Scheduling and Optimization of Genetic Logic Circuits on Flow-Based Microfluidic Biochips

Yu-Jhih Chen1,a, Sumit Sharma2,c, Sudip Roy2,d and Tsung-Yi Ho1,b
1Dept. of Computer Science, National Tsing Hua University, Taiwan.
2CoDA Laboratory, Dept. of Computer Science & Engineering, Indian Institute of Technology Roorkee, India.


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 flowbased microfluidic biochip to isolate each reaction zone. The state-of-the-art technique assumes different reaction times for each gates in a genetic logic circuit. This assumption is pessimistic as each gate has different reaction rate from others. Hence, it will cause unnecessary waiting time for faster gates and this may in turn increase the total experiment completion time significantly. In this paper, we propose a genetic logic circuit synthesis technique for flow-based microfluidic biochip considering different reaction time of each logic gate. Simulation results show that the proposed scheme reduces the total 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.

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