Abstract
Synthetic biologists design genetic logic circuit using living cells. A challenge in this task is the difficulty in constructing bigger logic circuits with several living cells due to the crosstalk effect among the biological cells. In order to remove the crosstalk effect, current practice is to use separate chambers on a flow-based microfluidic biochip to isolate each reaction zone. A flow-based microfluidic biochip can provide high precision control using microscale devices for the flow of biological substances. Hence, it can contruct more reliable and scalable genetic logic systems for synthetic biology experiments. The state-of-the-art technqiue assumes the reaction rates of different genetic logic gates are identical. This assumption is pessimistic as each genetic logic gate has the reaction rate different from others. Hence, it will cause unnecessary waiting time for fast logic gates and this, in turn, lengthen the whole experiment completion time significantly. In this thesis, we propose a new scheduling scheme for genetic logic circuits in flow-based microfluidic biochips considering different reaction time of each logic gate. Simulation results show that the proposed scheme reduces the experiment completion time. We further minimize the number of control valves and optimize the routing of flow and control layers in the chip layout, which in turn reduces the design cost.