Topological Flow Structures in a Mathematical Model for Rotation-Mediated Cell Aggregation

In this paper we apply vector field topology methods to a mathematical model for the fluid dynamics of reaggregation processes in tissue engineering. The experimental background are dispersed embryonic retinal cells, which reaggregate in a rotation culture on a gyratory shaker, according to defined rotation and culture conditions. Under optimal conditions, finally complex 3D spheres result. In order to optimize high throughput drug testing systems of biological cell and tissue models, a major aim is to understand the role which the fluid dynamics plays in this process. To allow for a mathematical analysis, an experimental model system was set up, using micro-beads instead of spheres within the culture dish. The qualitative behavior of this artificial model was monitored in time by using a camera. For this experimental setup a mathematical model for the bead-fluid dynamics was derived, analyzed and simulated. The simulations showed that the beads form distinctive clusters in a layer close to the bottom of the petri dish. To analyze these patterns further, we perform a topological analysis of the velocity field within this layer of the fluid. We find that traditional two-dimensional visualization techniques like path lines, streak lines and current time-dependent topology approaches are not able to answer the posed questions, for example they do not allow to find the location of clusters. We discuss the problems of these techniques and develop a new approach that measures the density of advected particles in the flow to find the moving point of particle aggregation. Using the density field the path of the moving aggregation