This is the main code of the project “Interacting Active Surfaces” and follows the ideas in the manuscript:
The code is written in C++, with the idea of storing cells in different partitions and parallelised with MPI and OpenMP. The library makes use of the Trilinos library for the management of linear algebra objects such as vectors and matrices.
hiperlife is a high performance parallel library for finite elements. The aim of this library is to provide a computational framework to address problems of cell and tissue mechanobiology for a wide range of cases and users, with special focus on curved surfaces (the cell membrane, the cell cortex, epithelial monolayers, etc.). It is designed to handle the multi-physic nature of problems in mechanobiology, to manage unstructured grids that deal with complex geometries and to allow arbitrary higher-order basis functions that describe the curvature of interfaces. hiperlife is written in C++, uses the Message Passage Interface (MPI) paradigm for parallelism, and is built on top of several packages of the Trilinos Project. These particular choices set the basis for the main features of the library, namely, parallelism, flexibility, user-centred design and sustainability.
This small python project provides tools for the finite element analysis of annular ablation experiments.
This project was built for the article:
John Robert Davis, et al. (2022) ECM degradation in the Drosophila abdominal epidermis initiates tissue growth that ceases with rapid cell-cycle exit Current Biology 32 (6), 1285-1300.e4.
The MDStress project provides computational tools for local stress calculations from molecular simulations.
- GROMACS-LS: This is a modified version of the vanilla GROMACS code for local stress calculations. It is a post-processing tool to analyze trajectories from existing simulations. Read more…
- MDStress library: This is a standalone C++ library that can be incorporated into any code for local stress calculations. It implements various flavors of the spatial Irving-Kirkwood-Noll stress including the central force decomposition as well as the virial stress per atom. Read more…
If you are interested in incorporating the MDStress library into your code, please contact us.