On this page you will find links to all kinds of resources, from modeling tools to lab websites or interesting blogs. The links are ordered alphabetically and by theme.
Immersed boundary method
The immersed boundary method is a numerical method used to model fluid-structure interactions, both in 2D and 3D. Several variants exist: the "classic" immersed boundary method (IB), the immersed boundary with adaptive mesh refinement (IBAMR), and the immersed boundary with finite elements (IBFE). All the source code is open and freely available online!
For a general introduction to the IB, you can refer to this presentation I gave at the University of Amsterdam in December 2015. To delve deeper into the details of the IB, read Charles Peskin's foundational paper "The immersed boundary method" (Acta Numerica, 2002) available here. On the same webpage, you can access a detailed example of how to apply the IB to model a heart ("Fluid dynamics of the heart and its valves" by Peskin and McQueen, 1996), as well as many other interesting IB publications. If you want to get your hands dirty, try out some of the many examples in this great MATLAB tutorial developed by Nick Battista. The source code for running IBAMR simulations, developed by Boyce Griffith, is freely available here.
Here are links to the webpages of people, labs, and research groups I have or am currently working with:
Dimitra Dodou, Delft University of Technology
Experimental Zoology Group, Wageningen University and Research
Hanlon Lab, Marine Biological Laboratory
Holzman Lab, Inter-University Institute for Marine Sciences
Khatri Lab, University of California at Merced
Miller Lab, University of North Carolina at Chapel Hill
Mooney Lab, Woods Hole Oceanographic Institution
Nick Battista, University of North Carolina at Chapel Hill
Shavit Lab, Technion - Israel Institute of Technology