My research interests lie in developing efficient and scalable algorithms for the simulation of multi-scale models of cell populations. The algorithms I develop address two problems: how to make use of high-performance computing technologies to facilitate the simulation of detailed models of large cell populations; and how to efficiently simulate individual-based models of cell populations that are coupled to a continuum description of the cellular micro-environment. The algorithms are implemented in the open-source, collaborative software library Chaste (Cancer, Heart And Soft Tissue Environment), which is developed primarily at the University of Oxford.
The aim of my doctoral project is to simulate a large number of cells (of the order of hundreds of thousands to millions) using detailed off-lattice models. Current limitations lie in the range of tens of thousands of cells. Such simulations will enable novel problems to be addressed with these modelling modalities.
My current work focuses on the development of a parallel, distributed algorithm to simulate the off-lattice cell-centre model described by Fletcher (Aspects of tumour modelling from the subcellular to the tissue scale. Ph.D. thesis, University of Oxford, UK. (2010)). I use a spatial decomposition to distribute the work among processing units, and augment the serial routine implemented in Chaste to ensure that the model is simulated correctly.