GPU-based Simulation of Yeast Cell Flocculation

Flocculation of yeast cells is an important phenomenon that often occurs in beverage production and applications of white biotechnology. In this paper, a novel model for cell movement and cell-cell interaction to simulate yeast cell flocculation is presented. To simulate this process with acceptable runtimes, a GPU implementation based on OpenCL and Java is described. The implementation allows us to track the cell movement in a detailed manner by a 3D visualization during execution. Experimental results indicate that the GPU implementation is up to factor of 736 faster than a multithreaded C/C++ implementation on a multi-core workstation for simulations with up to 20.000 yeast cells. Moreover, the GPU implementation requires only up to 225 milliseconds to perform simulations with up to 1.000.000 yeast cells.