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
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DOI：
10.1088/1748-3190/ac4afa
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发表时间：
2022-01
影响因子：
3.4
通讯作者：
M. Santiago;Nicholas A. Battista;L. Miller;S. Khatri
中科院分区：
文献类型：
--
作者：
M. Santiago;Nicholas A. Battista;L. Miller;S. Khatri
在本文中，我们提出了一个开源软件库，它可以用来数值模拟化学浓度或热密度在粘性流体中的平流和扩散，其中移动的弹性边界驱动流体，充当源或汇。用Peskin浸没边界法求解粘性流体中弹性边界的全耦合流固耦合问题。浓度或热密度的增加或从边界的移除使用类似浸没边界的方法来解决，在该方法中，浓度使用正则化的增量函数从浸入边界扩散到流体。然后用对流-扩散方程描述浓度或密度随时间的变化，并进行数值求解。这一功能已被添加到我们的软件库IB2d中，该库提供了一个易于使用的二维浸没边界方法，并在MATLAB和Python语言中完全实现。我们提供了四个例子来说明该方法的有效性。作为第一个例子，模拟了一种简单的橡皮筋，它抵抗拉伸并吸收和释放化学浓度。给出了该基准情况下的完全收敛结果。文中还给出了另外三个生物例子：(1)一列振荡的圆柱体，代表一种用于滤料或嗅探的理想附属物；(2)背景流中的振动板，用于研究振动叶中的热量散失情况；(3)脉动软珊瑚的简化模型，其中二氧化碳被吸收，氧气作为副产品从移动的触须中释放出来。这种方法适用于生命科学中的广泛问题，包括触角的化学传感、植物和其他结构中的热量散失、发育过程中形态生物质的平流-扩散、海洋生物的滤食以及生物废物在流动中的释放。
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.