise of the novel methodology implemented here for the concentration or heat density, see [21]. Note here that we assume that the IB is neutrally buoyant unless otherwise stated.…”

Section: Mathematical Modelmentioning

confidence: 99%

“…The Dirac delta function, δ (x − X(s, t)), is once again used to couple this adsorption or desorption model, G(s, t), defined in the Lagrangian frame of reference with the concentration or density solved on the Eulerian grid. This approach is based on the modeling by Chen and Lai for surfactants [81] and further developed by the authors for studying the photosynthesis of symbiotic algae on pulsing corals [21]. This model, equation (5), can also be used with other methods, including sharp interface methods.…”

Section: Governing Equations For the Chemical Or Thermal Dynamicsmentioning

confidence: 99%

“…Although a broad body of computational work has been done to study fluid-structure interactions [9,[16][17][18][19][20], work that couples flow with concentration dynamics in these contexts is much more limited. Recently, the authors have developed a numerical method to couple concentration dynamics with a moving structure that drives the movement of fluid and acts as a source for the chemical concentration [21]. This method was inspired by a numerical method developed by Lai et al [22] to simulate interfacial flows with insoluble surfactants.…”

Section: Introductionmentioning

confidence: 99%

“…These algae provide the corals with most of their energy, and the pulsing behavior of the coral is believed to remove oxygen and increase the uptake of carbon dioxide. These active dynamics are thought to enhance the rate of photosynthesis up to an order of magnitude [21,70]. Photosynthesis in soft corals is an oxygen-limited process, and this method was initially applied to a problem that considers the advection and diffusion of oxygen with an IB acting as a source.…”

Section: Introductionmentioning

confidence: 99%

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Passive concentration dynamics incorporated into the library IB2d, a two-dimensional implementation of the immersed boundary method

et al. 2022

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In this paper, we present an open-source software library that can be used to numerically simulate the advection and diffusion of a chemical concentration or heat density in a viscous fluid where a moving, elastic boundary drives the fluid and acts as a source or sink. The fully- coupled fluid-structure interaction problem of an elastic boundary in a viscous fluid is solved using Peskin’s immersed boundary method. The addition or removal of the concentration or heat density from the boundary is solved using an immersed boundary-like approach in which the concentration is spread from the immersed boundary to the fluid using a regularized delta function. The concentration or density over time is then described by the advection-diffusion equation and numerically solved. This functionality has been added to our software library, IB2d, which provides an easy-to-use immersed boundary method in two dimensions with full implementations in MATLAB and Python. We provide four examples that illustrate the usefulness of the method. A simple rubber band that resists stretching and absorbs and releases a chemical concentration is simulated as a first example. Complete convergence results are presented for this benchmark case. Three more biological examples are presented: (1) an oscillating row of cylinders, representative of an idealized appendage used for filter-feeding or sniffing, (2) an oscillating plate in a background flow is considered to study the case of heat dissipation in a vibrating leaf, and (3) a simplified model of a pulsing soft coral where carbon dioxide is taken up and oxygen is released as a byproduct from the moving tentacles. This method is applicable to a broad range of problems in the life sciences, including chemical sensing by antennae, heat dissipation in plants and other structures, the advection-diffusion of morphogens during development, filter-feeding by marine organisms, and the release of waste products from organisms in flows.

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Section: Mathematical Modelmentioning

confidence: 99%

Section: Governing Equations For the Chemical Or Thermal Dynamicsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Passive concentration dynamics incorporated into the library IB2d, a two-dimensional implementation of the immersed boundary method

et al. 2022

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“…There are several models that couple the advection and diffusion of chemical species and their sources from immersed boundaries. [18][19][20] Typically, these models use sources that are then spread from the immersed boundary to the surrounding fluid using the regularized delta function. Restricting species from diffusing across the interface remains a challenge.…”

Section: Introductionmentioning

confidence: 99%

A model offluid–structureand biochemical interactions for applications to subclinical leaflet thrombosis

Barrett

Brown

Smith

et al. 2023

Numer Methods Biomed Eng

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Subclinical leaflet thrombosis (SLT) is a potentially serious complication of aortic valve replacement with a bioprosthetic valve in which blood clots form on the replacement valve. SLT is associated with increased risk of transient ischemic attacks and strokes and can progress to clinical leaflet thrombosis. SLT following aortic valve replacement also may be related to subsequent structural valve deterioration, which can impair the durability of the valve replacement. Because of the difficulty in clinical imaging of SLT, models are needed to determine the mechanisms of SLT and could eventually predict which patients will develop SLT. To this end, we develop methods to simulate leaflet thrombosis that combine fluidstructure interaction and a simplified thrombosis model that allows for deposition along the moving leaflets. Additionally, this model can be adapted to model deposition or absorption along other moving boundaries. We present convergence results and quantify the model's ability to realize changes in valve opening and pressures. These new approaches are an important advancement in our tools for modeling thrombosis because they incorporate both adhesion to the surface of the moving leaflets and feedback to the fluid-structure interaction.

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Interplay of elasticity and flow velocity on gorgonian feeding and implications for bioinspired design

Santiago,

Miller

2024

Annals of the New York Academy of Sciences

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Evidence shows that gorgonians are more resistant to ocean acidification and rising temperatures than hard corals and are vital to reef health and the reestablishment of disrupted coral reef communities. Gorgonian coral's resilience and its diversity of morphology and environment make it well‐suited as a model organism for bioinspired design applied to particle capture. We focus on flow near the polyps, using an updated form of the immersed boundary method to model the fluid–structure interaction of the flexible polyps and the surrounding ocean water. The inlet velocity and the polyp elasticity are simultaneously varied to gain insight into (1) how these parameters affect the emergent reconfiguration of their tentacles and (2) how the interaction of the reconfiguration and inlet velocity impacts passive particle capture. Two main behaviors are observed: a recirculation regime, in which particles recirculate in a region near the oral disk, and a unidirectional regime, in which the particles move unidirectionally through the tentacles without recirculation. Our results show that different regimes support different feeding strategies. We apply these results as bioinspired filtration, discussing how an elastic material could benefit specific engineering applications.

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Numerical method for modeling photosynthesis of algae on pulsing soft corals

Cited by 3 publications

References 81 publications

Passive concentration dynamics incorporated into the library IB2d, a two-dimensional implementation of the immersed boundary method

Passive concentration dynamics incorporated into the library IB2d, a two-dimensional implementation of the immersed boundary method

A model offluid–structureand biochemical interactions for applications to subclinical leaflet thrombosis

Interplay of elasticity and flow velocity on gorgonian feeding and implications for bioinspired design

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