System-level modeling and simulation of the cell culture microfluidic biochip ProCell

Microfluidic biochips offer a promising alternative to a conventional biochemical laboratory. There are two technologies for the microfluidic biochips: droplet-based and flow-based. In this paper we are interested in flow-based microfluidic biochips, where the liquid flows continuously through pre-defined micro-channels using valves and pumps. We present an approach to the system-level modeling and simulation of a cell culture microfluidic biochip called ProCell, Programmable Cell Culture Chip. ProCell contains a cell culture chamber, which is envisioned to run 256 simultaneous experiments (viewed as a 16 × 16 matrix). We use an inverted fluorescence microscope to observe the experiments in real-time, allowing kinetic data analysis. We are able to automatically adjust the current experimental setup thus allowing, for the first time, conditional experiments. We propose a biochip architecture model and a comprehensive fault model that captures permanent faults occurring during chip operation. Using the proposed modeling and simulation framework, we perform an architectural level evaluation of two cell culture chamber implementations. A qualitative success metric is also proposed to evaluate chip performance in the presence of partial failures. Our results show that significant improvements in efficiency can be obtained using redundancy, providing improved chances to complete an experiment even in the presence of faults. This decreases the experiment repetition rate while increasing system productivity, saving time and reducing costs.