Chaste: an open source C++ library for computational physiology and biology

Chaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to "re-invent the wheel" with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials

Three-dimensional CFD simulations with large displacement of the geometries using a connectivity-change moving mesh approach

This paper deals with three-dimensional (3D) numerical simulations involving 3D moving geometries with large displacements on unstructured meshes. Such simulations are of great value to industry, but remain very time-consuming. A robust moving mesh algorithm coupling an elasticity-like mesh deformation solution and mesh optimizations was proposed in previous works, which removes the need for global remeshing when performing large displacements. The optimizations, and in particular generalized edge/face swapping, preserve the initial quality of the mesh throughout the simulation. We propose to integrate an Arbitrary Lagrangian Eulerian compressible flow solver into this process to demonstrate its capabilities in a full CFD computation context. This solver relies on a local enforcement of the discrete geometric conservation law to preserve the order of accuracy of the time integration. The displacement of the geometries is either imposed, or driven by fluid–structure interaction (FSI). In the latter case, the six degrees of freedom approach for rigid bodies is considered. Finally, several 3D imposed-motion and FSI examples are given to validate the proposed approach, both in academic and industrial configurations

Chaste: a test-driven approach to software development for biological modelling

Chaste (‘Cancer, heart and soft-tissue environment’) is a software library and a set of test suites for computational simulations in the domain of biology. Current functionality has arisen from modelling in the fields of cancer, cardiac physiology and soft-tissue mechanics. It is released under the LGPL 2.1 licence.\ud \ud Chaste has been developed using agile programming methods. The project began in 2005 when it was reasoned that the modelling of a variety of physiological phenomena required both a generic mathematical modelling framework, and a generic computational/simulation framework. The Chaste project evolved from the Integrative Biology (IB) e-Science Project, an inter-institutional project aimed at developing a suitable IT infrastructure to support physiome-level computational modelling, with a primary focus on cardiac and cancer modelling

Simulating water-entry/exit problems using Eulerian-Lagrangian and fully-Eulerian fictitious domain methods within the open-source IBAMR library

In this paper we employ two implementations of the fictitious domain (FD) method to simulate water-entry and water-exit problems and demonstrate their ability to simulate practical marine engineering problems. In FD methods, the fluid momentum equation is extended within the solid domain using an additional body force that constrains the structure velocity to be that of a rigid body. Using this formulation, a single set of equations is solved over the entire computational domain. The constraint force is calculated in two distinct ways: one using an Eulerian-Lagrangian framework of the immersed boundary (IB) method and another using a fully-Eulerian approach of the Brinkman penalization (BP) method. Both FSI strategies use the same multiphase flow algorithm that solves the discrete incompressible Navier-Stokes system in conservative form. A consistent transport scheme is employed to advect mass and momentum in the domain, which ensures numerical stability of high density ratio multiphase flows involved in practical marine engineering applications. Example cases of a free falling wedge (straight and inclined) and cylinder are simulated, and the numerical results are compared against benchmark cases in literature.Comment: The current paper builds on arXiv:1901.07892 and re-explains some parts of it for the reader's convenienc