Speaker: Ivo Sbalzarini, Ph.D. (TU Dresden)
Professor on the Faculty of Computer Science of TU Dresden
Chair of Scientific Computing for Systems Biology at the Institute of Artificial Intelligence
Title: Numerical Methods for Solving Active Matter Models of Morphogenesis
We present numerical methods and a software framework for simulating active matter models of morphogenesis. Mechanistically understanding morphogenesis in living systems requires models that encode the physics and material properties of tissues alongside their biochemical regulation. The simulated models are subject to change as new experimental data arrive, or they are entirely data-derived. This frequently requires changing the simulation code, a process that becomes increasingly taxing when using high-performance or parallel computers. We present an intuitive C++ expression system with near-mathematical notation implemented in the parallel high-performance computing platform OpenFPM. We show how this framework enables numerical solutions of continuum active hydrodynamics models in 2D and 3D, as well as classic simulations of fluid dynamics. We also show how the governing equations and the numerical methods can be rapidly changed, and even auto-tuned, without rewriting the code, while taking full advantage of parallel high-performance computers and GPUs.