Open AccessA semi-automated finite difference mesh creation method for use with immersed boundary software IB2d and IBAMR
Author(s) -
Denis Michael Senter,
Dylan R. Douglas,
Christopher Strickland,
Steven Thomas,
Anne Talkington,
Laura Miller,
Nicholas Battista
Publication year - 2020
Publication title -
bioinspiration and biomimetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.905
H-Index - 69
eISSN - 1748-3190
pISSN - 1748-3182
DOI - 10.1088/1748-3190/ababb0
Subject(s) - boundary (topology) , discretization , immersed boundary method , finite element method , computer science , software , fluid–structure interaction , mesh generation , finite difference , computational science , finite difference method , boundary value problem , geometry , topology (electrical circuits) , mathematics , mathematical analysis , engineering , structural engineering , programming language , combinatorics
Numerous fluid-structure interaction problems in biology have been investigated using the immersed boundary method. The advantage of this method is that complex geometries, e.g., internal or external morphology, can easily be handled without the need to generate matching grids for both the fluid and the structure. Consequently, the difficulty of modeling the structure lies often in discretizing the boundary of the complex geometry (morphology). Both commercial and open source mesh generators for finite element methods have long been established; however, the traditional immersed boundary method is based on a finite difference discretization of the structure. Here we present a software library for obtaining finite difference discretizations of boundaries for direct use in the 2D immersed boundary method. This library provides tools for extracting such boundaries as discrete mesh points from digital images. We give several examples of how the method can be applied that include passing flow through the veins of insect wings, within lymphatic capillaries, and around starfish using open-source immersed boundary software.